Subject: Daily Scan of COVID-19 Scientific Publications / survol journalier des publications scientifiques du COVID-19,
2020-10-01
Good afternoon,
There are 570 citations in today’s scan. 502 were considered primary research or review literature.
Highlights today include:
CANADA
·
Bolotin et al. analyzed 21,676 residual specimens from Ontario, Canada collected between March-August, 2020 to investigate the effect of antibody decline
on SARS-CoV-2 seroprevalence estimates, using both Abbott and Ortho assays. The association between the two tests decreased each month (p<0.001), suggesting anti-N antibody decline.
·
Zhao et al. establish a preliminary expert stakeholder perspective on the relative importance of pandemic immunisation strategies for different COVID-19
pandemic scenarios at the time of initial COVID-19 vaccine availability.
During an anticipated period of initial vaccine scarcity for all pandemic scenarios, stakeholders generally considered the most important immunisation strategy to be protecting those who are most vulnerable to severe illness and death from COVID-19. This was
followed in importance by the strategies to protect healthcare capacity, and to minimise transmission of COVID-19. In this supply constrained context, an immunisation strategy to protect critical infrastructure was considered the least important.
·
Savage et al
through modelling assess and identify the risk of COVID-19 transmission, resource use and mortality in urban and rural communities in northwestern Ontario. Rural populations will likely be affected disproportionately more than urban populations. They
also develop an online tool for policy planners to help reduce health inequity and respond proactively to outcome disparities between urban and rural populations.
·
Fisman et al.
Data from Ontario, Canada was used incidence rates among different age groups. Observed disease incidence and testing rates were highest in oldest individuals and markedly lower in those aged < 20. After adjustment
for testing frequency, SMR were lowest in children and adults aged 70 and older, approximately the same in adolescents as in the population as a whole and elevated in young adults (aged 20-29 years), providing a markedly different picture of the epidemic than
seen with crude SMR or case-based incidence. Older adults are tested more frequently, likely due to increased disease severity, while children are under-tested. Adjustment for testing frequency results in a very different picture of SARS-CoV-2 infection
risk by age, one that is consistent with estimates obtained through serological testing.
·
Karaivanov et al.
estimated the impact of mask mandates and other non-pharmaceutical interventions (NPI) on COVID-19 case growth in Canada, including regulations on businesses and gatherings, school closures, travel and self-isolation, and long-term care homes. In the
first few weeks after implementation, the authors found that mask mandates are associated with a reduction of 25 percent in the weekly number of new COVID-19 cases. Counterfactual policy simulations suggest that mandating indoor masks nationwide in early July
could have reduced the weekly number of new cases in Canada by 25 to 40 percent in mid-August, translating into 700 to 1,100 fewer cases per week.
·
Cipriano et al. evaluated the impact of a large student population returning to a mid-sized city currently experiencing a low rate of COVID-19 on community
health outcomes, using a dynamic transmission model of COVID-19 subdivided into three interacting populations: general population, university students, and long-term care residents. Screening targeted at university students population provides significant
public health benefits to the community through averted infections, critical care admissions, and COVID-19 deaths.
PUBLIC HEALTH INTERVENTIONS
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Coppola et al
forecast the impacts of keeping an interpersonal distancing of one-meter between passengers on board (sub-urban and high-speed) trains. Interpersonal distancing and the reduced level of capacity on board vehicles are seen as effective to prevent the
contagion, but are perceived as not sustainable due to the induced increase in operating costs.
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Rosenstrom et al
evaluate the effectiveness of widespread adoption of masks or face coverings to reduce community transmission of the SARS-CoV-2 virus that causes Covid-19. Their results indicate that if 60% of the population wears masks that are 50% effective, this
decreases the cumulative infection attack rate (CAR) by 25%, the peak prevalence by 51%, and the population mortality by 25%. If 100% of people wear masks (or 60% wear masks that are 80% effective), this decreases the CAR by 38%, the peak prevalence by 67%,
and the population mortality by 40%.
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Goyal et al.
utilize a mathematical model to assess the impact of masking on transmission within individual transmission pairs and at the population level. Their model quantitatively links mask efficacy to reductions in viral load and
subsequent transmission risk. The results reinforce that the use of masks by both a potential transmitter and exposed person substantially reduces the probability of successful transmission, even if masks only lower exposure viral load by ~50. Slight increases
in masking relative to current levels would reduce the reproductive number substantially below 1, particularly if implemented comprehensively in potential super-spreader environments.
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Buckner et al.
assessed the optimal allocation of a limited and dynamic COVID-19 vaccine supply in the U.S. across socio-demographic groups differentiated by age and essential worker
status. They found that optimal prioritization consistently targets older essential workers. However, depending on the policy objective, younger essential workers are prioritized to minimize infections or seniors
in order to minimize mortality.
·
Matzinger and Skinner
plotted COVID-19 cases, hospitalizations and deaths and analyzed them using segmented regression. The data reveals that school closings dropped infection rates in half, lockdowns dropped the rates 3 to 4 fold, and other actions (such as closing bars
and mandating masks) brought the rates even further down. Hospitalizations and deaths paralleled cases, with 3-10 day lags.
TRANSMISSION
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Balaraman et al studied the susceptibility of SARS-CoV-2 replication in biting insects after ingesting a SARS-CoV-2 infected blood meal. The
results indicate that none of the biting insects, nor the insect cell lines support SARS-CoV-2 replication. They conclude, that biting insect do not pose a risk for transmission of SARS-CoV-2 to humans or animals
following a SARS-CoV-2 infected blood meal.
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Anchordoqui et al provide an assessment of the risk of SARS-CoV-2 infection during a 7-hour school day in
elementary schools. They show that the existing data are insufficient to establish a low (below 1%) probability of infection with high accuracy. The use of facemasks and social distancing could significantly decrease this risk.
·
Pace et al
(preprint) present data that do not support maternal-to-child transmission of SARS-CoV-2 via milk; however, risk of transmission via breast skin should be further evaluated. Milk produced by infected mothers was a source of anti-SARS-CoV-2 IgA and IgG
and neutralizes SARS-CoV-2 activity. Their results support recommendations to continue breastfeeding during mild-to-moderate maternal COVID-19 illness.
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Murbe et al. utilize a laser particle counter in cleanroom conditions to show children emit fewer aerosols during singing than what has been
known so far for adults. Aerosol emission among children was also higher during singing, when compared to speaking.
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Lelieveld, et al. present a simple, easy-to-use spreadsheet algorithm to estimate the infection risk for different
indoor environments, constrained by published data on human aerosol emissions, SARS-CoV-2 viral loads, infective dose and other parameters. We evaluate typical indoor settings such as an office, a classroom, a choir practice room and reception/party environments.
EPIDEMIOLOGY
·
Andersen et al
examine college reopenings' association with changes in human mobility within campuses and in COVID-19 incidence in the counties of the campuses, over a two-week period before and after college reopenings. They
find that after college reopenings for face-to-face instruction, COVID-19 incidence in the county increased on average by a statistically significant 0.024 per thousand residents, following increases in mobility on campus. Similarly, they estimated increased
transmission locally after reopening, with a rising trend in Rt. The increase in cases was larger in counties with colleges that drew students from areas with increasing incidence rates.
·
Nicolelis et al
(preprint) present a significant negative correlation between COVID-19's incidence, infection growth rate, and mortality to the percentage of people with antibody (IgM) levels for dengue fever in each of Brazil’s states. This finding raises the possibility
of an immunological cross-reactivity between DENV serotypes and SARS-CoV-2, which may have important implications for immunization.
·
Wood et al
examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalization with COVID-19, and/or testing positive for COVID-19 infection in a group of healthcare workers
in Scotland. Increased household exposure to young children was associated with an attenuated risk of testing positive for SARS-CoV-2 and appeared to also be associated with an attenuated risk of COVID-19 disease severe enough to require hospitalization.
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Rom-Kedar e al
look into the growing fraction of the general population that may be immune to COVID-19, following infection. They propose that this immune cohort be deployed as a buffer between the general population and the population most at risk from the disease.
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Kuryntseva, et al.
present a modified approach for detection of COVID-19 infection rate using wastewater analysis has been developed. The minimum infection rate that can be detected using this approach is 0.01%. The approach developed was used to investigate wastewater
from eleven sewage inspection chambers in the city of Kazan (Russia). It was demonstrated that the average infection rate of people using these sewers was over 0.4% in July 2020.
·
Johnson et al.
used epidemiological modelling to explore the feasibility and consequences of school reopening in the face of differing rates of COVID-19 prevalence and transmission. The findings indicate that in the absence of systematic surveillance testing, most
schools in the United States can expect to remain open for 20-60 days. At this point, one or more large disease clusters can be expected to be detected, forcing schools to close again. In turn, these disease clusters can be expected to propagate through the
community, with potentially hundreds to thousands of additional cases resulting from each school cluster.
·
Stowe et al. studied the interaction between influenza and SARS-CoV-2 infections in England. The risk of testing positive for SARS-CoV-2 was 68% lower
among influenza positive cases, suggesting possible pathogenic competition between the two viruses. Patients with a coinfection had a risk of death of 5.92 (95% CI, 3.21-10.91) times greater than among those with neither influenza nor SARS-CoV-2 suggesting
possible synergistic effects in coinfected individuals.
·
Ulyte et al. studied the SARS-CoV-2 antibody seroprevalance within schools in Switzerland. Overall seroprevalence was 2.8 %, ranging from 1.0% to 4.5%
across districts. Seroprevalence was 3.8% in grades 1-2, 2.5% in grades 4-5, and 1.5% in grades 7-8. At least one case was present in 36/55 tested schools and in 43/128 classes with ≥50% participation rate and ≥5 children tested. 73% of children reported
COVID-19 compatible symptoms since January 2020, but none were reported more frequently in seropositive compared to seronegative children.
THERAPEUTICS
·
Sapkal et al
reports the development and evaluation of equine hyper immune globulin raised against inactivated SARS-CoV-2 virus. Post immunization neutralization titres of the equines demonstrated high neutralizing antibodies. The average nAb titre of the purified
bulk was 22,927 and correlated with high IgG binding efficiency in ELISA. Provides evidence of the potential of generating highly purified F(ab’)2 from equines against SARS-CoV-2 that can demonstrate consistent and high neutralization activity.
·
Rajasingham et al
investigated whether hydroxychloroquine could prevent SARS CoV-2 in healthcare workers at high-risk of exposure. Results from this randomized, double-blind, placebo-controlled clinical trial concluded that pre-exposure prophylaxis with hydroxychloroquine
once or twice weekly did not significantly reduce laboratory-confirmed Covid-19 or Covid-19-compatible illness among healthcare workers.
DIAGNOSTICS
·
Goldfarb et al.
We assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline mouth rinse/gargle sample types for the molecular detection of SARS-CoV-2 in adults and school-aged children.
Saline mouth rinse/gargle samples had a sensitivity of 98% while saliva samples had a sensitivity of 79%. Saline mouth rinse/gargle samples demonstrated the highest combined user acceptability ratings and analytical performance when compared with saliva and
HCW collected NP swabs.
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Singh et al. describe a low-cost, aptamer-based SARS-CoV-2 salivary antigen assay designed around a glucometer. Clinical testing determined that the assay
detects SARS-CoV-2 infection across a range of viral loads with 100% sensitivity and specificity.
·
Brown et al.
obtained 209 matched venous and capillary blood (self-sampling )
samples from thirty nine participants and analysed them using a COVID-19 IgG ELISA to detect antibodies against SARS-CoV-2. They found that capillary blood self-sampling is a reliable and feasible alternative
to venepuncture for serological assessment in COVID-19.
CORONAVIROLOGY
·
Leung, et al.
used their previous epidemiological framework to analyze COVID-19 surveillance and sequence data, we estimated that the G614 mutant is 31% (28-34%) more transmissible than the D614 wildtype. As such, interventions that were previously effective in containing
or mitigating the D614 wildtype (e.g. in China, Vietnam, Thailand, etc.) might be less effective against the G614 mutant.
PUBLIC HEALTH RESPONSE
·
Adebsi et al. aim to understand the perception of the public towards hypothetical COVID-19
vaccine in Nigeria. Most of the respondents intend to take the COVID-19 vaccine when it becomes available. Among the 132 respondents that would not take the COVID-19 vaccine, the major reason for non-acceptance is unreliability of the clinical trials, followed
by the belief that their immune system is sufficient to combat the virus.
·
Zimba et al.
determine important drivers of decisions to obtain a SARS-CoV-2 test in the context of increasing community transmission. Turnaround time for test results had the highest relative importance (30.4%), followed by test type (28.3%), specimen
type (26.2%), and venue (15.0%). Participants preferred fast results on both past and current infection and using a noninvasive specimen, preferably collected at home. Simulations suggested that providing immediate or same day test results, providing both
PCR and serology, or collecting oral specimens would substantially increase testing uptake over the current typical testing option.
·
Bonner et al.
used data from
a national longitudinal survey in Australia that includes a list of testing barriers. The most common barriers selected from the list provided were that testing is painful (11%), not knowing how to get tested
(7%), and worry about getting infected at the testing centre (5%).
Regards,
Lisa Waddell, Tricia Corrin, Rukshanda Ahmad, Robyn Odell, Maribeth Mitri, Julie Theriault, Dobrila Todoric, Alejandra Dubois, Christina Bancej, Austyn Baumeister, Anam Khan, Musaab Younis, Lien Mi Tien, Dima Ayache, Angela Sloan, Kaitlin
Young, Chatura Prematunge, Ainsley Otten, Irene Yong, Drew Greydanus, Shalane Ha, Alex Gilbert, Jessie Varga, Vanessa Zubach, Meenu Sharma, Kristyn Burak
Focus areas: Modelling/ prediction, Epidemiology, Transmission, Clinical data, Surveillance, Coronavirology, Diagnostics / Pathogen detection, Therapeutics,
Vaccine Research, Public health interventions, Public Health response, Public Health Priorities, IPAC, Health care response, immunology, economics, animal model, zoonoses, Review Literature, Commentary/Editorial, news
Domaines cibles: Modélisation/prédiction, Épidémiologie, Transmission, Données cliniques, Surveillance, Coronavirologie, Diagnostics
/ Détection d'agents pathogènes, Thérapeutique, Recherche sur les vaccins, Interventions de santé publique, Priorités de santé publique, PCI,
Réponse des soins de santé, immunologie, économie, modèle animal, zoonoses, Revue de littérature, Commentaire/Éditorial, journaux
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PUBLICATIONS |
AUTHORS / AUTEURS |
SOURCE |
FOCI / DOMAINE |
SUMMARY / SOMMAIRE |
Superiority of cilostazol among antiplatelet FDA-approved drugs against COVID 19 M(pro) and spike protein: Drug repurposing approach |
Abosheasha, MA, El-Gowily, et al |
Drug Dev Res |
Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
We performed molecular docking-based virtual screening of antiplatelet FDA-approved drugs on the key two viral target
proteins: main protease (M(pro) ) and spike glycoprotein (S) as potential inhibitor candidates for COVID-19. In the present study, 15 antiplatelet FDA-approved drugs were investigated against the concerned targets using the Molecular Docking Server. Our study
revealed that only cilostazol has the most favorable binding interaction on M(pro) (PDB ID: 6LU7) and cilostazol, iloprost, epoprostenol, prasugrel, and icosapent ethyl have a higher binding affinity on spike glycoprotein (S) (PDB ID: 6VYB) compared with recent
anti-CoVID-19. Therefore, cilostazol is a promising FDA drug against COVID-19 by inhibiting both M(pro) and S protein. |
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When it is available, will we take it? Public perception
of hypothetical COVID-19 vaccine in Nigeria |
Adebisi, Yusuff Adebayo, Alaran, et al |
medRxiv |
Public Health response| Interventions de santé publique |
We conducted a cross-sectional survey in August 2020 across the 36 states of Nigeria using an online questionnaire. The questionnaire includes sections
on the demographic characteristics of the respondents and their perception regarding hypothetical COVID-19 vaccine. A total of 517 respondents completed and returned the informed consent along with the questionnaire electronically. Most of the respondents
intend to take the COVID-19 vaccine when it becomes available. Among the 132 respondents that would not take the COVID-19 vaccine, the major reason for non-acceptance is unreliability of the clinical trials, followed by the belief that their immune system
is sufficient to combat the virus. There are significant association with the respondents age and having reservations toward vaccination and COVID-19 vaccine acceptance. Furthermore, geographical location and acceptance of the COVID-19 vaccine are significantly
associated. Even though the majority of our respondents are willing to take the COVID-19 vaccine, our findings reiterate the need to reassure the public that any vaccine which becomes available is safe and effective |
|
Ahmed, Firoz, Islam, et al |
medRxiv |
Epidemiology| Épidémiologie Surveillance |
In the course of a COVID-19 pandemic, 0.33 million people got infected in Bangladesh, we made the first and successful attempt to detect SARS-CoV-2 viruses'
genetic material in the vicinity wastewaters of an isolation centre i.e. Shaheed Bhulu Stadium, situated at Noakhali. The idea was to understand the genetic loading variation, both temporal and distance-wise in the nearby wastewater drains when the number
of infected COVID-19 patients is not varying much. Our finding suggested that while the temporal variation of the genetic load decreased in small drains over the span of 50 days, the main sewer exhibited accumulation of SARS-CoV-2 RNA. Other interesting finding
displays that probably distance of sampling location in meters is not likely to have a significant impact on gene detection concentration, although the quantity of the RNA extracted in the downstream of the drain was higher. These findings are of immense value
from the perspective of wastewater surveillance of COVID-19, as they largely imply that we do not need to monitor every wastewater system, and probably major drains monitoring may illustrate the city health. |
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Aiken, AbigailRA, Starling, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
We assessed whether demand for self-managed medication abortion provided by a fully remote online telemedicine service increased following the emergence
of COVID-19. Design: We used regression discontinuity to compare the number of requests to online telemedicine service Women on Web in eight European countries before and after they implemented lockdown measures to slow COVID-19 transmission. Participants:
3,915 people who made requests for self-managed abortion to Women on Web between January 1st, 2019 and June 1st, 2020. Main Outcome Measures: Percent change in requests to Women on Web before and after the emergence of COVID-19 and associated lockdown measures.
Results: Five countries showed significant increases in requests, ranging from 28% in Northern Ireland to 139% in Portugal. Two countries showed no significant change in requests, and one country, Great Britain, showed an 88% decrease in requests. Countries
with significant increases in requests were either countries where abortion services are mainly provided in hospitals or where no abortion services are available and international travel was prohibited during lockdown. |
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Akter, Farhana, Mannan, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study investigated the clinical manifestations, outcomes and long-term complications of COVID-19 inpatients in Bangladesh while emphasizing on individuals
having diabetes. Methods: A cross-sectional study was conducted for a sample of COVID-19 inpatients across four different hospitals of Bangladesh between April 1st and June 30, 2020. Variation in clinical characteristics, contact history, comorbidities, treatment
pattern, and long-term complications were investigated. Results: There were 734 COVID-19 presentations in this study of which 19.8% of patients had diabetes. The most frequently occurring blood groups among patients with diabetes were B (+) ve (35%) and O
(+) ve (31%). A number of COVID-19 patients with diabetes have been suffering from long term complications post recovery including pain, discomfort, memory loss and sleep disturbance. Conclusion: Individuals with diabetes have experienced severe manifestation
of COVID-19 and post disease complications. |
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Mathematical Modelling of the Spread of the Coronavirus
under Social Restrictions |
Al-arydah, Mo, tassem, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In this work we will use mathematical modelling to assess the current social restrictions in controlling the spread
of the disease. We formulate a simple susceptible-infectious-recovery (SIR) model to describe the spread of the coronavirus under social restrictions. We analyze this model, then fit the model to 160 days induced death data in Italy, Iran, USA, Germany, France,
India, Spain and China. Results: We find a formula for the basic reproduction function (R(t)) and the maximum number of daily infected people. The percentage of disease death estimated by the model in Germany and France are 3.8% and 1.2% respectively, which
are close to reported percentages values. Finally, we estimate the time, after first reported death, spent under social restrictions to reduce the basic reproduction function (R(t)) to one unit. The times to do that in Italy, USA, Germany, France, Spain and
China are 40, 50, 34,58, 31, and 15 days respectively. |
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Sensing of COVID-19 Antibodies in Seconds via Aerosol
Jet Printed Three Dimensional Electrodes |
Ali, Md Azahar, Hu, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes Immunology | Immunologie |
In this research, we report sensing of antibodies specific to SARS-CoV-2 virus in seconds via an electrochemical platform
consisting of gold micropillar array electrodes decorated with reduced graphene oxide and functionalized with recombinant viral antigens. The device is shown to detect antibodies to SARS-CoV-2 spike S1 protein and its receptor-binding-domain (RBD) at concentrations
down to 1pM via electrochemical impedance spectroscopy and read by a smartphone-based user interface. The detection time for the two antibodies tested in this work is 11.5 seconds. S1 protein sensing of its antibodies is specific, which cross-reacts neither
with other antibodies nor with proteins such as Nucleocapsid antibody and Interleukin-6 protein. |
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AlMadhi, Marwa, Abdulrahman, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
In this study, we used retrospective observational data in Bahrain to investigate the association between ABO blood
group and risk of infection as well as susceptibility to a more severe ICU-requiring infection. We found that individuals with blood group B were at a higher risk of infection, while those with blood group AB were at a lower risk. No association was observed
between blood group and the risk of a severe ICU-requiring COVID-19 infection. We extended the analysis to study the association by antibodies present; anti-a (blood groups B and O) and anti-b (blood groups A and O). Antibodies were not found to be associated
with either risk of infection or susceptibility to severe infection. The current study, along with the variation in blood group association results, indicates that blood group may not be the most ideal biomarker to predict risk of COVID-19 infection. |
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Al-Rifai, Rami, Acuna, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
In this study, we characterized the first cohort of COVID-19 RT-PCR confirmed cases reported in the Abu Dhabi Emirate,
UAE, according to symptomatic state, and identified factors associated with the symptomatic state. Also, the strength of association between the symptomatic state and testing positive in three subsequent RT-PCR testing rounds was examined and quantified. Method
We analyzed data collected from the first cohort of the RT-PCR confirmed COVID-19 cases reported to the health authorities in the Abu Dhabi Emirate, UAE between February 28 and April 08, 2020. Self-reported sociodemographic, working status, travel history,
and chronic comorbidities of 1,249 COVID-19 cases were analyzed according to symptomatic state (symptomatic and asymptomatic). Results . Nearly, 56.0% were asymptomatic cases. The most frequent two symptoms were fever (58.0%) and cough (41.0%). The mean age
of symptomatic was significantly higher than that of asymptomatic cases. Compared to non-working populations, working in public places, healthcare settings, or in the aviation and tourism sector, were independently associated with the symptomatic state. Reporting
at least one chronic comorbidity was also associated with symptomatic cases. Compared to asymptomatic, symptomatic COVID-19 cases had consistent odds of two or more of testing positive to COVID-19 in three subsequent testing rounds. |
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Alvarez-Pomar, Lindsay, Rojas-Galeano, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
In this paper we describe experiments performed on a simulated COVID-19 epidemic in an artificial population using
an agent based model, so as to illustrate to what extent the interplay between such personal care habits contributes to mitigate the spread of the disease, assuming the lack of other population-wide non-pharmaceutical interventions or vaccines. Our model purpose
is illustrative and contributes to ratify the importance of disseminating the message regarding the collective benefits of mass adoption of personal protection and hygiene habits, as an exit strategy for COVID-19 in the new normal state. |
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Ambrosia, Chistopher, Christensen, et al |
medRxiv |
Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
Methods: We integrated patient symptom and test data using machine learning and Bayesian inference to quantify individual
patient risk of SARS CoV 2 infection. We trained models with 100,000 simulated patient profiles based on thirteen symptoms, estimated local prevalence, imaging, and molecular diagnostic performance from published reports. We tested these models with consecutive
patients who presented with a COVID 19 compatible illness at the University of California San Diego Medical Center over 14 days starting in March 2020. Results: Bayesian inference network, distance metric learning, and ensemble models discriminated between
patients with SARS CoV2 infection and alternate diagnoses with sensitivities of 81.6 to 84.2%, specificities of 58.8 to 70.6%, and accuracies of 61.4 to 71.8%. After integrating imaging and laboratory test statistics with the predictions of the Bayesian inference
network, changes in diagnostic uncertainty at each step in the simulated clinical evaluation process were highly sensitive to location, symptom, and diagnostic test choices. |
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Ameh, CharlesA, Banke-Thomas, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The objective of this study was to determine the health facility (HF) preparedness for reproductive, maternal and newborn
health (RMNH) service delivery during the outbreak from the perspective of RMNH providers and to determine what factors significantly predict this. An anonymous cross-sectional online survey of RMNH providers was conducted from 1st to 21st July 2020 in Lagos
state Nigeria. Two hundred and fifty-six RMNH workers participated, 35.2% reported that RMNH services were unavailable at some time since March 2020, 39% felt moderate or extreme work-related burnout, 84% were moderately or extremely concerned about the availability
of PPE and related guidelines, and only 11.7% were extremely satisfied with the preparedness of their HFs. |
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Hearing the voices of Australian healthcare workers
during the COVID-19 pandemic |
Ananda-Rajah, Michelle, Veness, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
This study explores the working conditions and issues faced by Australian HCWs. Methods: Qualitative analysis of free-text
responses from Australian HCWs from 3 August to 5 August 2020 from an open letter calling for better respiratory protection for HCWs, transparent reporting of HCW COVID-19 infections and diversity in national infection control policy development. Results:
Among 2,733 HCWs who signed the open letter during the study period, 407 free-text responses were analysed. Doctors and nurses accounted for 58% and 35% of respondents, respectively. Dominant themes included concerns about: work health and safety standards;
guidelines on respiratory protection including the omission of fit-testing of P2/N95 respirators; deficiencies in the availability, quality, appropriateness and training of personal protective equipment; a top-down workplace culture that enabled bullying in
response to concerns about safety that culminated a loss of trust in leadership, self-reported COVID-19 infections in some respondents and moral injury. |
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Risk assessment of COVID-19 airborne infection during
hybrid learning |
Anchordoqui, Luis Alfredo, Chudnovsky, et al |
medRxiv |
Transmission Public health interventions*| Interventions de santé publique |
We provide an assessment of the risk of SARS-CoV-2 infection during a 7-hour school day in elementary schools. We show
that existing data are insufficient to establish a low (below 1%) probability of infection with high accuracy. The use of facemasks and social distancing could significantly decrease this risk. |
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College Openings, Mobility, and the Incidence of
COVID-19 Cases |
Andersen, MartinS, Bento, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
In this paper, we examine college reopenings' association with changes in human mobility within campuses and in COVID-19
incidence in the counties of the campuses, over a two-week period before and after college reopenings. Using a difference-in-differences design comparing areas with a college campus, before and after reopening, to areas without a campus, we find that after
college reopenings for face-to-face instruction, COVID-19 incidence in the county increased on average by a statistically significant 0.024 per thousand residents, following increases in mobility on campus. Similarly, we estimated increased transmission locally
after reopening, with a rising trend in Rt. The increase in cases was larger in counties with colleges that drew students from areas with increasing incidence rates. |
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Ansumali, Santosh, Kumar, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
To facilitate an intuition for the spatio-temporal development of the pandemic and to help resource deployment planning,
we analyze and describe how the disease burden almost-predictably shifted from large metropolitan districts to sub-urban districts. Methods. We gathered the publicly available granular data from 186 different districts (equivalent of counties) on their COVID-19
infections and deaths during the 15 April to 31 August 2020 period. The epidemiological data of these districts was fit to a susceptible-asymptomatic-infected-recovered-dead (SAIRD) model and the underlying epidemic parameters for each of these districts during
the course of 4 months was estimated. Findings. The center of the burden of the current-active infections which on May 15 was in the large metro districts with most international access shifted continuously and smoothly shifted towards districts which could
be accessed by domestic airports and by trains. A linear trend-analysis showed a continuous improvement in most epidemic parameters consistently across the districts with four categories of accessibility from an international travel perspective - large metro,
metro, urban and sub-urban districts. The reproduction numbers, recovery rate per infected person per day, and the death rate of symptomatic individuals improved from May 15 to August 31 in large metro districts and sub-urban districts. |
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Antonio-Villa, Neftali, Bello-Chavolla, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
Here, we aimed to explore the epidemiology, symptoms, and risk factors associated with adverse outcomes in HCWs in
Mexico City. METHODS: We explored data collected by the National Epidemiological Surveillance System in Mexico City, in HCWs who underwent real-time RT-PCR test. We explored COVID-19 outcomes in HCWs and the performance of symptoms to detect SARS-CoV-2 infection.
RESULTS: As of September 20th, 2020, 57,758 HCWs were tested for SARS-CoV-2 and 17,531 were confirmed; 6,610 were nurses (37.70%), 4,910 physicians (28.0%), 267 dentists (1.52%) and 5,744 laboratory personnel and other HCWs (32.76%). Overall, 2,378 HCWs required
hospitalization (4.12%), 2,648 developed severe COVID-19 (4.58%), and 336 required mechanical-ventilatory support (0.58%). Lethality was recorded in 472 (0.82%) cases. We identified 635 asymptomatic SARS-CoV-2 infections (3.62%). Compared with general population,
HCWs had higher incidence, testing, asymptomatic and mortality rates. No individual symptom offers adequate performance to detect SARS-CoV2. Older HCWs with chronic non-communicable diseases and severe respiratory symptoms were associated with higher risk
for adverse outcome; physicians were at higher risk compared with nurses and other HCWs. |
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An easy, reliable and rapid SARS-CoV2 RT-LAMP based
test for Point-of-Care and diagnostic lab |
Ar Gouilh, Meriadeg, Cassier, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
This study presents and evaluates a rapid and all-in-one SARS-CoV-2 RT-LAMP based molecular detection system, including
RNA extraction or not, for point-of-care or massive testing of naso-pharyngeal swabs. The point-of-care format uses LoopX©, a small portative device ensuring optimal LAMP reaction and automated reading with 95.2% and 95.5% sensitivity and specificity respectively. |
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Theoretical investigation of pre-symptomatic SARS-CoV-2
person-to-person transmission in households |
Arav, Yehuda, Klausner, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission |
we have formulated a detailed mathematical model of discrete human actions (such as coughs, sneezes, and touching)
and the decay of the virus in the environment. To take into account both discrete and continuous events we have extended the common modelling approach and employed a hybrid stochastic mathematical framework. We focused on transmission within a household, the
venue with the highest risk of infection and validated the model results against the observed secondary attack rate and the serial interval distribution. Detailed analysis of the model results identified the dominant driver of pre-symptomatic transmission
as the contact route via hand-face transfer and showed that wearing masks and avoiding physical contact are an effective prevention strategy. |
|
Argawu, Alemayehu |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
this study aimed to model and forecast of COVID-19 new cases in these top 10 infected African countries. Methods: In
this study, the COVID 19 new cases data have been modeled and forecasted using curve estimation regression and time series models for these top 10 infected African countries from Feb 14 to Sep 6, 2020. Results: From July to August, the prevalence of COVID-19
cumulative cases was declined in South Africa, Cote dʹIvoire, Egypt, Ghana, Cameron, Nigeria, and Algeria by 31%, 26%, 22%, 20%, 14%, 12%, and 4%, respectively. But, it was highly raised in Ethiopia and Morocco by 41%, and 38% in this period, respectively.
In Kenya, it was raised only by 1%. In this study, the cubic regression models for the ln(COVID-19 new cases) data were relatively the best fit for Egypt, Ethiopia, Kenya, Morocco, Nigeria and South Africa. In the analysis, the trends of COVID-19 new cases
will be declined for Algeria and Ethiopia, and the trends will be constantan for Cameroon, Cote-dIvoire, Ghana and Nigeria. But, it will be raised slightly for Egypt and Kenya, and significantly for Morocco and South Africa from September 7 to October 6, 2020. |
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Arim, Matias, Herrera-Esposito, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
We show that saturation of NPIs with the increase in infected individuals, an expected consequence of limited contact
tracing and healthcare capacities, produces a positive feedback in the disease growth rate and a threshold between two alternative states--containment and outbreak. These alternative states were previously related with the strength of NPIs but not with the
infection number. Furthermore, the transition between these states involves an abrupt acceleration in disease dynamics, which we report here for several COVID-19 outbreaks around the world. Including saturating NPIs expands the range of observed dynamics,
promoting slower rates during the initial phase and, after the tipping point, an accelerated dynamic capturing the loss in effectiveness of the NPIs. Our model results show how NPIs saturation may induce an Allee effect that produces abrupt transitions, with
periods of disease containment and periods of rapid growth. |
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Quantifying heterogeneity in SARS-CoV-2 transmission
during the lockdown in India |
Arinaminpathy, Nimalan, Das, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
Here, we used data collected from contact tracing during the lockdown in Punjab, a major state in India, to quantify
this heterogeneity, and to examine implications for transmission dynamics. We found evidence of heterogeneity acting at multiple levels: in the number of potentially infectious contacts per index case, and in the per-contact risk of infection. Incorporating
these findings in simple mathematical models of disease transmission reveals that these heterogeneities act in combination to strongly influence transmission dynamics. Standard approaches, such as representing heterogeneity through secondary case distributions,
could be biased by neglecting these underlying interactions between heterogeneities. We discuss implications for policy, and for more efficient contact tracing in resource-constrained settings such as India. Our results highlight how contact tracing, an important
public health measure, can also provide important insights into epidemic spread and control. |
|
Ariza, Beatriz Elena, Torres, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
Our report is one of the first in Latina America on seroprevalence and seroconversion rates in medical healthcare workers.
It emphasizes the importance of avoiding focusing only on symptomatic individuals to screen this population for SARS-CoV-2 infection, since of all individuals that have evidence of previous infection many (37.93%) may be pre-symptomatic or asymptomatic and
may contribute to infection/disease spread. |
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Arora, Sudipti, Nag, et al |
medRxiv |
Epidemiology| Épidémiologie Transmission Surveillance |
We investigated the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA at different treatment
stages of 15 wastewater treatment plants (WWTPs) in two North Indian states of Rajasthan and Uttarakhand. Untreated (influent), biologically treated, and disinfected wastewater samples were collected from May to August 2020. The findings indicate that there
are no SARS-CoV-2 related risks involved with using the treated effluent for non-potable applications. In contrast, untreated wastewater may be a potential route of viral transmission to the wastewater treatment plants and sanitation workers. |
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Severity scores in COVID-19 pneumonia: a multicenter, retrospective, cohort
study |
Artero, Arturo, Madrazo, et al |
Research Square prepub |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The purpose of this study was to compare severity scores used for community acquired pneumonia to identify high-risk
patients. We examined 10,238 patients with COVID-19. Mean age of patients was 66.6 years and 57.9% were males. The most common comorbidities were: hypertension (49.2%), diabetes (18.8%) and chronic obstructive pulmonary disease (12.8%). Acute respiratory distress
syndrome (34.7%) and acute kidney injury (13.9%) were the most common complications. In-hospital mortality was 20.9%. PSI and CURB-65 showed the highest AUROC (0.835 and0.825, respectively). qSOFA and MuLBSTA had a lower AUROC (0.728 and 0.715, respectively).
qSOFA was the most specific score (specificity 95.7%) albeit its sensitivity was only 26.2%. PSI had the highest sensitivity (84.1%) and a specificity of 72.2%. |
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The effect of COVID-19 on the economy: evidence from
an early adopter of localized lockdowns |
Asahi, Kenzo, Undurraga, et al |
medRxiv |
Economics | Économie |
Drawing from a rich dataset of localized lockdowns in Chile, we used econometric methods to measure the reduction in
local economic activity from lockdowns when applied to smaller or larger geographical areas. We measured economic activity by tax collection at the municipality-level. Results show lockdowns were associated with a 10-15% drop in local economic activity, a
two-fold reduction compared to municipalities not under lockdown. A three-to-four-month lockdown had a similar effect on economic activity than the year of the 2009 great recession. We found that costs are proportional to the population under lockdown, without
differences when lockdowns were measured at the municipality or city-wide levels. |
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Quantifying the impact of quarantine duration on
COVID-19 transmission |
Ashcroft, Peter, Lehtinen, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Transmission Public health interventions*|
Interventions de santé publique Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI) |
We present a mathematical model that leverages empirically determined distributions of incubation period, infectivity,
and generation time to quantify how the duration of quarantine affects transmission. With this model we address the impact of shortening the quarantine for returning travellers and traced contacts of confirmed cases, both in terms of prevented transmission
and the ratio of prevented transmission to days spent in quarantine. We also consider the impact of i) test-and-release strategies; ii) additional hygiene measures imposed upon release after a negative test; iii) the development of symptoms during quarantine;
iv) the relationship between quarantine duration and adherence; and v) the specificity of quarantine. A greater gain of utility can be achieved through a test-and-release strategy, and this can be even further strengthened by imposed hygiene measures post-release.
We also find that unless a test-and-release strategy is considered, the specificity of quarantine does not affect the optimal duration of quarantine. |
|
Asimakopoulou, K, Hoorens, et al |
Health Expect |
Public Health response| Interventions de santé publique |
This paper reports UK data on comparative optimism. In particular, examined the belief that negative events surrounding
risk and recovery from COVID-19 are perceived as more likely to happen to others rather than to oneself. Data were collected through an international survey (N = 6485) exploring people's thoughts and psychosocial behaviours relating to COVID-19. Respondents
demonstrated comparative optimism where they believed that as compared to others of the same age and gender, they were unlikely to experience a range of controllable (eg accidentally infect/ be infected) and uncontrollable (eg need hospitalization/ intensive
care treatment if infected) COVID-19-related risks in the short term (P < .001). They were comparatively pessimistic (ie thinking they were more at risk than others for developing COVID-19-related infection or symptoms) when thinking about the next year. |
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Assefa, Kibir Temesgen, Gashu, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The general objective of this study was to assess the impact of COVID-19 infection on maternal and reproductive health
care services among mothers getting service in governmental health institutions of Dessie town. This study concluded that COVID-19 significantly affects the quality and utilization of maternal and reproductive health care services. The study also showed that
utilization of these services was decreased due to fear of clients to go to health institutions. Ministry of health should continue maternity and reproductive health care services such as family planning to be prioritized as an essential core health service. |
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Convalescent Plasma for COVID-19: A multicenter,
randomized clinical trial |
Avendano-Sola, Cristina, Ramos-Martinez, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique RCT |
We conducted a multi-center, randomized clinical trial in patients hospitalized for COVID-19. All patients received
standard of care treatment, including off-label use of marketed medicines, and were randomized 1:1 to receive one dose (250-300 mL) of CP from donors with IgG anti-SARS-CoV-2. Convalescent plasma could be superior to standard of care in avoiding progression
to mechanical ventilation or death in hospitalized patients with COVID-19. The strong dependence of results on a limited number of events in the control group prevents drawing firm conclusions about CP efficacy from this trial. |
|
Ayed, Manal Mohamed Ahmed, Mohamed, et al |
Research Square prepub |
Public Health response| Interventions de santé publique |
The study evaluated the impact of educational intervention on secondary school students’ knowledge, practical knowledge
and attitudes regarding to COVID-19. A statistically significant difference between secondary students' knowledge attitudes, and practices before and after educational intervention. 202 (77.7%) had a poor pretest attitude level followed by fair (20.0%) and
good 6 (2.3%). In the posttest, all 260 students had a good attitude level which improved after educational intervention implementation. (57.7%) had poor pretest practice levels followed by fair (38.3%) and good 10 (4.0%). |
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|
azevedo, valderilioF, Peruffo, et al |
medRxiv |
Public health interventions*| Interventions de santé publique Public Health response|
Interventions de santé publique |
We aimed establish measures to contain and suppress the spread of COVID-19, associating education, active case tracking,
and humanitarian aid in two needy communities in Brazil. The adherence to the measures and evolution of the number of cases were verified during the project. Community isolation may be the best way to contain the spread of pandemics in fragile populations
with low socio-economic status. Educational actions combined with rapid testing and humanitarian aid were objective forms to promote community isolation. |
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|
Azhar, Mohd, Phutela, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a direct Cas9 based enzymatic readout
for detecting nucleotide sequences and identifying nucleobase identity without the requirement of trans-cleavage activity of reporter molecules. Using a lateral flow readout within 1h, FELUDA shows 100% sensitivity and 97% specificity across all range of viral
loads in clinical samples. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection at home. |
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Prolonged SARS-CoV-2 replication in an immunocompromised
patient |
Baang, Ji Hoong, Smith, et al |
medRxiv |
Clinical data| Données cliniques |
We describe a case of chronic COVID-19 in a patient with lymphoma and associated B-cell immunodeficiency. Viral cultures
and sequence analysis demonstrate ongoing replication of infectious SARS-CoV-2 virus for at least 119 days. The patient had three admissions related to COVID-19 over a four-month period and was treated twice with remdesivir and convalescent plasma with resolution
of symptoms. The lack of seroconversion and prolonged course illustrate the importance of humoral immunity in resolving SARS-CoV-2 infection. This case highlights challenges in managing immunocompromised hosts, who may act as persistent shedders and sources
of transmission. |
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Pre-existing T cell memory as a risk factor for severe
1 COVID-19 in the elderly |
Bacher, Petra, Rosati, et al |
medRxiv |
Immunology | Immunologie |
Here we demonstrate that all unexposed individuals harbor SARS-CoV-2-specific memory T cells with marginal cross-reactivity
to common cold corona and other unrelated viruses. This data suggest that a low avidity pre-existing T cell memory negatively impacts on the T cell response quality against neoantigens such as SARS-CoV-2, which may predispose to develop inappropriate immune
reactions especially in the elderly. We propose the immunological age as an independent risk factor to develop severe COVID-19 |
|
Bahrs, Christina, Kimmig, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
The objectives of this study were to compare SARS-CoV-2 IgG seroprevalence and compliance to wear personal protective
equipment (PPE) between HCWs working within (high-risk) or outside (intermediate-risk) units treating suspected or confirmed COVID-19 patients. No evidence for higher seroprevalence against SARS-CoV-2 in HCWs working in high-risk COVID-19 areas could be observed,
probably due to high compliance to wear PPE. Compared to administration employees, we observed no additional risk to acquire SARS-CoV-2 infections by patient care. |
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Non-stationary Spatio-Temporal Modeling of COVID-19
Progression in The U.S |
Bai, Yue, Safikhani, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
In this paper, we propose a modeling framework which not only accounts for such policies but also utilizes the spatial
and temporal information to characterize the pattern of COVID-19 progression. Specifically, a piecewise susceptible-infected-recovered (SIR) model is developed while the dates at which the transmission/recover rates change significantly are defined as "break
points" in this model. The proposed model is applied to several U.S. states and counties, and the results confirm the effect of "stay-at-home orders" and some states' early "re-openings" by detecting break points close to such events. Further, the model performed
satisfactorily short-term forecasts of the number of new daily cases at regional levels by utilizing the estimated spatio-temporal covariance structures. |
|
Bajaj, NamanS, Pardeshi, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
This study provides concrete evidence to show the superiority of the modified SIR model over the Logistic model based
on analysis. Municipal corporations having control should make use of this study to make decisions and test their effectiveness, and more corporations should be empowered to benefit from this study. |
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Subclinical ocular inflammation in persons recovered
from ambulatory COVID-19 |
Bakhoum, MathieuF, Ritter, et al |
medRxiv |
Clinical data| Données cliniques |
Here, we used spectral domain optical coherence tomography (SD-OCT) to detect the presence of inflammatory cells in
the vitreous cavity, an immune-privileged microenvironment, in persons recovered from COVID- 19. Our results provide quasi-histologic evidence that neuroinflammation is present in persons who recovered from COVID-19, only one of whom required hospitalization.
Our results also suggest that persons who feel that their recovery is incomplete have evidence of subclinical eye inflammation, which may be a marker of residual inflammation elsewhere as well. |
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Susceptibility of midge and mosquito vectors to SARS-CoV-2
by natural route of infection |
Balaraman, Velmurugan, Drolet, et al |
bioRxiv |
Transmission Coronavirology| Coronavirologie |
Arthropods transmit numerous viral, parasitic, and bacterial diseases; however, the potential role of arthropods in
SARS-CoV-2 transmission is not fully understood. Thus far, a few studies have demonstrated that SARS-CoV-2 replication is not supported in cells from certain insect species nor in certain species of mosquitoes after intrathoracic inoculation. In this study,
we expanded the work of SARS-CoV-2 susceptibility to biting insects after ingesting a SARS-CoV-2 infected blood meal. Species tested included Culicoides sonorensis biting midges, as well as Culex tarsalis and Culex quinquefasciatus mosquitoes, all known biological
vectors for numerous RNA viruses. Arthropods were allowed to feed on SARS-CoV-2 spiked blood and at various time points post infection analyzed for the presence of viral RNA and infectious virus. Additionally, cell lines derived from C. sonorensis (W8a), Ae.
aegypti (C6/36), Cx. quinquefasciatus (HSU), and Cx. tarsalis (CxTrR2) were tested for SARS-CoV-2 susceptibility. Our results indicate that none of the biting insects, nor the insect cell lines support SARS-CoV-2 replication. We conclude, that biting insect
do not pose a risk for transmission of SARS-CoV-2 to humans or animals following a SARS-CoV-2 infected blood meal. |
|
Balcells, María Elvira, Rojas, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique RCT |
We aimed to evaluate the efficacy and safety of early convalescent plasma (CP) therapy in COVID-19 progression. This
is an open-label, single-center, randomized clinical trial performed in an academic center in Santiago, Chile from May 10, 2020, to July 18, 2020, with final follow-up August 17, 2020. The intervention consisted in immediate CP (early plasma group) versus
no CP unless developing pre-specified criteria of deterioration (deferred plasma group). Of 58 randomized patients (mean age, 65.8 years, 50% male), 57 (98.3%) completed the trial. A total of 13 (43.3%) participants from the deferred group received plasma
based on clinical aggravation. We found no benefit in the primary outcome (32.1% vs 33.3%, OR 0.95, 95% CI 0.32-2.84, p>0.99) in the early versus deferred CP group. In-hospital mortality rate was 17.9% vs 6.7% (OR 3.04, 95% CI 0.54-17.2, p=0.25), mechanical
ventilation 17.9% vs 6.7% (OR 3.04, 95% CI 0.54-17.2, p=0.25), and prolonged hospitalization 21.4% vs 30% (OR 0.64, 95%CI, 0.19-2.1, p=0.55) in early versus deferred CP group, respectively. Viral clearance rate on day 3 (26% vs 8%, p=0.20) and day 7 (38% vs
19%, p=0.37) did not differ between groups. Two patients experienced serious adverse events within 6 or less hours after plasma transfusion. |
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Balwinder, Singh, Shirsath, et al |
Agric Syst |
Economics | Économie |
This study assessed the potential for COVID-related reductions in the agriculture workforce to disrupt production of
the dominant rice-wheat cropping pattern in these states, we use a spatial ex ante modelling framework to evaluate four scenarios representing a range of plausible labor constraints on the timing of rice transplanting. Averaged over both states, results suggest
that rice productivity losses under all delay scenarios would be low as compare to those for wheat, with total system productivity loss estimates ranging from 9%, to 21%, equivalent to economic losses of USD $674 m to $1.48 billion. Late rice transplanting
and harvesting can also aggravate winter air pollution with concomitant health risks. |
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|
Bandopadhyay, Purbita, Rozario, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique RCT |
In a randomized control trial on convalescent plasma therapy (CPT) in severe COVID-19, we characterized the nature,
in terms of abundance of forty eight cytokines, and dimensions, in terms of their interrelationships, of the hyper-immune activation-associated cytokine storm in patients suffering from acute respiratory distress syndrome. We found plasma MCP3 level to be
a key correlate for mitigation of hypoxia, irrespective of therapeutic regimen. We also identified an anti-inflammatory role of CPT independent of its neutralizing antibody content, and a linear regression analysis revealed that neutralizing antibodies as
well as the anti-inflammatory effect of CPT both contribute to marked immediate reductions in hypoxia, as compared to patients on standard therapy. |
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|
A Cost Analysis of Childbirth for Pregnant Women
with COVID-19 in the Epicentre of Nigeria |
Banke-Thomas, Aduragbemi, Makwe, et al |
medRxiv |
Economics | Économie |
We conducted a hospital-based cost analysis to estimate the out-of-pocket cost of spontaneous vaginal delivery (SVD)
and caesarean delivery (CD). Specifically, we collected facility-based and household costs of all nine pregnant women with COVID-19 who were managed between 1st April and 30th August 2020 at the largest teaching hospital in Lagos, the epicentre of COVID-19
in Nigeria. Findings showed that total utilization cost ranged from US$494 (N190,150) for SVD with mild COVID-19 to US$4,553 (N1,751,165) for emergency CD with severe COVID-19. Though 32-66% of facility-based cost has been subsidized, cost of SVD and CD have
doubled and tripled respectively during the pandemic compared to those paid pre-COVID. Out of the facility-based costs paid, cost of personal protective equipment (PPE) was the major cost driver (50%) for SVD and CD. Supplemental oxygen was a major cost driver
when women had severe COVID-19 symptoms and required long admission (48%). Excluding treatment costs specifically for COVID-19, mean facility-based costs for SVD and CD are US$228 (N87,750) and US$948 (N364,551) respectively. |
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Barraza, NR, Pena, et al |
Chaos Solitons Fractals |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
This work introduces a new markovian stochastic model that can be described as a non-homogeneous Pure Birth process.
We propose a functional form of birth rate that depends on the number of individuals in the population and on the elapsed time, allowing us to model a contagion effect. Thus, we model the early stages of an epidemic. The number of individuals then becomes
the infectious cases and the birth rate becomes the incidence rate. We obtain this way a process that depends on two competitive phenomena, infection and immunization. Variations in those rates allow us to monitor how effective the actions taken by government
and health organizations are. From our model, three useful indicators for the epidemic evolution over time are obtained: the immunization rate, the infection/immunization ratio and the mean time between infections (MTBI). We apply this model to the present
SARS-CoV-2 pandemic still in its early growth stage in Latin American countries. As it is shown, the model accomplishes a good fit for the real number of both positive cases and deaths. We analyze the evolution of the three indicators for several countries
and perform a comparative study between them. |
|
|
Barrett, ThomasJ, Patterson, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
For four highly-affected countries, we determine population susceptibilities by directly comparing country-wide observed
epidemic dynamics data with that with their main metropolitan regions. We find significant susceptibility reductions in the metropolitan regions as a result of earlier seeding, with a relatively longer phase of exponential growth before the introduction of
public health interventions. During the post-growth phase, the lower susceptibility of these regions contributed to the decline in cases, independent of intervention effects. Forward projections indicate that non-metropolitan regions will be more affected
during recurrent epidemic waves compared with the initially heavier-hit metropolitan regions. Our findings have consequences for disease forecasts and resource utilisation. |
|
|
Baruah, Hemanta Kumar |
medRxiv |
Epidemiology| Épidémiologie |
We have studied the current COVID-19 spread situation in Assam, a State of India. We have found that currently the
spread pattern is indeed exponential and that it is not going to show a reducing trend soon. As a result, it is not possible yet to forecast about the time of peaking of the epidemic in Assam. It can be said that the COVID-19 situation in this Indian State
is very alarming even after five and a half months of the start of the epidemic in the State. It may so happen that in Assam the spread would continue to grow exponentially even after the situation changes in India as a whole. |
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Role of IgG against N-protein of SARS-CoV2 in COVID19
clinical outcomes |
Batra, Mayank, Tian, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The effect of high titers of IgG against N-protein on clinical outcomes of SARS-CoV2 disease has not been described.
We studied 400 RT-PCR confirmed SARS-CoV2 patients to determine independent factors associated with poor outcomes, including MICU admission, prolonged MICU stay and hospital admissions, and in-hospital mortality. We found that several factors, including Charlson
comorbidity Index (CCI), high levels of IL6, and presentation with dyspnea were associated with poor clinical outcomes. It was shown that higher CCI and higher IL6 levels were independently associated with in-hospital mortality. Anti-N protein IgG was detected
in the serum of 55 (55%) patients at the time of admission. A high concentration of antibodies, defined as signal to cut off ratio (S/Co)> 1.5 (75 percentile of all measurements), was found in 25 (25%) patients. The multivariable logistic regression models
showed that between being an African American, higher CCI, lymphocyte counts, and S/Co ratio> 1.5, only S/Co ratio were independently associated with MICU admission and longer length of stay in hospital. |
|
Commercial COVID-19 serial seroconversion panel for
validation of SARS-CoV-2 antibody assays |
Belda, Francisco, Cherenzia, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Background: Seroconversion panels (SCP) are an important tool for investigating antibody responses and developing serological
assays. A SCP was generated from a single SARS-CoV-2 positive plasma donor over 87 days. Methods: This SCP was tested against five SARS-CoV-2 antibody tests (IgG, IgM and total Ig). All test kits utilized recombinant antigens that are specific to SARS-CoV-2.
Results: The SCP showed IgG responses for SARS-CoV-2 after day 50. IgM levels peaked on day 50 (prior to IgG) and declined in subsequent samples. Conclusion: This SCP is a useful tool for validation of SARS-CoV-2 antibody assays. |
|
Bell, SadieL, Clarke, et al |
medRxiv |
Public Health response| Interventions de santé publique |
We used a multi-methods approach - involving an online cross-sectional survey and semi-structured interviews - to investigate
parents' and guardians' views on the acceptability of a future COVID-19 vaccine. 1252 parents and guardians (aged 16+ years) who reported living in England with a child aged 18 months or under completed the survey. Nineteen survey respondents were interviewed.
Most participants reported they would definitely accept or were unsure but leaning towards accepting a COVID-19 vaccine for themselves (Definitely 55.8%; Unsure but leaning towards yes 34.3%) and their child/children (Definitely 48.2%; Unsure but leaning towards
yes 40.9%). Less than 4% of participants reported that they would definitely not accept a COVID-19 vaccine for themselves or their child/children. Participants were more likely to accept a COVID-19 vaccine for themselves than for their child/children. Participants
that self-reported as Black, Asian, Chinese, Mixed or Other ethnicity were almost 3 times more likely to reject a COVID-19 vaccine for themselves and their children than White British, White Irish and White Other participants. Respondents from lower income
households were also more likely to reject a COVID-19 vaccine. The main reason for vaccine acceptance was for self-protection from COVID-19. Common concerns were around COVID-19 vaccine safety and effectiveness, which were largely prompted by the newness and
rapid development of the vaccine. |
|
|
Bello, Shaibu Oricha, Igumbor, et al |
medRxiv |
Epidemiology| Épidémiologie Coronavirology| Coronavirologie |
In this study, we analyzed available complete SARS-CoV-2 sequences using the CpG index as a signature of Zinc finger
antiviral protein (ZAP) activity to examine population variations in innate intracellular antiviral competencies. The result suggests that differential ZAP activity may be a major determinant of the outcome of SARS-CoV-2 infection. SARS-CoV-2 sequences from
Africa, Asia, and pools of asymptomatic patients had I_CpG signature evidence of high ZAP activity, while SARS-CoV-2 sequences from North America and Intensive Care Unit or Deceased patients had I_CpG signature of low ZAP activity. ZAP activity is linked to
the interferon system. Low ZAP activity may be part of the explanation for the increased morbidity of SARS-CoV-2 in the elderly and with comorbidities like diabetes, obesity, and hypertension. It may also provide some insight into the discrepancies between
invitro anti-SARS-CoV-2 activities of candidate therapies and performance in clinical trials. Furthermore, our results suggest that asymptomatic patients may paradoxically shed a more dangerous virus. |
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Norwich COVID-19 Testing Initiative: feasibility
project evaluation |
Berger Gillam, Tara, Cole, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
This study aimed to pilot mass COVID-19 testing on a university research park, to assess the feasibility and acceptability
of scaling up to all staff and students. This was a cross-sectional feasibility study on a university research park in the East of England. Staff and students (5,625) on the research park were eligible to participate. Polymerase chain reaction (PCR) testing
was offered to all participants. Participants were offered 4 swabs, which they self-administered over a two-week period. 798/1053 (76%) of those who registered provided at least one swab and of these, 687 (86%) provided all four. 681/687 (99%) had all negative
results. 6 participants had one inconclusive result. There were no positive results. 458/798 (57%) participants responded to a post-testing questionnaire. 446/458 (97.5%) of those who responded agreed that they would be interested in repeat testing in the
future. |
|
Bernardes, JoanaP, Mishra, et al |
medRxiv |
Clinical data| Données cliniques |
Here, we performed a longitudinal multi-omics study using a two-centre German cohort of 13 patients (from Cologne and
Kiel, cohort 1). We analysed the bulk transcriptome, bulk DNA methylome, and single-cell transcriptome (>358,000 cells, including BCR profiles) of peripheral blood samples harvested from up to 5 time points. We observed an increase of proliferating, activated
plasmablasts in severe COVID-19, and show a distinct expression pattern related to a hyperactive cellular metabolism of these cells. We further identified a notable expansion of type I IFN-activated circulating megakaryocytes and their progenitors, indicative
of emergency megakaryopoiesis, which was confirmed in cohort 2. These changes were accompanied by increased erythropoiesis in the critical phase of the disease with features of hypoxic signalling. Finally, projecting megakaryocyte- and erythroid cell-derived
co-expression modules to longitudinal blood transcriptome samples from cohort 3 confirmed an association of early temporal changes of these features with fatal COVID-19 disease outcome. |
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A Cost/Benefit Analysis of Clinical Trial Designs
for COVID-19 Vaccine Candidates |
Berry, Donald, Berry, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique |
We compare and contrast the expected duration and number of infections and deaths averted among several designs for
clinical trials of COVID-19 vaccine candidates, including traditional randomized clinical trials and adaptive and human challenge trials. Using epidemiological models calibrated to the current pandemic, we simulate the time course of each clinical trial design
for 504 unique combinations of parameters, allowing us to determine which trial design is most effective for a given scenario. A human challenge trial provides maximal net benefits---averting an additional 1.1M infections and 8,000 deaths in the U.S. compared
to the next best clinical trial design---if its set-up time is short or the pandemic spreads slowly. In most of the other cases, an adaptive trial provides greater net benefits. |
|
Bhaduri, Ritwik, Kundu, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
We consider an extension of the Susceptible-Exposed-Infected-Removed (SEIR) model under both selection bias and misclassification.
We derive closed form expression for the basic reproduction number under such data anomalies using the next generation matrix method. We conduct extensive simulation studies to quantify the effect of misclassification and selection on the resultant estimation
and prediction of future case counts. Finally we apply the methods to reported case-death-recovery count data from India, a nation with more than 5 million cases reported over the last seven months. We show that correcting for misclassification and selection
can lead to more accurate prediction of case-counts (and death counts) using the observed data as a beta tester. The model also provides an estimate of undetected infections and thus an under-reporting factor. For India, the estimated under-reporting factor
for cases is around 21 and for deaths is around 6. We develop an R-package (SEIRfansy) for broader dissemination of the methods. |
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COVID-19 dynamics across the US: A deep learning
study of human mobility and social behavior |
Bhouri, Mohamed Aziz, Costabal, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
This paper presents a deep learning framework for epidemiology system identification from noisy and sparse observations
with quantified uncertainty. The method is applied to a mobility and social behavior-based SEIR model of COVID-19 spread. The model is trained on Google and Unacast mobility data spanning a period of 66 days, and is able to yield accurate future forecasts
of COVID-19 spread in 203 US counties within a time-window of 15 days. Strikingly, a sensitivity analysis that assesses the importance of different mobility and social behavior parameters reveals that attendance of close places, including workplaces, residential,
and retail and recreational locations, has the largest impact on the basic reproduction number. The model enables us to rapidly probe and quantify the effects of government interventions, such as lock-down and re-opening strategies. |
|
Bierig, Tobias, Collu, et al |
bioRxiv |
Coronavirology| Coronavirologie |
This study describes a construct and protocol for the expression and purification of yellow fluorescent protein (YFP)
labeled 2019-nCoV spike RBD. The fusion protein, in the vector pcDNA 4/TO, comprises an N-terminal interferon alpha 2 (IFNα2) signal peptide, an eYFP, a FLAG-tag, a human rhinovirus 3C protease cleavage site, the RBD of the 2019-nCoV spike protein and a C-terminal
8x His-tag. We stably transfected HEK 293 cells. Following expansion of the cells, the fusion protein was secreted from adherent cells into serum-free medium. Ni-NTA IMAC purification resulted in very high protein purity, based on analysis by SDS-PAGE. Deglycosylation
experiments confirmed the presence of N-linked glycosylations in the secreted protein. Complex formation with the peptidase domain of human angiotensin-converting enzyme 2 (ACE2), the receptor for the 2019-nCoV spike RBD, was confirmed by SEC, both for the
YFP-fused spike RBD and for spike RBD alone, after removal of YFP by proteolytic cleavage. |
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Impact of COVID-19 on the mortality rates for the
resident population of the Umbria region in Italy |
Bietta, Carla, Morini, et al |
medRxiv |
Epidemiology| Épidémiologie |
In this paper, we have discussed the mortality figures in the Umbria region after analyzing the data from the national
Health registry between December 2019 to April 2020; the period of infection and its comparison with the data from previous five years. The factors governing these figures were studied including temperature, standard mortality rates, territorial distribution,
death due to all cases as well as the non-COVID deaths. A sharp increase in mortality figures was observed for the month of march and low temperature also had a role to play. However the difference when compared to previous 5 years was not significant as was
expected at the start of the study. A single factor cannot be responsible for the total mortality figures in a region as is frequently predicted. |
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BILLONG, samuel Ismael, Kouamou, et al |
Research Square prepub |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
This paper proposes a hybrid SIR model which takes into consideration the spatio-temporal dynamics of individuals.
The model is based on the discrete stochastic diffusion equations. To build the equation system, the 2D diffusion equations are coupled to the human displacement probability law pattern through a discretization made by the finite volume method for complex
geometries. Beyond the health consequences it causes, COVID-19 (coronavirus) is a test case used to validate the proposed model. The authors used the case of a developed country before confinement to fit to the chosen displacement pattern, and to analyze the
sensitivity of the parameters of the model taking into account the accuracy of the statistics provided. |
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|
Blackburn, JonathanM, Anuar, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We have developed a novel, quantitative, multi-antigen, multiplexed, array-based immunoassay platform, ImmuSAFE COVID+
(ImmuSAFE) comprising 6 functionally validated domains or regions of the N protein of SARS-CoV-2 expressed using Sengenics KREX technology. This array platform enables determination of both the position and breadth of anti-SARS-CoV-2 antibody responses following
natural infection or vaccination. To validate our platform, 100 serum samples (confirmed sero-positive COVID-19 cases, n=50; pre-pandemic HIV positive controls, n=50) were tested for IgG seropositivity to the N antigen, yielding 100% specificity and 100% sensitivity.
All 50 cases showed positive antibody reactivity towards at least one N protein epitope, whilst all 50 controls showed antibody reactivity below threshold values. Broad variation was also observed in the magnitude and breadth of antibodies present, represented
as an Epitope Coverage score (EPC). A positive correlation was observed between increasing age and EPC values, with individuals under 40 years old having a mean EPC score of 3.1, whilst individuals above the age of 60 had a mean EPC of 5.1. This finding may
have broad implications for the natural history of COVID-19 disease in different individuals. |
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Identifying gaps in COVID-19 health equity data reporting
in Canada using a scorecard approach |
Blair, Alexandra, Warsame, et al |
medRxiv |
Public Health Priorities| Priorités de santé publique |
This study aimed to assess health equity-oriented COVID-19 data reporting across Canadian provinces and territories,
using a scorecard approach. Overall, information on cases and deaths was more complete than for tests, hospitalizations and population size denominators needed for rate estimation. Information provided on jurisdictions and their regions, overall, tended to
be more available (average score of 53%, "B") than for equity-related indicators (average score of 21%, "D"). Only British Columbia and Alberta provided case-delimited data, and only Alberta provided information for local areas. No jurisdiction reported on
outcomes according to patients' individual-level immigration status, race, or income. Only Ontario and Quebec provided detailed information for long-term care settings and detention facilities. |
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SARS-CoV-2 seroprevalence survey estimates are
affected by anti-nucleocapsid antibody decline |
Bolotin, Shelly, Tran, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
We analyzed 21,676 residual specimens from Ontario, Canada collected between March-August, 2020 to investigate the
effect of antibody decline on SARS-CoV-2 seroprevalence estimates. Testing specimens orthogonally using the Abbott (anti-nucleocapsid) and then the Ortho (anti-spike) assays, seroprevalence estimates ranged from 0.4%-1.4%, despite ongoing disease activity.
The geometric mean concentration (GMC) of antibody-positive specimens decreased over time (p=0.015), and the GMC of antibody-negative specimens increased over time (p=0.0018). The association between the two tests decreased each month (p<0.001), suggesting
anti-N antibody decline. Lowering the Abbott index cut-off from 1.4 to 0.7 resulted in a 16% increase in positive specimens. |
|
Bonner, Carissa, Batcup, et al |
medRxiv |
Public Health response| Interventions de santé publique |
There is very little research on the behaviours and behavioural barriers involved in getting tested, both in Australia
and worldwide, despite there being some evidence that these barriers do exist. Only 49% (n=1369) of people strongly agreed they would get tested if they had COVID-19 symptoms, but most people agreed to some extent that they would get tested (96%). The most
common barriers selected from the list provided were that testing is painful (11%), not knowing how to get tested (7%), and worry about getting infected at the testing centre (5%). Many participants (10%) indicated other reasons, and open responses included
many additional barriers to testing than those provided in the initial list. These covered all components of the COM-B model. |
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The "Great Lockdown": Inactive Workers and Mortality
by Covid-19 |
Borri, Nicola, Drago, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
This paper estimates the causal effect of the economic lockdown in Italy on mortality by Covid-19 and on mobility patterns.
Our results show that the intensity of the economic lockdown is associated to a statistically significant reduction in mortality by Covid-19 and, in particular, for age groups between 40-64 and older. Back of the envelope calculations indicate that 4,793 deaths
were avoided, in the 26 days between April 5 to April 30, in the 3,518 municipalities which experienced a more intense lockdown. Assuming linearity, a 1 percentage point reduction in the share of active population caused a 1.32 percentage points reduction
in mortality by Covid-19. We also find that the economic lockdown, as expected, led to a reduction in human mobility. Several robustness checks corroborate our empirical findings. |
|
Bradfield, Zoe, Wynter, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
Evidence on the experience of those receiving or providing maternity care is important to guide practice through this
challenging time. A cross-sectional study was conducted in Australia and a total of 3701 completed responses were received. While anxiety related to COVID-19 was high among all five cohorts, there were statistically significant differences between the responses
from each cohort for most survey items. Women were more likely to indicate concern about their own and family's health and safety in relation to COVID-19 whereas midwives, doctors and midwifery students were more likely to be concerned about occupational exposure
to COVID-19 through working in a health setting than those receiving care through attending these environments. Midwifery students and women's partners were more likely to respond that they felt isolated because of the changes to the way care was provided.
Despite concerns about care received or provided not meeting expectations, most respondents were satisfied with the quality of care provided, although midwives and midwifery students were less likely to agree. |
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Variation across population subgroups of COVID-19
antibody testing performance |
Brantley, HalleyL, Yoo, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes Public
Health response| Interventions de santé publique |
Understanding variations in the performance of serological tests for SARS-CoV-2 across varying demographics is relevant
to clinical interpretations and public policy derived from their results. Appropriate use of serological assays to detect anti-SARS-CoV-2 antibodies requires estimation of their accuracy over large populations and an understanding of the variance in performance
over time and across demographic groups. In this manuscript we focus on anti-SARS-CoV-2 IgG, IgA, and IgM antibody tests approved under emergency use authorizations and determine the recall of the serological tests compared to RT-PCR tests by Logical Observation
Identifiers Names and Codes (LOINCs). Variability in test performance was further examined over time and by demographics. The recall of the most common IgG assay (LOINC 94563-4) was 91.2% (95% CI: 90.5%, 91.9%). IgA (LOINC 94562-6) and IgM (94564-2) assays
performed significantly worse than IgG assays with estimated recall rates of 20.6% and 27.3%, respectively. A statistically significant difference in recall (p = 0.019) was observed across sex with a higher recall in males than females, 92.1% and 90.4%, respectively.
Recall also differed significantly by age group, with higher recall in those over 45 compared to those under 45, 92.9% and 88.0%, respectively (p < 0.001). While race was unavailable for the majority of the individuals, a significant difference was observed
between recall in White individuals and Black individuals (p = 0.007) and White individuals and Hispanic individuals (p=0.001). The estimates of recall were 89.3%, 95.9%, and 94.2% for White, Black, and Hispanic individuals respectively. |
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Analysis of geo-temporal evolution and modeling of
the COVID-19 epidemic in Libya |
Bredan, Amin, Benamer, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
The epidemic in Libya was modeled using the classical Susceptible-Exposed-Infected-Recovered (SEIR) mathematical model
of infectious disease epidemics. Three scenarios were developed based on three estimates of the fraction of the population exposed to the disease (1.5, 2.5 and 3.5%). The modeling portrays the peak of the epidemic around early August and estimates that the
number of deaths will flatten out around early November at between 250 and 600, depending on the parameter employed. More deaths than those estimated implies that is more widespread than assumed. Greater promotion of awareness and understanding of social distancing
practices and their value is needed, particularly in the south, and better protection of the elderly should decrease mortality. |
|
Brinks, Ralph, Kuechenhoff, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
In this work, we assess the four frequently used measures with respect to incomplete case-detection: 1) cumulative
case-count, 2) incidence rate, 3) effective reproduction number and 4) doubling time. We apply an age-structured SIR model to simulate a SARS-CoV-2 outbreak followed by a lockdown in a hypothetical population. Different scenarios about temporal variations
in case-detection are applied to the four measures during outbreak and lockdown. The biases resulting from incomplete case-detection on the four measures are compared. It turns out that the most frequently used epidemiological measure, the cumulative case
count is most prone to bias in all of our settings. The effective reproduction number is the least biased measure. |
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Self-sampling of capillary blood for serological
testing of SARS-CoV-2 by COVID-19 IgG ELISA |
Brown, Lottie, Byrne, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Serological testing is emerging as a powerful tool to progress our understanding of COVID-19 exposure, transmission
and immune response. Large-scale testing is limited by the need for in-person blood collection by staff trained in venepuncture. Capillary blood self-sampling and postage to laboratories for analysis could provide a reliable alternative. Two-hundred and nine
matched venous and capillary blood samples were obtained from thirty nine participants and analysed using a COVID-19 IgG ELISA to detect antibodies against SARS-CoV-2. Thirty seven out of thirty eight participants were able to self-collect an adequate sample
of capillary blood (≥50 μl). Using plasma from venous blood collected in lithium heparin as the reference standard, matched capillary blood samples, collected in lithium heparin-treated tubes and on filter paper as dried blood spots, achieved a Cohen′s kappa
coefficient of >0.88 (near-perfect agreement). Storage of capillary blood at room temperature for up to 7 days post sampling did not affect concordance. Our results indicate that capillary blood self-sampling is a reliable and feasible alternative to venepuncture
for serological assessment in COVID-19. |
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Dynamic Prioritization of COVID-19 Vaccines When
Social Distancing is Limited for Essential Workers |
Buckner, Jack Hoyt, Chowell, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique Public Health response| Interventions de santé publique |
We assess the optimal allocation of a limited and dynamic COVID-19 vaccine supply in the U.S. across socio-demographic
groups differentiated by age and essential worker status. The transmission dynamics are modeled using a compartmental (SEIR) model parameterized to capture our current understanding of the transmission and epidemiological characteristics of COVID-19, including
key sources of group heterogeneity (susceptibility, severity, and contact rates). We investigate tradeoffs between three alternative policy objectives: minimizing infections, years of life lost, or deaths. Moreover, we model dynamic vaccine prioritization
policies that respond to changes in the epidemiological status of the population as SARS-CoV-2 continues its march. Because contacts tend to be concentrated within age groups, there is diminishing marginal returns as vaccination coverage increases in a given
group, increasing the group's protective immunity against infection and mortality. We find that optimal prioritization consistently targets older essential workers. However, depending on the policy objective, younger essential workers are prioritized to minimize
infections or seniors in order to minimize mortality. Optimal prioritization outperforms non-targeted vaccination strategies by up to 18% depending on the outcome optimized. For example, in our baseline model, cumulative mortality decreased on average by 17%
(25,000 deaths in the U.S. population) over the course of the outbreak. |
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National Longitudinal Mediators of Psychological
Distress During Stringent COVID-19 Lockdown |
Bulbulia, JosephA, Piven, et al |
medRxiv |
Public Health response| Interventions de santé publique |
We leverage powerful time-series data from a national longitudinal sample measured before the COVID-19 pandemic and
during the world's eighth most stringent COVID-19 lockdown (New Zealand, March-April 2020, N = 940) and apply Bayesian multilevel mediation models to rigorously test five theories of pandemic distress. Findings: (1) during lockdown, rest diminished distress;
without rest psychological distress would have been about 1.74 times greater; (2) an elevated sense of community reduced distress, a little, but elevated government satisfaction was inert. Thus, the psychological benefits of lockdown extended to political
discontents; (3) most lockdown distress arose from dissatisfaction from personal relationships. Social captivity, more than isolation, proved challenging; (4-5) Health and business satisfaction were stable; were they challenged substantially more distress
would have ensued. Thus, lockdown benefited psychological health by affording safety, yet only because income remained secure. These national longitudinal findings clarify the mental health effects of stringent infectious disease containment. |
|
Buss, LewisF, Prete, et al |
medRxiv |
Epidemiology| Épidémiologie Public Health response| Interventions de santé publique |
Here we show that the transmission of SARS-CoV-2 in Manaus, located in the Brazilian Amazon, increased quickly during
March and April and declined more slowly from May to September. In June, one month following the epidemic peak, 44% of the population was seropositive for SARS-CoV-2, equating to a cumulative incidence of 52%, after correcting for the false-negative rate of
the antibody test. The seroprevalence fell in July and August due to antibody waning. After correcting for this, we estimate a final epidemic size of 66%. Although non-pharmaceutical interventions, plus a change in population behavior, may have helped to limit
SARS-CoV-2 transmission in Manaus, the unusually high infection rate suggests that herd immunity played a significant role in determining the size of the epidemic. |
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Assessment of Commercial SARS-CoV-2 Antibody Assays,
Jamaica |
Butterfield, TiffanyR, Bruce-Mowatt, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
The performance of the Roche Elecsys® Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 IgG, Euroimmun SARS-CoV-2 IgA, Euroimmun
SARS-CoV-2 IgG ELISA, and Trillium IgG/IgM rapid assays was evaluated in Jamaica. Serum samples collected ≥14 days after onset of symptoms, or ≥14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging
from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. Grouping moderate to critical disease showed a significant association with a SARS-CoV-2 antibody positive result
for all assays. Diagnostic specificity, assessed by testing serum samples collected during 2018-2019 from healthy persons and from persons with antibodies to a wide range of viral infections, ranged from 96.7-100.0%. For all assays examined, SARS-CoV-2 real-time
PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive were significantly different for samples testing antibody positive versus negative. |
|
Camargo, Emerson Lucas Silva, Oliveira, et al |
medRxiv |
Public Health response| Interventions de santé publique |
This cross-sectional study's objective was to analyze the factors associated with MSM's low psychological well-being
in the COVID-19 pandemic context. Only 44.4% of the sample presented high levels of well-being. Low psychological well-being appeared associated with the youngest age group (PR: 2.76; CI95%: 1.90-4.01), polyamorous relationships (PR: 2.78; CI95%: 1.51-5.11),
not complying with social isolation measures (PR: 6.27; CI95%: 4.42-8.87), not using the social media to find partners (PR: 1.63; CI95%: 1.06-2.53), having multiple sexual partners (PR: 1.80; CI95%: 1.04-3.11), having reduced the number of partners (PR: 2.67;
CI95%: 1.44-4.95), and group sex (PR: 1.82; CI95%: 1.23-2.69). |
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DNA Methylation Architecture of the ACE2 gene in
Nasal Cells |
Cardenas, Andres, Rifas-Shiman, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Diagnostics / Pathogen
detection| Diagnostics / Détection d'agents pathogènes |
We collected nasal swabs from anterior nares of 547 children, measured DNA methylation (DNAm), and tested differences
at 15 ACE2 CpGs by sex, age, race/ethnicity and epigenetic age. ACE2 CpGs were differentially methylated by sex with 12 sites having lower DNAm (mean=12.71%) and 3 sites greater DNAm (mean=1.45%) among females relative to males. We observed differential DNAm
at 5 CpGs for Hispanic females (mean absolute difference=3.22%) and lower DNAm at 8 CpGs for Black males (mean absolute difference=1.33%), relative to white participants. Longer DNAm telomere length was associated with greater ACE2 DNAm at 11 and 13 CpGs among
males (mean absolute difference=7.86%) and females (mean absolute difference=8.21%), respectively. Nasal ACE2 DNAm differences could contribute to our understanding COVID-19 severity and disparities reflecting upstream environmental and social influences. |
|
Carrat, Fabrice, de Lamballerie, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
This study aimed to estimate the seroprevalence of SARS-CoV-2 infection in May-June 2020 after the lockdown in adults
living in three regions in France and to identify the associated risk factors. Between May 4, 2020 and June 23, 2020, 16,000 participants were asked to provide DBS, and 14,628 were included in the analysis, 983 with a positive ELISA-S, 511 with a positive
ELISA-NP, 424 with SN>=40 and 941 (Standard Deviation=31) with a positive MI. Adjusted estimates of seroprevalence (positive ELISA-S) were 10.0% (95%CI 9.1%;10.9%) in IDF, 9.0% (95%CI 7.7%; 10.2%) in GE and 3.1% (95%CI 2.4%; 3.7%), in NA. The adjusted prevalence
of positive ELISA-NP, SN and MI were 5.7%, 5.0% and 10.0% in IDF, 6.0%, 4.3% and 8.6% in GE, and 0.6%, 1.3% and 2.5% in NA, respectively. A higher seroprevalence was observed in younger participants and when at least one child or adolescent lived in the same
household. A lower seroprevalence was observed in smokers compared to non-smokers. |
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|
Carsetti, Rita, Zaffina, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie |
To understand the basis of the protective immune response in COVID-19, we performed a longitudinal follow-up, flow-cytometric
and serological analysis of innate and adaptive immunity in 64 adults with a spectrum of clinical presentations: 28 healthy SARS-CoV-2-negative contacts of COVID-19 cases; 20 asymptomatic SARS-CoV-2-infected cases; 8 patients with Mild COVID-19 disease and
8 cases of Severe COVID-19 disease. Our data show that high frequency of NK cells and early and transient increase of specific IgA, IgM and, to a lower extent, IgG are associated to asymptomatic SARS-CoV-2 infection. By contrast, monocyte expansion and high
and persistent levels of IgA and IgG, produced relatively late in the course of the infection, characterize severe disease. Modest increase of monocytes and different kinetics of antibodies are detected in mild COVID-19. The importance of innate NK cells and
the short-lived antibody response of asymptomatic individuals and patients with mild disease suggest that only severe COVID-19 may result in protective memory established by the adaptive immune response. |
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|
Carvallo, Hector Eduardo, Hirsch, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique |
We have designed an experimental treatment called IDEA based on four affordable drugs already available on the market
in Argentina, based on the following rationale: -Ivermectin solution at a relatively high dose to lower the viral load in all stages of COVID 19 -Dexamethasone 4-mg injection, as anti-inflammatory drug to treat hyperinflammatory reaction to COVID-infection
-Enoxaparin injection as anticoagulant to treat hypercoagulation in severe cases. -Aspirin 250-mg tablets to prevent hypercoagulation in mild and moderate cases. A clinical study has been conducted on COVID-19 patients at Eurnekian Hospital in the Province
of Buenos Aires, Argentina. The study protocol and its final outcomes are described in this article. Results were compared with published data and data from patients admitted to the hospital receiving other treatments. None of the patient presenting mild symptoms
needed to be hospitalized. Only one patient died (0.59 % of all included patients vs. 2.1 % overall mortality for the disease in Argentina today; 3.1 % of hospitalized patients vs. 26.8 % mortality in published data). IDEA protocol appears to be a useful alternative
to prevent disease progression of COVID-19 when applied to mild cases and to decrease mortality in patients at all stages of the disease with a favorable risk-benefit ratio. |
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Modeling COVID-19 as a National Dynamics with a SARS-CoV-2
Prevalent Variant: Brazil - A Study Case |
Celaschi, Sergio |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
COVID-19 global dynamics is modeled by an adaptation of the deterministic SEIR Model, which takes into account two
dominant lineages of the SARS-CoV-2, and a time-varying reproduction number to estimate the disease transmission behavior. The pandemic in Brazil was selected as a first study case. By the end of 2020, the predicted numbers of confirmed cases in Brazil, within
95% credible intervals, may reach 6 Million (5 to 7), and fatalities would accounts for 180 (130 to 220) thousands. The total number of infected individuals is estimated to reach (13 +/- 1) Million, 6.2% of the Brazilian population. Regarding the original
SARS-CoV-2 form and its variant, the only model assumption is their distinct incubation rates. The variant form reaches a maximum of 96% of exposed individuals as previously reported for South America. |
|
Cerda, Pau, Ribas, et al |
Antimicrob Agents Chemother |
Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
Here, we demonstrate that the antiparasitic drug suramin inhibits SARS-CoV-2 replication, protecting Vero E6 cells
with a 50% effective concentration (EC50) of ∼20 μM, which
is well below the maximum attainable level in human serum. Suramin also decreased the viral load by 2 to 3 logs when Vero E6 cells or cells of a human lung epithelial cell line (Calu-3 2B4 [referred to here as “Calu-3”]) were treated. Time-of-addition and
plaque reduction assays performed on Vero E6 cells showed that suramin acts on early steps of the replication cycle, possibly preventing binding or entry of the virus. In a primary human airway epithelial cell culture model, suramin also inhibited the progression
of infection. The results of our preclinical study warrant further investigation and suggest that it is worth evaluating whether suramin provides any benefit for COVID-19 patients, which obviously requires safety studies and well-designed, properly controlled
randomized clinical trials. |
|
|
Chapman, LloydAC, Kushel, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique Public Health response| Interventions de santé publique |
This study aimed to estimate the probability of averting outbreaks in homeless shelters under different infection control
strategies. Basic reproduction number (R0) estimates for the observed outbreaks ranged from 2.9 to 6.2. The probability of averting an outbreak diminished with higher transmissibility (R0) within the simulated shelter and increasing transmission intensity
in the local community. With moderate transmission intensity in the local community, the estimated probabilities of averting an outbreak in a low-risk (R0=1.5), moderate-risk (R0=2.9), and high-risk (R0=6.2) shelter were: 0.33, 0.11 and 0.03 for daily symptom-based
screening; 0.52, 0.27, and 0.04 for twice-weekly PCR testing; 0.47, 0.20 and 0.06 for universal masking; and 0.68, 0.40 and 0.08 for these strategies combined. |
|
|
Chartier, KarenG, Guidry, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The current study seeks to understand the links between social media use and alcohol consumption during the early months
of the COVID-19 pandemic. Twitter and Instagram users, but not Facebook users, drank more frequently at wave 3 than non-users. For Instagram users, more frequent alcohol use at wave 3 was at least partially attributed to the frequency of drinking at wave 1.
The interaction between Twitter use and working or studying from home was statistically significant. The combination of being on Twitter and working or studying from home was associated with drinking more days a week. |
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|
Chatterjee, Sheshadri Shekhar, Chakrabarty, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
This cross-sectional study investigated mental distress among HCWs during the early phase of the coronavirus disease-2019
(COVID-19). 140 HCWs of a tertiary care hospital in India were assessed for perceived stress and insomnia. Doctors were the most anxious among the HCWs. Both doctors and nurses perceived a greater level of irritability than the other HCWs. Compared to the
doctors and nurses, other HCWs were more likely to experience insomnia. Lower age, higher education, female gender, and urban habitat were associated with the perception of anxiety. Older age, quarantine, single marital-status predicted irritability. Female
gender, single marital-status, and greater ailments contributed to perceived hopelessness. Quarantine significantly predicted insomnia. |
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Knowledge, attitudes and practices of COVID 19 among
Medical Laboratory Professionals in Zambia |
Chawe, Adon, Mfune, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
We conducted a quick online questionnaire to investigate the knowledge, attitudes and practices of medical laboratory
personnel regarding COVID-19 in Zambia. A total of 208 medical laboratory professionals participated in the study. There were more males (58.2%) than females. The majority of respondents had good knowledge (84.1%) and practice (75%) regarding COVID-19. Less
than half (n=97, 46.6%) reported willingness to participate in a vaccination program. Predictors of good knowledge included; having a Bachelors degree (AOR: 5.0, CI: 1.15-23.9) and having prior COVID-19 related training (AOR: 8.83, CI: 2.03-38.4). Predictors
of good practice included; having a masters or PhD qualification (AOR: 5.23, CI: 1.15-23.9) and having prior COVID-19 related training (AOR: 14.01, CI: 6.47-30.4). |
|
Two Color Single Molecule Sequencing on GenoCare
1600 Platform to Facilitate Clinical Applications |
Chen, Fang, Liu, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
With the rapid development of precision medicine industry, DNA sequencing becomes increasingly important as a research
and diagnosis tool. For clinical applications, medical professionals require a platform which is fast, easy to use, and presents clear information relevant to definitive diagnosis. We have developed a single molecule desktop sequencing platform, GenoCare 1600.
Fast library preparation (without amplification) and simple instrument operation make it friendlier for clinical use. Here we presented sequencing data of E. coli sample from GenoCare 1600 with consensus accuracy reaches 99.99%. We also demonstrated sequencing
of microbial mixtures and COVID-19 samples from throat swabs. Our data show accurate quantitation of microbial, sensitive identification of SARS-CoV-2 virus and detection of variants confirmed by Sanger sequencing. |
|
Chen, VL, Hawa, et al |
Dig Dis Sci |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study characterize the impact of hepatic steatosis (HS) on disease severity and liver injury in COVID-19. In
a cohort of 342 patients, metabolic disease was highly prevalent including nearly 90% overweight. HS was associated with increased transaminitis and need for intubation, dialysis, and vasopressors. There was no association between HS and jaundice or portal
hypertensive complications. In a sensitivity analysis including only patients with liver imaging > 30 days before onset of COVID-19, imaging evidence of hepatic steatosis remained associated with disease severity and risk of transaminitis. |
|
|
Chen, Zhitong, Garcia, et al |
medRxiv |
Coronavirology| Coronavirologie Infection Prevention and Control/ Prévention et contrôle
des infections (IPAC/PCI) |
SARS-CoV-2 infectious virions are viable on various surfaces (e.g., plastic, metals, cardboard) for several hours.
This presents a transmission cycle for the human infection that can be broken by developing new inactivation approaches. We employed an efficient cold atmospheric plasma (CAP) with argon feed gas to inactivate SARS-CoV-2 on various surfaces including plastic,
metal, cardboard, basketball composite leather, football leather, and baseball leather. These results demonstrate the great potential of CAP as a safe and effective means to prevent virus transmission and infections. |
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Causal Impact of Masks, Policies, Behavior on Early
Covid-19 Pandemic in the U.S |
Chernozhukov, Victor, Kasahara, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
The paper evaluates the dynamic impact of various policies adopted by US states on the growth rates of confirmed Covid-19
cases and deaths as well as social distancing behavior measured by Google Mobility Reports, where we take into consideration people's voluntarily behavioral response to new information of transmission risks in a causal structural model framework. Our analysis
finds that both policies and information on transmission risks are important determinants of Covid-19 cases and deaths and shows that a change in policies explains a large fraction of observed changes in social distancing behavior. Our main counterfactual
experiments suggest that nationally mandating face masks for employees early in the pandemic could have reduced the weekly growth rate of cases and deaths by more than 10 percentage points in late April and could have led to as much as 19 to 47 percent less
deaths nationally by the end of May, which roughly translates into 19 to 47 thousand saved lives. We also find that, without stay-at-home orders, cases would have been larger by 6 to 63 percent and without business closures, cases would have been larger by
17 to 78 percent. We find considerable uncertainty over the effects of school closures due to lack of cross-sectional variation; we could not robustly rule out either large or small effects. |
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Perceived risk of infection and smoking behavior change during COVID-19 in Ohio |
Chertok, IRA |
Public Health Nurs |
Public Health response| Interventions de santé publique |
The purpose of this cross-sectional study was to examine factors associated with reducing smoking exposure during the
COVID-19 outbreak. 810 adults in Ohio (77.9% non-smokers, 22.1% current smokers) completed an online survey. For the overall sample, the odds of indoor smoking bans were significantly associated with never smoked, college education, single-family residence,
not living with smokers, and perceived importance of avoiding public places. For smokers, the desire to quit smoking since the COVID-19 outbreak was associated with diabetes and perceived risk of severe infection. |
|
Chiara-Chilet, Christian, Luna-Vilchez, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study describes the clinical, epidemiological and treatment characteristics of children presenting COVID-19 at
the Instituto Nacional de Salud del Niño San Borja (INSN-SB). We included 91 patients, 33 being females (36.3%). The most affected age group was children > 2 years of age (63 cases) with a median age of 6 years (IQR 3-10), and 61.5% were from Lima. The previous
contact was determined in 30.8% of cases. A positive SARS CoV-2 PCR result was obtained in 50.6%. The presence of comorbidity was 53.8%. The most frequent symptoms were: fever (39.6%), general malaise (23.1%), cough (19.8%), and respiratory distress (14.3%).
The presence of multisystem inflammatory syndrome in children (MIS-C) was confirmed in 6 patients. Antibiotics were administered in 76.9%. The most frequent radiological pattern was bilateral interstitial infiltrates (57.7%). Mortality was higher in patients
in the ICU than in the hospitalization ward (27.3% vs. 4.3%, respectively; p = 0.02). |
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|
Chikontwe, Philip, Luna, et al |
medRxiv |
Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
In this study, we propose an attention-based end-to-end weakly supervised framework for the rapid diagnosis of COVID-19
and bacterial pneumonia based on multiple instance learning (MIL). We further incorporate unsupervised contrastive learning for improved accuracy with attention applied both in spatial and latent contexts, herein we propose Dual Attention Contrastive based
MIL (DA-CMIL). DA-CMIL takes as input a several patient CT slices (considered as a bag of instances) and outputs a single label. Attention based pooling is applied to implicitly select key slices in latent space, and spatial attention learns slice spatial
context for interpretable diagnosis. A contrastive loss is applied at the instance level to encode similarity in features from the same patient against pooled patient features. Empirical results show our algorithm achieves an overall accuracy of 98.6% and
an AUC of 98.4%. Moreover, ablation studies show the benefit of contrastive learning with MIL. |
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|
Effects of non-pharmaceutical interventions on COVID-19:
A Tale of Three Models |
Chin, Vincent, Ioannidis, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
In this paper, we compare the inference regarding the effectiveness of the various non-pharmaceutical interventions
(NPIs) for COVID-19 obtained from three SIR models, all developed by the Imperial College COVID-19 Response Team. We demonstrate that inference is highly nonrobust to model specification. In particular, inference regarding the relative effectiveness of NPIs
changes substantially with the model and decision makers who are unaware of, or ignore, model uncertainty are underestimating the risk attached to any decisions based on that model. Our primary observation is that by applying to European countries the model
that the Imperial College team used for the USA states (model 2), complete lockdown has no or little effect, since it was introduced typically at a point when R_t was already very low. Moreover, using several state-of-the-art metrics for Bayesian model comparison,
we demonstrate that model 2 (when applied to the European data) is better supported by the data than the model published in Nature. In particular, serious doubt is cast on the conclusions in Flaxman et al., whether we examine the data up to May 5th (as in
Flaxman et al.) or beyond the point when NPIs began to be lifted. Only by objectively considering a wide variety of models in a statistically principled manner, can one begin to address the effectiveness of NPIs such as lockdown. |
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SARS-CoV-2 PCR cycle threshold at hospital admission
associated with Patient Mortality |
Choudhuri, Jui, Carter, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The relationship of initial Ct at hospitalization and patient mortality has not been thoroughly investigated. We conducted
a retrospective study of all SARS-CoV-2 positive, hospitalized patients from 3/26/2020 to 8/5/2020 who had SARS CoV-2 Ct data within 48 hours of admission (n=1044). In this cohort the mean Ct at admission was higher for survivors (28.6, SD=5.8) compared to
non-survivors (24.8, SD=6.0, P<0.001). Patients with a lower Ct value on admission were found to have a higher odds ratio (0.91, CI 0.89-0.94, p<0.001) of in hospital mortality after adjusting for age, gender, body mass index (BMI) and history of hypertension
and diabetes. Patients with Ct values in 3rd Quartile (Ct 27.4-32.8) and 4th Quartile (Ct >32.9) have a lower odds of in-hospital death (P<0.001) in comparison to the 1st Quartile. On comparing between Ct quartiles, the mortality, BMI and glomerular filtration
rate (GFR) were significantly different (p<0.05) between the groups. The cumulative incidence of all-cause mortality and discharge was found to differ between Ct quartiles (Grays Test P<0.001 for both.) |
|
Cipriani, A, Capone, et al |
Intern Emerg Med |
Clinical data| Données cliniques |
This study described the clinical characteristics and outcomes of a cohort of Italian inpatients, admitted to a medical
COVID-19 Unit, and investigated the relative role of cardiac injury on in-hospital mortality. A total of 109 COVID-19 inpatients (female 36%, median age 71 years) were included. During in-hospital stay, 20 patients (18%) died and, compared with survivors,
these patients were older, had more comorbidities and higher levels of high-sensitivity cardiac troponin I (Hs-cTnI), both at first evaluation and peak levels. A dose-response curve between Hs-cTnI and in-hospital mortality risk up to 200 ng/L was detected.
Hs-cTnI, chronic kidney disease, and chronic coronary artery disease mediated most of the risk of in-hospital death, with Hs-cTnI mediating 25% of such effect. Smaller effects were observed for age, lactic dehydrogenase, and D-dimer. |
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IMPACT OF UNIVERSITY RE-OPENING ON TOTAL COMMUNITY
COVID-19 BURDEN |
Cipriano, LaurenE, Haddara, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique Public Health response| Interventions de santé publique |
We evaluated the impact of a large student population returning to a mid-sized city currently experiencing a low rate
of COVID-19 on community health outcomes. We consider whether targeted routine or one-time screening in this population can mitigate community COVID-19 impacts. We developed a dynamic transmission model of COVID-19 subdivided into three interacting populations:
general population, university students, and long-term care residents. In a city with low levels of COVID-19 activity, the return of a relatively large student population substantially increases the total number of COVID-19 infections in the community. In
a scenario in which students immediately engage in a 24% contact reduction compared to pre-COVID levels, the total number of infections in the community increases by 87% (from 3,900 without the students to 7,299 infections with the students), with 71% of the
incremental infections occurring in the general population, causing social and economic restrictions to be re-engaged 3 weeks earlier and an incremental 17 COVID-19 deaths. Scenarios in which students have an initial, short-term increase in contacts with other
students before engaging in contact reduction behaviours can increase infections in the community by 150% or more. In such scenarios, screening asymptomatic students every 5 days reduces the number of infections attributable to the introduction of the university
student population by 42% and delays the re-engagement of social and economic restrictions by 1 week. Compared to screening every 5 days, one-time mass screening of students prevents fewer infections, but is highly efficient in terms of infections prevented
per screening test performed. |
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Assessment of the Haemophagocytic lymphohistiocytosis HScore in patients with COVID-19 |
Clark, KEN, Nevin, et al |
Clin Infect Dis |
Clinical data| Données cliniques |
The clinical manifestation of moderate to severe COVID-19 has parallels to secondary haemophagocytic lymphohistiocytosis
(HLH) both clinically and based on molecular inflammatory response. We found no evidence to support the utility of risk stratifying COVID-19 patients using risk scoring methodology designed for HLH. |
|
Clay, JamesM, Stafford, et al |
medRxiv |
Public Health response| Interventions de santé publique |
We assessed change in alcohol-use and hazardous drinking during the first lockdown, and tested the hypothesis that
variation would be predicted by stress and inhibitory-control in 13,453 respondents in the UK as part of a longitudinal survey. The survey found that alcohol use increased in up to 30% of the population during COVID-19, resulting from a combination of factors
including poor inhibitory control and stress. |
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|
Colombo, Marco, Mellor, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
The authors propose relaxing the assumption of homogeneity to allow for individual variation in susceptibility in the
context of SIR models of infection. The authors created a model that shows improved fit and 14-day forward prediction. Allowing for heterogeneity was also found to reduce the estimate of “counterfactual” deaths that would have occurred if there had been no
interventions from 3.2 million to 262,000, implying that most of the slowing and reversal of COVID-19 mortality is explained by the build-up of herd immunity. The estimate of the herd immunity threshold depends on the value specified for the infection fatality
ratio (IFR): a value of 0.3% for the IFR gives 15% for the average herd immunity threshold. |
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Treatment of Moderate to Severe Respiratory COVID-19--A
Cost-Utility Analysis |
Congly, StephenE, Varughese, et al |
medRxiv |
Economics | Économie |
We developed a cost-effectiveness analysis of remdesivir and dexamethasone in the United States context with additional
global considerations assessed by willingness-to-pay thresholds. We found that supportive care for moderate/severe COVID-19 cost $11,112.98/0.8256 QALY. Remdesivir in moderate/dexamethasone in severe infections was the most cost-effective with an incremental
cost-effectiveness ratio of $19,764.56/QALY gained compared to supportive care. |
|
Coppola, Pierluigi, De Fabiis, et al |
Research Square prepub |
Public health interventions*| Interventions de santé publique |
This paper aims at giving a contribution to the undergoing social distancing debate by presenting the results of a
study to forecast the impacts of keeping an interpersonal distancing of one-meter between passengers on board (sub-urban and high-speed) trains. The results of the study have been shared and discussed with a panel of chief executives of industries, consultancies
in the mobility sector and Public Transportation (PT) companies. It has emerged that interpersonal distancing and the reduced level of capacity on board vehicles are seen as effective to prevent the contagion, but are perceived as not sustainable due to the
induced increase in operating costs. This is confirmed by the simulation carried out during the study which have showed the need of new urban policies not only limited to the transportation domain (e.g. changes in the times of schools, commerce and industries)
in order to manage the demand peaks at the stations and on-board vehicles. |
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LOW BIRTH WEIGHT AS A RISK FACTOR FOR SEVERE COVID-19
IN ADULTS |
Crispi, Fatima, Crovetto, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We analyzed a prospective cohort of 397 patients (18-70y) with laboratory-confirmed SARS-CoV-2 infection attended in
a tertiary hospital, where 15% required admission to Intensive Care Unit (ICU) in order to assess low birth weight (LBW) as a risk factor for severe Covid-19. Overall, LBW seems to be an independent risk factor for severe COVID-19 in non-elderly adults and
might improve the performance of risk stratification algorithms. |
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Genome sequencing of sewage detects regionally prevalent
SARS-CoV-2 variants |
Crits-Christoph, Alexander, Kantor, et al |
medRxiv |
Epidemiology| Épidémiologie Surveillance Coronavirology| Coronavirologie |
Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area
to generate complete and near-complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. We additionally characterized minor SARS-CoV-2 alleles in the wastewater and detected
viral genotypes which were also found within clinical genomes throughout California. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context. |
|
Cruz, LeticiaR, Baladron, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique RCT |
In this exploratory study (proof-of-concept), we administered intravenous CIGB-325 at 2.5 mg/kg along with standard-of-care
for treating SARS-Cov2 positive patients in Cuba which is based on alpha 2b-IFN plus kaletra/hydroxyquinoline. CIGB-325 induced transient mild and/or moderate adverse events like pruritus, flushing and rash in some patients. Both therapeutic regimens were
similar respect to SARS-Cov2 clearance in nasopharynx swabs over the time. |
|
|
Vaccination strategies against COVID-19 and the diffusion of anti-vaccination views |
Curiel, Rafael Prieto, Ramirez, et al |
arXiv |
Public Health response| Interventions de santé publique |
Here, we analyse epidemic spreading and optimal vaccination strategies, measured with the average years of life lost,
in two network topologies (scale-free and small-world) assuming full adherence to vaccine administration. We consider the spread of anti-vaccine views in the network, using a similar diffusion model as the one used in epidemics, which are adopted based on
a persuasiveness parameter of anti-vaccine views. Results show that even if an anti-vaccine narrative has a small persuasiveness, a large part of the population will be rapidly exposed to them. Assuming that all individuals are equally likely to adopt anti-vaccine
views after being exposed, more central nodes in the network are more exposed and therefore are more likely to adopt them. Comparing years of life lost, anti-vaccine views could have a significant cost not only on those who share them, since the core social
benefits of a limited vaccination strategy (reduction of susceptible hosts, network disruptions and slowing the spread of the disease) are substantially shortened. |
|
Prognostic value of sTREM-1 in COVID-19 patients:
a biomarker for disease severity and mortality |
da Silva Neto, PedroV, de Carvalho, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study aims to investigate the association between soluble TREM-1 (sTREM-1) and COVID-19 as a prognostic biomarker
to predict the disease severity, lethality and clinical management. Within COVID-19 patients, the highest severity was associated with the most significant elevated plasma levels sTREM-1. Using receiver operating curve analysis (ROC), sTREM-1 was found to
be predictive of disease severity (AUC= 0.988) and the best cut-off value for predicting in-hospital severity was ≥ 116.5 pg/mL with the sensitivity for 93.3% and specificity for 95.8%. |
|
Dabbous, HanyM, El-Sayed, et al |
Research Square prepub |
Clinical data| Données cliniques Therapeutics| Thérapeutique RCT |
We aimed to explore the safety and efficacy of favipiravir in treatment of COVID-19 mild and moderate cases in a randomized-controlled
open-label interventional phase 3 clinical trial NCT04349241. 50 patients received favipiravir 3200mg at day1 followed by 600mg twice (day2-day10). 50 patients received hydroxychloroquine 800mg at day1 followed by 200mg twice (day2- 10) and oral oseltamivir
75mg/12hour/day for 10 days. Both arms were comparable as regards demographic characteristics and comorbidities. The average onset of SARS-CoV-2 PCR negativity was 8.1 and 8.3 days in HCQ-arm and favipiravir-arm respectively. 55.1% of those on HCQ-arm turned
PCR negative at/or before 7th day from diagnosis compared to 48% in favipiravir-arm (p=0.7). Four patients in FVP arm developed transient transaminitis on the other hand heartburn and nausea were reported in about 20 patients in HCQ-arm. Only one patient in
HCQ-arm died after developing acute myocarditis resulted in acute heart failure. Favipiravir is a safe effective alternative for hydroxychloroquine in mild or moderate COVID-19 infected patients. |
|
|
Dada, Sara, Ashworth, et al |
medRxiv |
Public Health response| Interventions de santé publique |
This study analyzes the public speeches and statements made by heads of government in 20 countries around the world.
The purpose is to understand the different language, rhetoric, and priorities expressed by men and women leaders in responding to the COVID-19 pandemic. Five primary themes emerged across a total of 122 speeches on COVID-19 made by heads of government: economics
and financial relief, social welfare and vulnerable populations, nationalism, responsibility and paternalism, and emotional appeals. While all leaders described the economic impact of the pandemic, women leaders spoke more frequently about the impact on local
or individual scale. Women leaders were also more often found describing a wider range of social welfare services, including addressing to: mental health, substance abuse, and domestic violence. |
|
|
Quantifying the Effects of Social Distancing on the
Spread of COVID-19 |
Daghriri, Talal, Ozmen, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
We developed an agent-based simulation model by using Netlogo simulation software to quantify the effect of social
distancing on the spread of COVID-19 disease. The results of our study show that social distancing affects the spread of COVID-19 significantly, where the spread of disease and infection rates decrease once social distancing procedures are implemented at higher
levels. |
|
Dai, Ziwei, Locasale, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission
Public health interventions*| Interventions de santé publique |
We develop a mathematical model of the dynamics of COVID-19 to link quantitative features of viral shedding, human
exposure and transmission in nine countries impacted by the ongoing COVID-19 pandemic, and state-wide transmission in the United States of America (USA). The model was then used to evaluate the efficacy of interventions against virus transmission. We found
that cooperativity was important to capture country-specific transmission dynamics and leads to resistance to mitigating transmission in mild or moderate interventions. The behaviors of the model emphasize that strict interventions greatly limiting both virus
shedding and human exposure are indispensable to achieving effective containment of COVID-19. |
|
|
Dankwa, Emmanuelle, Hall, et al |
medRxiv |
Clinical data| Données cliniques |
This the ISARIC (International Severe Acute Respiratory and emerging Infections Consortium) clinical data report for
September 3rd, 2020. Up to the date of this report, data have been entered for 96074 individuals from 562 sites across 42 countries. Report includes demographic and presenting features, outcomes, and treatments. |
|
|
Investigating the likely association between genetic
ancestry and COVID-19 manifestations |
Das, Ranajit, Ghate, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
In this study, we aimed to evaluate the potential association between an individual's genetic ancestry and the extent
of COVID-19 disease presentation employing Europeans as the case study. In addition, using a genome wide association (GWAS) approach we sought to discern the putative single nucleotide polymorphism (SNP) markers and genes that may be likely associated with
differential COVID-19 manifestations by comparative analyses of the European and East Asian genomes. We found significant positive correlation (r=0.58, P=0.03) between West European hunter gatherers (WHG) ancestral fractions and COVID-19 death/recovery ratio
for data as of 5th April 2020. This association discernibly amplified (r=0.77, P=0.009) upon reanalyses based on data as of 30th June 2020, removing countries with small sample sizes and adding those that are a bridge between Europe and Asia. |
|
Davanzo, GustavoG, Codo, et al |
medRxiv |
Immunology | Immunologie |
Our objective was to explore the role of the CD4 molecule in SARS-CoV-2 infection. Here we show that SARS-CoV-2 infects
human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates
the entry of SARS- CoV-2 in T helper cells in a mechanism that also requires ACE2 and TMPRSS2. |
|
|
Davey, Sarah Lee, Lee, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The aim of this study was to evaluate perceived levels of heat stress and its consequences in HCWs required to wear
PPE during the COVID-19 pandemic in the UK. The survey received 224 responses from 192 (85.7%) women and 32 (14.3%) men. Even though 71.9% of respondents wore the less thermally challenging PPE (i.e. Type 2), a median of 3 (IQR: 2,5) heat-related symptoms
were reported including syncope (7.7%). A median of 1 (IQR: 0-3) cognitive task was adversely affected with attentional focus being the most affected. |
|
|
Davis, JonathanW, Pillow, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
This study aims to determine if including a filter in the bubble CPAP circuit impacts stability of pressure delivery.
Results indicate that the placement of the filter at the pre-generator position in a bubble CPAP circuit should be avoided due to unstable mean pressure. Filters are likely to become saturated with water over time. The post-generator position may accommodate
a filter, but regular pressure monitoring and early replacement are required. |
|
|
The epidemiological characteristics of COVID-19 in
Libya during the ongoing-armed conflict |
Daw, MohamedA, El-Bouzedi, et al |
medRxiv |
Epidemiology| Épidémiologie |
This study analyzed the epidemiological situation of the COVID-19 pandemic in Libya, examined the impact of the armed
conflict in Libya on the spread of the pandemic, and proposes strategies for dealing with the pandemic during this conflict. A total of 698 cases of COVID-19 were reported in Libya during a period of three months. The number of cases varied from one region
to another and was affected by the fighting. The largest number of cases was reported in the southern part of the country, which has been severely affected by the conflict in comparison to the eastern and western parts of the country. |
|
Daye, M, Cihan, et al |
Dermatol Ther |
Healthcare Response | Réponse des soins de santé |
This study evaluated the skin problems and dermatological life quality of the health care workers (HCWs) due to personal
protection equipment (PPE) use, who are at high risk for Covid-19 infection. The median age of 440 participants was 33.5 (21.0-65.0) years old. Skin problems were found to be 90.2%, the most common were dryness, itching, cracking, burning, flaking, peeling
and lichenification. The presence of skin problems (P < 0.001) was higher in those who did not use moisturizers. Of all, 22.3% (n = 98) stated that the use of PPE increased the severity of their previously diagnosed skin diseases and allergies (P < 0.01).
Only 28.0% (n = 123) stated that they know the skin symptoms that may develop by using PPE. The proper hand washing rate was higher as education level increased (P < 0.001). Skin problems were higher in those using mask with metal nose bridge (p:0.02; p:0.003,
respectively). As the mask using period prolonged, acne was more common (p:0.02). DLQI was significantly affected in women (P = 0.003), and with increased skin problems related to PPE (P < 0.001). |
|
|
De Maio, Flavio, Palmieri, et al |
medRxiv |
Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI)
Healthcare Response | Réponse des soins de santé |
Here, we show pre-incubation of viral particles with free Graphene oxide (GO) inhibits SARS-CoV-2 infection of VERO
cells. The findings presented here constitute an important nanomaterials-based strategy to significantly increase face mask and other PPE efficacy in protection against the SARS-CoV-2 virus and COVID-19 that may be applicable to additional anti-SARS-CoV-2
measures including water filtration, air purification, and diagnostics. |
|
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AI for radiographic COVID-19 detection selects shortcuts
over signal |
DeGrave, AlexJ, Janizek, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
The purpose of this study was to examine the reliability of artificial neural networks to detect COVID-19 in chest
radiographs. We demonstrate that recent deep learning systems to detect COVID-19 from chest radiographs rely on confounding factors rather than medical pathology, creating an alarming situation in which the systems appear accurate, but fail when tested in
new hospitals. |
|
The Psychological Effect of COVID-19 and Lockdown on the Population: Evidence
from Italy |
Delmastro, Marco, Zamariola, et al |
Research Square prepub |
Public Health response| Interventions de santé publique |
For the first time to our knowledge, we measured depressive symptoms on 6,700 Italian individuals, representative of
the Italian population in terms of age, gender, and geographical areas revealing higher scores of depressive symptoms in females, younger adults, people reporting professional uncertainty and lower socio-economic status. A positive correlation was also found
for individuals living alone, those who could not leave home for going to work, and people with a case of COVID-19 in the family, whereas the region of residence was not a significant predictor of depressive symptoms. These findings underline the importance
of considering the psychological effects of COVID-19 and providing support to individuals seeking mental health care. |
|
How do the general population behave with facemasks
to prevent COVID-19 in the community? |
Deschanvres, Colin, Haudebourg, et al |
medRxiv |
Public Health response| Interventions de santé publique |
We evaluated the frequency and quality of facemask use in general populations with different socio-spatial backgrounds,
and contextual factors associated with the appropriate use of the facemask in the west of France. A total of 3354 observations were recorded. A facemask was worn by 56.4% (n=1892) of individuals, varying from 49% (n=1359) in non-mandatory areas and 91.7% (n=533)
in mandatory areas, including surgical facemasks (56.8%, n=1075) and cloth masks (43.2%, n=817). The facemask was correctly positioned in 75.2% (n=1422) of cases. |
|
Deshpande, R, Dash, et al |
J Assoc Physicians India |
Epidemiology| Épidémiologie Clinical data| Données cliniques Healthcare Response |
Réponse des soins de santé |
The current study was aimed at describing prevalence and characteristics of COVID19 in hemodialysis population across
different HD centers across Mumbai. We found a prevalence rate of COVID19 in 6.4%, with 9 patients (12%) died during the study period. A fair proportion of Non covid HD patients (1.5%) also died due to lack of access to dialysis. At baseline, mean age of presentation
was 54.5 years. On routine test 80% were asymptomatic at presentation. Patients with COPD, requiring ICU care and those on ventilation faired poorly. Contrary to assumption patients with underlying cardiovascular disease didn't show poor outcome. Total of
4.1% health care workers turned positive during the study period with mean age of 31 years and median of 28years. Out of them 5 (45.4%) were symptomatic. All recovered from the illness without any sequelae. Seventy two percent of healthcare workers were on
Hydroxy-chloroquine chemoprophylaxis didn't reach statistical significance in preventing the infection. In our study elderly age with comorbidities had poor prognosis. |
|
|
di Iulio, Julia, Bartha, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
Here we identify patterns of gene response comprising transfer signatures that can be learned from deposited datasets
and tested for predictive power in independent transcriptomes associated with clinical metadata and we present two use cases of transfer signatures for infection and vaccination (COVID-19, tuberculosis, and H1N1). Our work establishes the validity of this
approach and explores the nature of human immunophenotypes. |
|
|
Dillner, Joakim, Elfström, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie |
We analyzed 12928 healthy hospital employees in Sweden for SARS-CoV-2 antibodies and compared results to participant
sick leave records in order to determine risk for future illness. Subjects with viral serum antibodies were not at excess risk for future sick leave (Odds Ratio (OR): 0.85 (95% Confidence Interval (CI) (0.85 (0.43-1.68)). By contrast, subjects with antibodies
had an excess risk for sick leave in the past weeks (OR: 3.34 (2.98-3.74)). |
|
|
Djaoue, S, Guilsou Kolaye, et al |
Chaos Solitons Fractals |
Modelling/ prediction| Modélisation/prédiction Transmission Public health interventions*|
Interventions de santé publique |
In this paper, we formulated a general model of COVID-19model transmission using biological features of the disease
and control strategies based on the isolation of exposed people, confinement (lock-downs) of the human population, testing people living risks area, wearing of masks and respect of hygienic rules. It is observed that the asymptomatic infectious group of individuals
may play a major role in the spreading of transmission. Moreover, various mitigation strategies are investigated using the proposed model. A numerical evaluation of control strategies has been performed. We found that isolation has a real impact on COVID-19
transmission. When efforts are made through the tracing to isolate 80% of exposed people the disease disappears about 100 days. Although partial confinement does not eradicate the disease it is observed that, during partial confinement, when at least 10% of
the partially confined population is totally confined, COVID-19 spread stops after 150 days. The strategy of massif testing has also a real impact on the disease. In that model, we found that when more than 95% of moderate and symptomatic infected people are
identified and isolated, the disease is also really controlled after 90 days. The wearing of masks and respecting hygiene rules are fundamental conditions to control the COVID-19. |
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Predictive Modelling of COVID-19 New Cases in Algeria
using An Extreme Learning Machines (ELM) |
Djeddou, Messaoud, Hameed, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In the present study, public health database from the Algeria health ministry has been used to train and test the extreme
learning machine (ELM) models for the purpose of predicting new COVID-19 cases in Algeria. The predictive accuracy of the seven models has been assessed via several statistical parameters. The results showed that the proposed ELM model achieved an adequate
level of prediction accuracy with smallest errors (MSE= 0.16, RMSE=0.4114, and MAE= 0.2912), and highest performances (NSE = 0.9999, IO = 0.9988, R2 = 0.9999). |
|
Duchemin, Tom, Noufaily, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Surveillance |
We proposed an adaptation of the Quasi-Poisson regression-based Farrington algorithm for multi-site surveillance. The
proposed algorithm consists of a Negative-Binomial mixed effect regression with a new re-weighting procedure to account for past outbreaks and increase sensitivity of the model. We perform a wide range simulations to assess the performance of the model in
terms of False Positive Rate and Probability of Detection. We propose an application to sick leave rate in the context of COVID-19. The proposed algorithm provides good overall performance and opens up new opportunities for multi-site data surveillance. |
|
|
Dudley, DawnM, Newman, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection
in clinically confirmed samples, albeit with approximately 100-fold lower sensitivity than qRT-PCR. We demonstrate that adding lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Overall, the limit
of detection (LOD) of RT-LAMP using direct nasopharyngeal swab or saliva samples without RNA extraction is 1x105-1x106 copies/ml. |
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Impact of SARS-CoV-2 antibodies at delivery in women,
partners and newborns |
Egerup, Pia, Olsen, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie |
The aim was to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns
in Copenhagen. A total of 1,361 parturient women, 1,236 partners and 1,342 newborns participated in the study. No associations between previous COVID-19 disease and obstetric- or neonatal complications were found. The adjusted serological prevalence was 2.9%
in women and 3.8% in partners. |
|
Emmerich, Petra, Murawski, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Here, we assess the false positive rates obtained with four commercially available IgG ELISAs in serum panels originating
from three different African countries. Wer found significantly increased false positive rates were observed in African pre-COVID-19 serum panels originating from countries with a high malaria burden (Ghana and Nigeria, calling into question the eligibility
of these assays for seroprevalence studies in these regions. |
|
|
Eng, Genghmun |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
In this work the authors build off prior work 'initial model baseline' to develop a new model 'resurgence' in order
to model the pandemic in the US after widespread reduction in restrictions. Results indicate that: (a) the gradual increase in doubling time from society-wide shut-downs is likely due to eliminating of a large number of population gathering points that could
have enabled CoVID-19 spread; and (b) having a non-zero fast pandemic shutoff is likely due to more people wearing masks more often. |
|
|
Erster, Oran, Shkedi, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We tested the sensitivity and efficiency of SARS-CoV-2 detection in clinical samples collected directly into a mix
of lysis buffer and RNA preservative, thus inactivating the virus immediately after sampling. We show that using NSLB instead of VTM can improve the sensitivity, safety, and rapidity of COVID-19 tests at a time most needed. |
|
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PMC7505604; Solution of a COVID-19 model via new generalized Caputo-type fractional
derivatives |
Erturk, VS, Kumar, et al |
Chaos Solitons Fractals |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In this manuscript, we solve a model of the novel COVID-19 epidemic by using Corrector-predictor scheme. For the considered
system exemplifying the model of COVID-19, the solution is established within the frame of the new generalized Caputo type fractional derivative. The existence and uniqueness analysis of the given initial value problem are established by the help of some important
fixed point theorems like Schauder's second and Weissinger's theorems. Arzela-Ascoli theorem and property of equicontinuity are also used to prove the existence of unique solution. A new analysis with the considered epidemic COVID-19 model is effectuated.
Obtained results are described using figures which show the behaviour of the classes of projected model. The results show that the used scheme is highly emphatic and easy to implementation for the system of non-linear equations. |
|
Estimate of the actual number of COVID-19 cases from
the analysis of deaths |
Etchenique, Roberto, Quiroga, et al |
medRxiv |
Epidemiology| Épidémiologie |
Using the calculated values for the Infection Fatality Rate (IFR) of COVID-19 it is possible to estimate the prevalence
of cases of infection in the city of Buenos Aires, Argentina, throughout the pandemic. The use of confirmed cases as a metric and their replacement by more reliable parameters such as death figures are discussed. The results are analyzed according to age ranges
and possible sources of error in the estimates are established. |
|
Fabiani, Massimo, Mateo-Urdiales, et al |
medRxiv |
Epidemiology| Épidémiologie |
We analysed 213,180 COVID-19 cases, including 15,974 (7.5%) non-Italian nationals. We found that, compared to Italian
cases, non-Italian cases were diagnosed at a later date and were more likely to be hospitalised [(adjusted relative risk (ARR)=1.39, 95% confidence interval (CI): 1.33-1.44)] and admitted to ICU (ARR=1.19, 95% CI: 1.07-1.32), with differences being more pronounced
in those coming from countries with lower HDI. We also observed an increased risk of death in non-Italian cases from low-HDI countries (ARR=1.32, 95% CI: 1.01-1.75). A delayed diagnosis in non-Italian cases could explain their worse outcomes compared to Italian
cases. Ensuring early access to diagnosis and treatment to non-Italians could facilitate the control of SARS-CoV-2 transmission and improve health outcomes in all people living in Italy, regardless of nationality. |
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|
Farah, Ibrahim, Lalli, et al |
medRxiv |
Public health interventions*| Interventions de santé publique |
Based on the precision medicine platform Shivom, a novel and secure data sharing and data analytics marketplace, we
developed a versatile pandemic preparedness platform that allows healthcare professionals to rapidly share and analyze genetic data. The platform solves several problems of the global medical and research community, such as siloed data, cross-border data sharing,
lack of state-of-the-art analytic tools, GDPR-compliance, and ease-of-use. The platform serves as a central marketplace of 'discoverability'. The platform combines patient genomic & omics data sets, a marketplace for AI & bioinformatics algorithms, new diagnostic
tools, and data-sharing capabilities to advance virus epidemiology and biomarker discovery. The bioinformatics marketplace contains some preinstalled COVID-19 pipelines to analyze virus- and host genomes without the need for bioinformatics expertise. The platform
will be the quickest way to rapidly gain insight into the association between virus-host interactions and COVID-19 in various populations which can have a significant impact on managing the current pandemic and potential future disease outbreaks. |
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|
Favara, DavidM, McAdam, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The value of routinely testing staff treating cancer patients is not known. Patient-facing oncology department staff
at work during the COVID-19 pandemic consented to have a nasopharyngeal swab SARS-CoV-2 antigen test by polymerase chain reaction (PCR) and blood tests for SARS-CoV-2 antibody using a laboratory Luminex-based assay and a rapid point-of-care (POC) assay on
2 occasions 28 days apart in June and July 2020. Findings show the high prevalence of SARS-CoV-2 IgG sero-positivity in oncology nurses, and the high decline of positivity over 4 weeks supports regular antigen and antibody testing in this staff group for SARS-CoV-2
as part of routine patient care prior to availability of a vaccine. |
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|
Fiorillo, A, Sampogna, et al |
Eur Psychiatry |
Public Health response| Interventions de santé publique |
This study evaluated the impact of lockdown on depressive, anxiety and stress symptoms. The final sample consisted
of 20,720 participants. 12.4% of respondent (N=2,555) reported severe or extremely severe levels of depressive symptoms, 17.6% (N=3,627) of anxiety symptoms and 41.6% (N=8,619) reported to feel at least moderately stressed by the situation at the DASS-21.
According to the multivariate regression models, the depressive, anxiety and stress symptoms significantly worsened from the week April 9-15 to the week April 30-May 4 (p<.0001). Moreover, female respondents and people with pre-existing mental health problems
were at higher risk of developing severe depression and anxiety symptoms (p<.0001). |
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|
COVID-19 Case-Age Distribution: Correction for Differential
Testing by Age |
Fisman, David, Greer, et al |
medRxiv |
Epidemiology| Épidémiologie |
Data from Ontario, Canada was used incidence rates among different age groups. Observed disease incidence and testing
rates were highest in oldest individuals and markedly lower in those aged < 20. Temporal trends in disease incidence and testing were observed, but standardizing morbidity and testing ratios eliminated temporal trends (i.e., relative patterns by age and sex
remained identical regardless of epidemic phase). After adjustment for testing frequency, SMR were lowest in children and adults aged 70 and older, approximately the same in adolescents as in the population as a whole and elevated in young adults (aged 20-29
years), providing a markedly different picture of the epidemic than seen with crude SMR or case-based incidence. Test-adjusted SMR were validated using seroprevalence data (Pearson correlation coefficient 0.82, P = 0.04). Surveillance for SARS-CoV-2 infection
is typically performed using only test-positive case data, without adjustment for testing frequency. Older adults are tested more frequently, likely due to increased disease severity, while children are under-tested. Adjustment for testing frequency results
in a very different picture of SARS-CoV-2 infection risk by age, one that is consistent with estimates obtained through serological testing. |
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Seroprevalence of anti-SARS-CoV-2 IgG at the epidemic
peak in French Guiana |
Flamand, Claude, Enfissi, et al |
medRxiv |
Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
A cross-sectional survey was performed between 15 July 2020 and 23 July 2020 in 4 medical biology laboratories and
5 health centers of French Guiana, representing a period shortly after the epidemic peak. Samples were screened for the presence of anti-SARS-CoV-2 IgG directed against domain S1 of the SARS-CoV-2 spike protein using the anti-SARS-CoV-2 enzyme-linked immunosorbent
assay (ELISA) from Euroimmun. The overall seroprevalence was 15.4% [9.3%-24.4%] among 480 participants, ranging from 4.0% to 25.5% across the different municipalities. The seroprevalence did not differ according to gender (p=0.19) or age (p=0.51). Among SARS-CoV-2
positive individuals, we found that 24.6% [11.5%-45.2%] reported symptoms consistent with COVID-19. |
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PMC7492182; Hemorrhagic stroke and COVID-19 infection: Coincidence or causality? |
Fraiman, P, Freire, et al |
eNeurologicalSci |
Clinical data| Données cliniques |
Amyloid Protein Precursor gene duplication is a rare cause of early-onset Alzheimer's disease that can be associated
with Cerebral Amyloid Angiopathy. This condition predisposes cerebrovascular events, specifically, intracerebral hemorrhagic stroke. This report describes a case of first-time intracerebral hemorrhage in a patient with APP gene duplication during SARS-CoV-2
infection, a typically pro-thrombotic and pro-inflammatory condition, as a possible trigger for this condition. |
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THE REMOTE ANALYSIS OF BREATH SOUND IN COVID-19 PATIENTS:
A SERIES OF CLINICAL CASES |
Furman, EvgenyG, Charushin, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Respiratory sounds have been recognized as a possible indicator of behavior and health. Computer analysis of these
sounds can indicate of characteristic sound changes caused by COVID-19 and can be used for diagnosis of this illness. The communication aim is development of fast remote computer-assistance diagnosis of COVID-19, based on analysis of respiratory sounds.
Fast Fourier transform (FFT) was applied for analyses of respiratory sounds recorded near the mouth of 9 COVID-19 patients and 4 healthy volunteers. Comparing of FFT spectrums of the respiratory sounds of the patients and volunteers we proposed numerical healthy-ill
criterions. The proposed computer method, based on analysis of the FFT spectrums of respiratory sounds of the patients and volunteers, allows one to automatically diagnose COVID-19 with sufficiently high diagnostic values. This method can be applied at development
of noninvasive self-testing kits for COVID-19. |
|
Gandhi, Sailaxmi, Sahu, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The present study aimed at exploring the perception of nurses and nursing students regarding psychological preparedness
for the pandemic (COVID-19) management. Findings revealed that mean score for PPDTS, GSE, BRCS and Optimism was 73.44 (SD=10.82, 33.19 (SD=5.23), 16.79 (SD=2.73) and 9.61 (SD=2.26) respectively indicating that the subjects had moderate level of psychological
preparedness, self-efficacy and resilience but higher level of optimism. Psychological preparedness, self-efficacy, optimism and resilience were positively correlated to each other. Self- efficacy, optimism, and resilience emerged as predictors of psychological
preparedness. The findings suggested that self-efficacy, optimism and resilience can be considered as predictors for psychological preparedness in pandemic management. Appropriate training could influence self-efficacy while programs addressing resilience
and coping may strengthen psychological preparedness which can help in further management of ongoing pandemic. |
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|
Garnett, Claire, Jackson, et al |
medRxiv |
Public Health response| Interventions de santé publique |
This study aims to assess what factors were associated with reported changes to usual alcohol drinking behaviour during
the start of lockdown in the UK. In a representative sample of adults in the UK, about half of drinkers reported drinking the same amount of alcohol as usual during the start of the COVID-19 related lockdown, with a quarter drinking more and a quarter drinking
less than usual. Drinking more than usual was associated with being younger, female, high socioeconomic position, having an anxiety disorder, and being stressed about finances or COVID-19. These groups may benefit targeted alcohol reduction support if there
are further periods of lockdown. |
|
|
Gaudart, Jean, Landier, et al |
medRxiv |
Epidemiology| Épidémiologie |
To better understand factors associated with incidence, mortality and lethality heterogeneity across the 96 administrative
departments of metropolitan France, we thus conducted a geoepidemiological analysis based on publicly available data, using hierarchical ascendant classification (HAC) on principal component analysis (PCA) of multidimensional variables, and multivariate analyses
with generalized additive models (GAM). Our results confirm a marked spatial heterogeneity of in-hospital COVID 19 incidence and mortality, following the North East / South West diffusion of the epidemic. The delay elapsed between the first COVID-19 associated
death and the onset of the national lockdown on March 17th, 2020, appeared positively associated with in-hospital incidence, mortality and lethality. Mortality was also strongly associated with incidence. Mortality and lethality rates were significantly higher
in departments with older population, but they were not significantly associated with the number of intensive-care beds available in 2018. We did not find any significant association between incidence, mortality or lethality rates and incidence of new chloroquine
and hydroxychloroquine dispensations in pharmacies either, nor between COVID 19 incidence and climate, nor between economic indicators and in-hospital COVID 19 incidence or mortality. |
|
|
Gehin, Antoine, Goorah, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Our objectives were to model and understand the evolution of the Mauritius outbreak using mathematical analysis, a
logistic growth model and an SEIR compartmental model with quarantine and a reverse sigmoid effective reproduction number and to relate the results to the public health control measures in Mauritius. The evolution of the outbreak in Mauritius was consistent
with one modulated by a time-varying effective reproduction number resulting from the epidemic control measures implemented by Mauritius authorities and the PPMs adopted by Mauritius inhabitants. The value of R_e≈1.6 on the reopening of supermarkets on Day
16 was sufficient for the outbreak to grow to large-scale proportions in case the Mauritius population did not comply with the PPMs. However, the number of cases remained contained to a small number which is indicative of a significant contribution of the
PPMs in the public health response to the COVID-19 outbreak in Mauritius. |
|
|
George, Jaiben, Gautam, et al |
medRxiv |
Public Health response| Interventions de santé publique |
we analysed the content, type and quality of Q&As in Quora regarding this pandemic, and compared the information with
that on World Health Organization (WHO) website. 462 (48%) questions were classified as positive, while 391 (41%) were negative. Number of views were higher for negative questions (11421 vs 7300, p=0.004). Majority of the questions were on social impact (N=217,
23%), followed by politics (N=122, 13%) and disease management (N=96, 10%). Positive questions had more accurate, but less popular answers (p<0.05). Information related to 229 (28%) questions were present on WHO website, while partial information was present
for 103 (11%) questions |
|
|
COVID-19: Risks of Re-emergence, Re-infection, and
Control Measures -- A Long Term Modelling Study |
Ghosh, Subhas Kumar, Ghosh, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique |
In this work we define a modified SEIR model that accounts for the spread of infection during the latent period, infections
from asymptomatic or pauci-symptomatic infected individuals, potential loss of acquired immunity, people's increasing awareness of social distancing and the use of vaccination as well as non-pharmaceutical interventions like social confinement. We estimate
model parameters in three different scenarios - in Italy, where there is a growing number of cases and re-emergence of the epidemic, in India, where there are significant number of cases post confinement period and in Victoria, Australia where a re-emergence
has been controlled with severe social confinement program. Our result shows the benefit of long-term confinement of 50% or above population and extensive testing. With respect to loss of acquired immunity, our model suggests higher impact for Italy. We also
show that a reasonably effective vaccine with mass vaccination program can be successful in significantly controlling the size of infected population. |
|
Giacopelli, Giuseppe |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
The aim of this contribution is to propose a individual-based model of Lombardy COVID-19 outbreak at full-scale, where
full-scale means that will be simulated all the 10 millions inhabitant population of Lombardy person by person, in a commercial computer. All this to test the impact of our daily actions in epidemic, investigate social networks connectivity and in the end
have an insight on the impact of an hypothetical vaccine. |
|
|
Goldfarb, DavidM, Tilley, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline
mouth rinse/gargle sample types for the molecular detection of SARS-CoV-2 in adults and school-aged children. 50 participants (aged 4 to 71 years) were included; of these, 40 had at least one positive sample and were included in the primary sample yield analysis.
Saline mouth rinse/gargle samples had a sensitivity of 98% (39/40) while saliva samples had a sensitivity of 79% (26/33). Both saline mouth rinse/gargle and saliva samples showed stable viral RNA detection after 2 days of room temperature storage. Mouth rinse/gargle
samples had the highest (mean 4.9) and HCW-collected NP swabs had the lowest acceptability scores (mean 3.1). Saline mouth rinse/gargle samples demonstrated the highest combined user acceptability ratings and analytical performance when compared with saliva
and HCW collected NP swabs. This sample type is a promising swab-independent option, particularly for outpatient self-collection in adults and school aged children. |
|
|
Reinfection with SARS-CoV-2 and Failure of Humoral
Immunity: a case report |
Goldman, JasonD, Wang, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these
confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively
describe reinfection with a new strain harboring the spike variant D614G. With antibody and B cell analytics, we show correlates of adaptive immunity, including a differential response to D614G. Finally, we discuss implications for vaccine programs and begin
to define benchmarks for protection against reinfection from SARS-CoV-2. |
|
Goldstein, Edward |
medRxiv |
Epidemiology| Épidémiologie |
Here, we examine the relation between detectability of SARS-CoV-2 infection (i.e. the percent of detected COVID-19
cases among all cases of SARS-CoV-2 infection in the population) and levels of mortality for COVID-19 for the 85 different regions (federal subjects) of the Russian Federation. Methods: Lower case-fatality rate (CFR, the proportion of deaths among reported
COVID-19 cases in the population) corresponds to higher detectability of the SARS-COV-2 infection. We used data from the Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor) on the number of detected
COVID-19 cases and the number of deaths from COVID-19 in the 85 different regions. Results: The correlation between case-fatality rates for cases/deaths reported by Sep. 17, 2020 and rates of mortality for COVID-19 per 100,000 for deaths reported by Sep. 17,
2020 in different regions of the Russian Federation is 0.68 (0.55,0.78). The region with both the highest COVID-19 mortality rate per 100,000 and the highest CFR (lowest detectability of SARS-CoV-2 infection) is the city of St. Petersburg. |
|
|
PMC7498206; QT interval measurement with portable device during COVID-19 outbreak |
González, NT, Acosta, et al |
Int J Cardiol Heart Vasc |
Clinical data| Données cliniques Healthcare Response | Réponse des soins de santé |
During the COVID-19 outbreak, we designed a protocol for monitoring the QT interval using a portable device with Bluetooth
connectivity. After a validation study with 50 patients, we found a very good correlation between the QT interval measured both with this device and with the conventional body surface ECG. In this article, we provide a brief overview of the protocol and then
analyse the QT changes observed in a group of patients during their hospitalization and treatment for SARS-CoV-2 infection. 81 patients with confirmed SARS-CoV-2 infection were enrolled in the protocol (age 63.4 SD 17.2 years; 70.3% men), while being treated
with lopinavir/ritonavir, azithromycin and hydroxychloroquine, both individually or combined. Ten patients developed long drug-related QT interval, and the QT prolongation was statically significant for all treatment schemes. All patients with drug induced
QT prolongation corrected the QT interval following the indications of the protocol, and no patients died of arrhythmic causes after its implementation. |
|
COVID-19 pediatric mortality rates are heterogenous
between countries |
Gonzalez-Garcia, Nadia, Miranda-Lora, et al |
medRxiv |
Epidemiology| Épidémiologie |
This study aims to explore differences in the pediatric mortality rate between countries. 23 countries were included
in the analysis. Pediatric mortality varied from 0 to 12.1 deaths per million people of the corresponding age group, with the highest rate in Peru. In most countries, deaths were more frequent in the 0-4 years old age group, except for Brazil. The pediatric/
general COVID-19 mortality showed a great variation between countries and ranged from 0 (Republic of Korea) to 10.4% (India). Pediatric and Pediatric/general COVID mortality have a strong correlation with 2018 neonatal mortality (r=0.77, p<0.001 and r= 0.88,
p<0.001 respectively), while it has a moderate or absent (r=0.47, p=0.02 and r=0.19, p=0.38, respectively) correlation with COVID-19 mortality in the general population. |
|
Goodall, JackW, Reed, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This observational cohort study aimed to characterize the independent associations between the clinical outcomes of
hospitalized patients and their demographics, comorbidities, blood tests and bedside observations. All patients admitted to Northwick Park Hospital, London, United Kingdom between 12 March and 15 April 2020 with COVID-19 were retrospectively identified. The
mortality rate was 36.0%. Age (adjusted hazard ratio (aHR) 1.53), respiratory disease (aHR 1.37), immunosuppression (aHR 2.23), respiratory rate (aHR 1.28), hypoxia (aHR 1.36), Glasgow Coma Score <15 (aHR 1.92), urea (aHR 2.67), alkaline phosphatase (aHR 2.53),
C-reactive protein (aHR 1.15), lactate (aHR 2.67), platelet count (aHR 0.77) and infiltrates on chest radiograph (aHR 1.89) were all associated with mortality. These important data will aid clinical risk stratification and provide direction for further research. |
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Goyal, Ashish, Reeves, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique |
Here we utilize a mathematical model to assess the impact of masking on transmission within individual transmission
pairs and at the population level. Our model quantitatively links mask efficacy to reductions in viral load and subsequent transmission risk. Our results reinforce that the use of masks by both a potential transmitter and exposed person substantially reduces
the probability of successful transmission, even if masks only lower exposure viral load by ~50%. Slight increases in masking relative to current levels would reduce the reproductive number substantially below 1, particularly if implemented comprehensively
in potential super-spreader environments. |
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SARS-CoV-2 in wastewater settled solids is associated
with COVID-19 cases in a large urban sewershed |
Graham, Katherine, Loeb, et al |
medRxiv |
Epidemiology| Épidémiologie |
We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to
inform the pre-analytical and analytical approaches, and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent samples. Likewise,
SARS-CoV-2 RNA was more readily detected in solids using one-step digital droplet (dd)RT-PCR than with two-step RT-QPCR and two-step ddRT-PCR, likely owing to reduced inhibition with the one-step ddRT-PCR assay. We subsequently analyzed a longitudinal time
series of 89 settled solids samples from a single plant for SARS-CoV-2 RNA as well as coronavirus recovery (bovine coronavirus) and fecal strength (pepper mild mottle virus, PMMoV) controls. SARS-CoV-2 RNA targets N1 and N2 concentrations correlate positively
and significantly with COVID-19 clinical confirmed case counts in the sewershed. Together, the results demonstrate that measuring SARS-CoV-2 RNA concentrations in settled solids may be a more sensitive approach than measuring SARs-CoV-2 in influent. |
|
Inexpensive, versatile and open-source methods for
SARS-CoV-2 detection |
Graham, ThomasGW, Dugast-Darzacq, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
we evaluated several protocols for RNA extraction and RT-qPCR that are simpler and less expensive than prevailing methods.
First, we show that isopropanol precipitation provides an effective means of RNA extraction from nasopharyngeal (NP) swab samples. Second, we evaluate direct addition of NP swab samples to RT-qPCR reactions without an RNA extraction step. We describe a simple,
inexpensive swab collection solution suitable for direct addition, which we validate using contrived swab samples. Third, we describe an open-source master mix for RT-qPCR and show that it permits detection of viral RNA in NP swab samples. Lastly, we show
that an end-point fluorescence measurement provides an accurate diagnostic readout without requiring a qPCR thermocycler. Adoption of these simple, inexpensive methods has the potential to significantly reduce the time and expense of COVID-19 testing. |
|
Identification of potential biomarkers and inhibitors
for SARS-CoV-2 infection |
Gu, Hanming, Yuan, et al |
medRxiv |
Coronavirology| Coronavirologie |
we aim to identify biological markers and associated biological processes of COVID-19 using a bioinformatics approach
to elucidate their potential pathogenesis. The gene expression profile of the GSE152418 dataset was originally produced by using the high-throughput Illumina NovaSeq 6000. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and Gene Ontology (GO) enrichment
analyses were applied to identify functional categories and biochemical pathways. KEGG and GO results suggested that biological pathways such as Cancer pathways and Insulin pathways were mostly affected in the development of COVID-19. Moreover, we identified
several genes including EP300, CREBBP, and POLR2A were involved in the virus activities in COVID-19 patients. We further predicted that some inhibitors may have the potential to block the SARS-CoV-2 infection based on the L1000FWD analysis. |
|
Gubensek, J, Vajdic Trampuz, et al |
Epidemiol Infect |
Transmission Clinical data| Données cliniques Healthcare Response | Réponse des soins
de santé |
We report a follow-up of the in-centre contacts of three positive chronic haemodialysis patients. Under strict preventive
measures, only one patient out of 21 patient-contacts and 29 personnel-contacts tested positive within 2 weeks after the last contact. This patient, case #3, most likely became infected during unprotected, |
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Analysis of the COVID-19 pandemic in Bavaria: adjusting
for misclassification |
Guenther, Felix, Bender, et al |
medRxiv |
Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
We present a method for adjusting the observed epidemic curve of daily new COVID-19 onsets for possible misclassification
in infection diagnostics. We discuss different assumptions for specificity and sensitivity of the person-specific COVID-19 diagnostics based on PCR-tests, which are the basis for the daily reported case counts. A specificity of less than one implies occurrence
of false positive cases, which becomes particularly relevant with an increased number of tests. The recent increase in cases in Bavaria could therefore be smaller than reported. However, an increase in case counts can still be seen from Mid-July until September
2020. The additional consideration of a sensitivity less than one, i.e., the occurrence of false negative tests, results in an epidemic curve in which the daily case counts are increased by a constant factor, but the structure of the curve does not change
considerably. |
|
Guimarães, AntonioC, C, et al |
medRxiv |
Epidemiology| Épidémiologie |
Objective: To analyze quantitatively and comparatively the deaths by COVID-19 of the four largest municipalities in
the North of Rio de Janeiro and Baixada Litorânea of Rio de Janeiro, within the national context. Methods: We used data from the Civil Registry and demographic information to elaborate a general picture of the pandemic up to the 31st epidemiological week in
several aspects: evolution, scope, age, sex, race and impact on other causes of death. Results: We characterized the evolution of the pandemic. We found an exponential dependence on the mortality rate by age and a higher lethality in the male population. We
determined that COVID-19 represents an important fraction of the causes of death in 2020, being associated with a significant excess of deaths in relation to 2019 and also with the change in mortality patterns due to other causes. |
|
|
Guo, Longhua, Boocock, et al |
medRxiv |
Epidemiology| Épidémiologie |
To learn about the transmission history of SARS-CoV-2 in LA County, we sequenced 142 viral genomes from unique patients
seeking care at UCLA Health System. 86 of these genomes are from samples collected before April 19, 2020. We found that the early outbreak in LA, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe.
We identified a US-specific strain, B.1.43, which has been found predominantly in California and Washington State. While samples from LA County carry the ancestral B.1.43 genome, viral genomes from neighbouring counties in California and from counties in Washington
State carry additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus
were effective at preventing transmission, but may have been undermined by the many introductions of SARS-CoV-2 into the region. Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health
response. |
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COVID-19 outbreak and Urban dynamics: Regional variations in India |
Gupta, Devarupa, Biswas, et al |
Research Square prepub |
Epidemiology| Épidémiologie |
This study focused on the spatial transmission of the pandemic among the 640 districts in India over time, and aimed
to understand the urban-centric nature of the infection. Metropolitans contributed three-fourths of total cases from the beginning. The transport networks attributed significantly in transmitting the virus from the urban containment zones. Later, there was
a gradual shift of infections from urban to rural areas; however, the numbers kept increasing in the former. Districts with airports reported more with influx of international passengers. A profound east-west division in April with higher infections in the
southern and western districts existed. By mid-May eastern India saw a steep rise in active cases. Moran’s I analysis showed a low autocorrelation initially which increased over time. Hotspot clustering was observed in western Maharashtra, eastern Tamil Nadu,
Gujarat and around Kolkata by the second week of August. The diffusion was due to travel, exposure to infected individuals and among the frontline workers. Spatial regression models confirmed that urbanization was positively correlated with higher incidences
of infections. Transit mediums, especially rail and aviation were positively associated. These models validated the crucial role of spatial proximity in diffusion of the pandemic. |
|
Ha, SierraK, Nguyen, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The aim of this study was to investigate self-reported discrimination and concern for physical assault due to the COVID-19
pandemic among disaggregated Asian subgroups in the US. Chinese respondents experienced the largest change (15% increase) in proportion of respondents reporting discrimination from 2019 to 2020 (P<.01). Chinese, Korean, Japanese, Vietnamese, and Other API
showed up to 3.9 times increased odds of self-reported racial/ethnic discrimination due to COVID-19 and, with the addition of Filipino, experienced up to 5.4 times increased odds of concern for physical assault due to COVID-19 compared to Whites. |
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Distribution equality as an optimal epidemic mitigation
strategy |
Hacohen, Adar, Cohen, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
We design a dissemination strategy that naturally follows the predicted spreading patterns of the epidemic, optimizing
not just for supply volume, but also for its congruency with the anticipated demand. Specifically, we show that epidemics spread relatively uniformly across all destinations, and hence we introduce an equality constraint into our dissemination that prioritizes
supply homogeneity. This strategy may, at times, slow down the supply rate in certain locations, however, thanks to its egalitarian nature, which mimics the flow of the viral spread, it provides a dramatic leap in overall mitigation efficiency, saving more
lives with orders of magnitude less resources. |
|
Haroon, Shamil, Subramanian, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The objective of this study was to assess a possible association between prescription of renin-angiotensin system
(RAS) inhibitors and the incidence of COVID-19 and all-cause mortality. Current use of ACE inhibitors was not associated with the risk of suspected or confirmed COVID-19 whereas use of ARBs was associated with a statistically non-significant 38% relative increase
in risk compared to use of CCBs. However, no significant associations were observed between prescription of either ACE inhibitors or ARBs and all-cause mortality during the peak of the pandemic. |
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Early Humoral Response Correlates with Disease Severity
and Outcomes in COVID-19 Patients |
Hashem, AnwarM, Algaissi, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We investigated the kinetics of IgM, IgG against the spike (S) and nucleoproteins (N) proteins and their neutralizing
capabilities in hospitalized patients with RT-PCR confirmed COVID-19 infection. Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations.
Notably, anti-S and -N IgG, peaked 20-40 day after disease onset, and were still detectable for at least up to 70 days, with nAbs observed during the same time period. Moreover, nAbs titers were strongly correlated with IgG antibodies. Significantly higher
levels of nAbs as well as anti-S1 and N IgG and IgM antibodies were found in patients with more severe clinical presentations, patients requiring admission to intensive care units (ICU) or those with fatal outcomes. Interestingly, lower levels of antibodies,
particularly anti-N IgG and IgM in the first 15 days after symptoms onset, were found in survivors and those with mild clinical presentations. Collectively, these findings provide new insights into the characteristics and kinetics of antibody responses in
COVID-19 patients with different disease severity. |
|
Hausburg, Melissa, Banton, et al |
medRxiv |
Clinical data| Données cliniques |
we present a follow-up analysis of a longitudinal study characterizing COVID-19 immune responses from a father and
son with distinctly different clinical courses. The father required a lengthy hospital stay for severe symptoms, whereas his son had mild symptoms and no fever yet tested positive for SARS-CoV-2 for 29 days. Father and son, as well as another unrelated COVID-19
patient, displayed a robust increase of SERPING1, the transcript encoding C1 esterase inhibitor (C1-INH). We further bolstered this finding by incorporating a serum proteomics dataset and found that serum C1-INH was consistently increased in COVID-19 patients.
C1-INH is a central regulator of the contact and complement systems, potentially linking COVID-19 to complement hyperactivation, fibrin clot formation, and immune depression. Furthermore, despite distinct clinical cases, significant parallels were observed
in transcripts involved interferon and B cell signaling. As symptoms were resolving, widespread decreases were seen in immune-related transcripts to levels below those of healthy controls. Our study provides insight into the immune responses of likely millions
of people with extremely mild symptoms who may not be aware of their infection with SARS-CoV-2 and implies a potential for long-lasting consequences that could contribute to reinfection risk. |
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Henry, Brandon Michael, Benoit, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
he aim of this study was to evaluate the anti-inflammatory response to COVID-19, by assessing interleukin-10 (IL-10)
and IL-10/lymphocyte count ratio and their association with patient outcomes. A total of 52 COVID-19 patients were enrolled. IL-10 and IL-10/lymphocyte count were significantly higher in patients with severe disease. In multivariable analysis, a one-unit increase
in IL-10 was associated with 42% increased odds of severe COVID-19 (p=0.031), whilst a one-unit increase IL-10/lymphocyte ratio was also associated with 32% increase in odds of severe COVID-19 (p=0.013). |
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Probabilistic analysis of COVID-19 patients' individual
length of stay in Swiss intensive care units |
Henzi, Alexander, Kleger, et al |
medRxiv |
Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
We aim to provide early predictions of individual patients' intensive care unit length of stay, which might improve
resource allocation and patient care during the on-going pandemic. The model gives probabilistically and marginally calibrated predictions which are more informative than the empirical length of stay distribution of the training data. However, marginal calibration
was worse after approximately 20 days in the whole cohort and in different subgroups. Long staying COVID-19 patients have shorter length of stay than regular acute respiratory distress syndrome patients. We found differences in LoS with respect to age categories
and gender but not in regions of Switzerland with different stress of intensive care unit resources. |
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Ozone therapy for patients with COVID-19 pneumonia:
a Quasi-Randomized Controlled Trial |
Hernandez, Alberto, Vinals, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
Objective: To determine the impact of the use of ozonated blood on time to clinical improvement in patients with severe
COVID-19 pneumonia. Participants: Eighteen patients with COVID-19 infection (laboratory confirmed) severe pneumonia admitted to hospital between 20th March and 19th April 2020. Nine patients (50%) received ozonated autohemotherapy beginning on the day of
admission. Ozonated autohemotherapy was associated with shorter time to clinical improvement (median [IQR]), 7 days [6-10] vs 28 days [8-31], p=0.04) and better outcomes at 14-days (88.8% vs 33.3%, p=0.01). In risk-adjusted analyses, ozonated autohemotherapy
was associated with a shorter mean time to clinical improvement (-11.3 days, p=0.04, 95% CI -22.25 to -0.42). |
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Hernández-Pérez, Luis Germán, Ponce-Ortega, et al |
Research Square prepub |
Modelling/ prediction| Modélisation/prédiction Healthcare Response | Réponse des soins
de santé |
This paper presents an optimization strategy based on mathematical programming to solve resource management problems
regarding hospitalization of sick patients, considering emergency scenarios, such as those that can occur in a pandemic. The proposed optimization methodology is applied to case studies based on data obtained from affected people by severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), which is the virus that causes coronavirus disease 2019 (COVID-19). The distances were taken as example from severely affected cities in USA. The obtained results offer attractive alternatives for the specified objective
function in an acceptable computation time. |
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Using COVID-19 deaths as a surrogate to measure the
progression of the pandemics |
Hernandez-Suarez, Carlos, Murillo-Zamora, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Here we suggest how to use the observed deaths by COVID-19 in an arbitrary population as a surrogate for the progression
of the epidemic with the purpose of decision making. We compare several estimates of IFR (Infection Fatality Risk) for SARS-CoV-2 with our estimate that uses the number of additional deaths in households in a database population of 159,150 laboratory-confirmed
(RT-qPCR) COVID-19 by SARS-COV-2 in Mexico. The main result is that if the number of deaths in a region is close to 2 per thousand individuals, the fraction of remaining susceptible may be too small for the vaccine to make a difference in the total number
of infected. |
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Modeling lung perfusion abnormalities to explain early COVID-19 hypoxemia |
Herrmann, J, Mori, et al |
Nat Commun |
Modelling/ prediction| Modélisation/prédiction Clinical data| Données cliniques |
Herein, a mathematical model demonstrates that the large amount of pulmonary venous admixture observed in patients
with early COVID-19 can be reasonably explained by a combination of pulmonary embolism, ventilation-perfusion mismatching in the noninjured lung, and normal perfusion of the relatively small fraction of injured lung. Although underlying perfusion heterogeneity
exacerbates existing shunt and ventilation-perfusion mismatch in the model, the reported hypoxemia severity in early COVID-19 patients is not replicated without either extensive perfusion defects, severe ventilation-perfusion mismatch, or hyperperfusion of
nonoxygenated regions. |
|
Hertz-Palmor, Nimrod, Moore, et al |
medRxiv |
Public Health response| Interventions de santé publique |
Here we investigated the associations between COVID-19 pandemic-related income loss with financial strain and mental
health trajectories over a 1-month course. Two independent studies were conducted in the U.S and in Israel at the beginning of the outbreak (March-April 2020, T1; N = 4 171) and at a 1-month follow-up (T2; N = 1 559). In both studies, income loss and financial
strain were associated with greater depressive symptoms at T1, above and beyond T1 anxiety, worries about health, and pre-COVID-19 income. Worsening of income loss was associated with exacerbation of depression at T2 in both studies. Worsening of subjective
financial strain was associated with exacerbation of depression at T2 in one study (US). |
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The Mean Unfulfilled Lifespan (MUL): A New Indicator
of a Disease Impact on the Individual Lifespan |
Heuveline, Patrick |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
To avoid making any assumption about future mortality, I propose measuring instead the Mean Unfulfilled Lifespan (MUL).
For fine-grained tracking of the pandemic, I also provide an empirical shortcut to MUL estimation for small areas or short periods. I estimate quarterly MUL values for the first half of 2020 in 144 national populations and 122 sub-national populations in Italy,
Mexico, Spain and the US. Across national populations, the highest quarterly values were reached in the second quarter in Peru (3.90 years) and in Ecuador (4.59 years). Higher quarterly values still were found in New York and New Jersey, where individuals
died respectively 5.41 and 5.56 years younger on average than their expected age at death. Using a shorter, seven-day rolling window, I estimate the MUL peaked at 7.32 years in Lombardy, 8.96 years in Madrid, and 8.93 years in New York, and even reached 12.86
years for the entire month of April in Guayas (Ecuador). |
|
Hibino, Sawako, Hayashida, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
Objective: To assess changes in COVID-19 seroprevalence among asymptomatic employees working in Tokyo during the second
wave. We conducted an observational cohort study. Healthy volunteers working for a Japanese company in Tokyo were enrolled from disparate locations to determine seropositivity against COVID19 from May 26 to August 25, 2020. Healthy volunteers from 1877 employees
of a large Japanese company were recruited to the study from 11 disparate locations across Tokyo. Six hundred fifteen healthy volunteers (mean + SD 40.8 + 10.0; range 19-69; 45.7 % female) received at least one test. Seroprevalence increased from 5.8 % to
46.8 % over the course of the summer. The most dramatic increase in SPR occurred in late June and early July, paralleling the rise in daily confirmed cases within Tokyo, which peaked on August 4. Out of the 350 individuals (mean + SD 42.5 + 10.0; range 19-69;
46.0 % female) who completed both offered tests, 21.4 % of those individuals who tested seronegative became seropositive and seroreversion was found in 12.2 % of initially seropositive participants. 81.1% of IgM positive cases at first testing became IgM negative
in approximately one month. |
|
|
Hicks, Sarah, Pohl, et al |
medRxiv |
Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
Using an ELISA-based approach to that combines data about IgG responses to both the Nucleocapsid and Spike-receptor
binding domain antigens, we show that near-optimal sensitivity and specificity can be achieved. We used this assay to assess the frequency of virus-specific antibodies in a cohort of elective surgery patients in Australia and estimated seroprevalence in Australia
to be 0.28% (0 to 0.72%). These data confirm the low level of transmission of SARS-CoV-2 in Australia before July 2020 and validate the specificity of our assay. |
|
|
Hinch, Robert, Probert, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and
realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including
both manual and digital contact tracing. It can simulate a population of 1 million people in seconds per day allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside
academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 is its Python interface, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare
options to suppress the COVID-19 epidemic. |
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|
Hoffmann, Stephanie, Spallek, et al |
Research Square prepub |
Epidemiology| Épidémiologie Healthcare Response | Réponse des soins de santé Immunology
| Immunologie |
Aim of this study is to assess the prevalence of SARS-CoV-2 infections in a cohort of 171 healthcare workers in a standard
care hospital in a rural German area. The outcomes are monthly measures of antibody prevalence over a 6-month period. Using univariate statistics, baseline characteristics will be analysed considering risk groups, exposure history, test frequencies, symptoms,
and antibody distribution. At T0 tests for qualitative detection of antibodies (Ig) against SARS-CoV-2 revealed a seroprevalence of 1.3%. The data contribute to the understanding of the virus spread in a particularly exposed population group and will be relevant
for management of the pandemic. Longitudinal analyses will reveal the progression of seroprevalence of antibodies and immunity over the time. |
|
|
Hong, K, Cao, et al |
Emerg Microbes Infect |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We here described the clinical and epidemiological characteristics of 37 recovered COVID-19 patients with prolonged
presence of viral RNA in Wuhan, China. The median age of the 37 patients was 62 years (IQR 50, 68), and 24 (64.9%) were men. They had common or severe COVID-19. With prolonged positive RT-PCR, most patients were clinically stable, 29 (78.4%) denied any symptoms.
A total of 431 PCR tests were carried out, with each patient at a median of 8 time points. The median time of PCR positivity to April 18 was 78 days (IQR 67.7, 84.5), and the longest 120 days. 22 of 37 patients had been discharged at a median of 44 days (IQR
22.3, 50) from disease onset, and 9 had lived with their families without personal protections for a total of 258 person-days and no secondary infection was identified through epidemiological investigation, nucleic acid and antibody screening. |
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|
SARS-CoV-2 D614G Variant Exhibits Enhanced Replication
ex vivo and Earlier Transmission in vivo |
Hou, YixuanJ, Chiba, et al |
bioRxiv |
Coronavirology| Coronavirologie Animal model | Modèle animal |
We engineered SARS-CoV-2 variants harboring the D614G substitution with or without nanoluciferase. The D614G variant
replicates more efficiency in primary human proximal airway epithelial cells and is more fit than wildtype (WT) virus in competition studies. With similar morphology to the WT virion, the D614G virus is also more sensitive to SARS-CoV-2 neutralizing antibodies.
Infection of human ACE2 transgenic mice and Syrian hamsters with the WT or D614G viruses produced similar titers in respiratory tissue and pulmonary disease. However, the D614G variant exhibited significantly faster droplet transmission between hamsters than
the WT virus, early after infection. Our study demonstrated the SARS-CoV2 D614G substitution enhances infectivity, replication fitness, and early transmission. |
|
Hozalski, RaymondM, LaPara, et al |
medRxiv |
Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI) |
In this study, we flushed and collected samples from showers in buildings that had been unoccupied for approximately
two months and quantified Legionella pneumophila using a commercial cultivation-based assay. In addition, all bacteria, Legionella spp., L. pneumophila, L. pneumophila serogroup 1, non-tuberculous mycobacteria (NTM), and Mycobacterium avium complex (MAC) were
analyzed using quantitative PCR (qPCR). Despite low or negligible total chlorine in the stagnant pre-flush water samples, L. pneumophila were not detected by either method; Legionella spp., NTM, and MAC, however, were widespread. Using quantitative microbial
risk assessment (QMRA), estimated risks of clinical illness from exposure to legionella and MAC via showering were generally low, but the risk of subclinical infection via Legionella spp. could exceed a 10-7 daily risk threshold if just a small fraction (≥0.1
%) of those legionellae detected by qPCR are highly infectious. Flushing cold and hot water lines rapidly restored a total chlorine (as chloramine) residual and decreased all bacterial gene targets to building inlet water levels within 30 min. Following flushing,
the chlorine residual rapidly dissipated and bacterial gene targets rebounded, approaching pre-flush concentrations after 6 to 7 days of stagnation. |
|
|
Huber, W, Lorenz, et al |
Int J Artif Organs |
Clinical data| Données cliniques |
This report presents a case management of an 80-year old patient with pulmonary, renal, circulatory, and hepatic failure.
Decided against the use of extracorporeal membrane oxygenation (ECMO) due to old age and a SOFA-score of 13. However, the patient was continuously treated with the extracorporeal multi-organ- "ADVanced Organ Support" (ADVOS) device (ADVITOS GmbH, Munich, Germany).
In the context of secondary pulmonary infection and progressive liver failure, the patient had a sudden cardiac arrest. In accordance with the presumed patient will, we decided against mechanical resuscitation. Irrespective of the outcome we conclude that
extracorporeal CO(2) removal and multiorgan-support were feasible in this COVID-19-patient. |
|
|
Ichimura, Takaharu, Mori, et al |
medRxiv |
Coronavirology| Coronavirologie Animal model | Modèle animal |
We report that Kidney Injury Molecule-1/T cell immunoglobulin mucin domain 1 (KIM-1/TIM-1) is expressed in lung and
kidney epithelial cells in COVID-19 patients and is a receptor for SARS-CoV-2. Human and mouse lung and kidney epithelial cells express KIM-1 and endocytose nanoparticles displaying the SARS-CoV-2 spike protein (virosomes). Uptake was inhibited both by anti-KIM-1
antibodies and by TW-37, our newly discovered inhibitor of KIM-1-mediated endocytosis. Enhanced KIM-1 expression by human kidney tubuloids increased uptake of virosomes. KIM-1 positive cells express less angiotensin-converting enzyme 2 (ACE2), the well-known
receptor for SARS-CoV-2. Using microscale thermophoresis, the EC50 for KIM-1-SARS-CoV-2 spike protein, and receptor binding domain (RBD) interactions, were 19 and 10 nM respectively. Thus KIM-1 is an alternative receptor to ACE2 for SARS-CoV-2. KIM-1 targeted
therapeutics may prevent and/or treat COVID-19. |
|
|
Idris, MohammedM, Banu, et al |
medRxiv |
Immunology | Immunologie |
In this study, we have investigated the expression of defensin genes in the buccal cavity during COVID-19 infection.40
SARS-CoV-2 infected positive and 40 negative swab samples were selected for the study. Based on the RT-PCR analysis involving gene specific primer for defensin genes, 10 defensin genes were found to be expressed in the Nasopharyngeal/Oropharyngeal cavity.
Six defensin genes were further found to be significantly downregulated in SARS-CoV-2 infected patients as against the control, negative samples based on differential expression analysis. The genes significantly downregulated were defensin beta 4A, 4B, 106B,
107B, 103A and defensin alpha 1B. Downregulation of several defensin genes suggests that innate immunity provided by defensins is or may be compromised in SARS-CoV-2 infection resulting in progression of the disease caused by the virus. |
|
|
Iftikhar, Hasnain, Iftikhar, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
. In this work, we used five different univariate time series models including; Autoregressive (AR), Moving Average
(MA), Autoregressive Moving Average (ARMA), Nonparametric Autoregressive (NPAR) and Simple Exponential Smoothing (SES) models for forecasting confirmed, death and recovered cases. The findings show that the time series models are useful in predicting COVID-19
confirmed, deaths and recovered cases. Furthermore, MA model outperformed the rest of all models for confirmed and deaths counts prediction, while ARMA is second best model. The SES model seems superior to other models for prediction of recovered counts, however
MA is competitive. |
|
|
Risk factors for mortality among hospitalized patients
with COVID-19 |
Incerti, Devin, Rizzo, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Objectives: To develop a prognostic model to identify and quantify risk factors for mortality among patients admitted
to the hospital with COVID-19. Participants: 17,086 patients hospitalized with COVID-19 between February 20, 2020 and June 5, 2020. Age was the most important risk factor. The performance of models that included all demographics and comorbidities (C-index
= 0.79) was only slightly better than a model that only included age (C-index = 0.76). Across the study period, predicted mortality was 1.2% for 18-year olds, 8.4% for 55-year olds, and 28.6% for 85-year olds. Predicted mortality across all ages declined over
the study period from 21.7% by March to 13.3% by May. |
|
Islam, Md Saiful, Emran, et al |
medRxiv |
Public Health response| Interventions de santé publique |
A cross-sectional offline survey was carried out enrolling 406 slum dwellers. The findings revealed that the majority
of slum dwellers in Bangladesh have limited knowledge of COVID-19. Poor practices (i.e., face mask and hand protection) were directly observed during the survey. |
|
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Monitoring SARS-CoV-2 circulation and diversity through
community wastewater sequencing |
Izquierdo Lara, RayW, Elsinga, et al |
medRxiv |
Epidemiology| Épidémiologie |
Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity
of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. hylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades
(19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within
a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome
which have not been described before. |
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The Effects of Indias COVID-19 Lockdown on Critical
Non-COVID Health Care and Outcomes |
Jain, Radhika, Dupas, et al |
medRxiv |
Epidemiology| Épidémiologie |
Comparing mortality trends among dialysis patients in the eight months around the lockdown with the previous year,
we document a 64% increase in mortality between March and May 2020 and an estimated 22-25% total excess mortality through July 2020. The mortality increase is greater among females and disadvantaged groups. Barriers to transportation and disruptions in hospital
services appear to be the main drivers of increased morbidity and mortality. The results highlight the unintended consequences of the lockdown on critical and life-saving non-COVID health services that must be taken into account in the implementation of future
policy efforts to control the spread of pandemics. |
|
Jalilian, Abdollah, Mateu, et al |
arXiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
This paper uses a spatio-temporal stochastic model to explain the temporal and spatial variations in the daily number
of new confirmed cases in Spain, Italy and Germany from late February to mid September 2020. Using a hierarchical Bayesian framework, found that the temporal trend of the epidemic in the three countries rapidly reached their peaks and slowly started to decline
at the beginning of April and then increased and reached their second maximum in August. However decline and increase of the temporal trend seems to be sharper in Spain and smoother in Germany. The spatial heterogeneity of the relative risk of COVID-19 in
Spain is also more pronounced than Italy and Germany. |
|
|
Jani, BhauteshD, Ho, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
Of the 1.3 million population, 32,533 (2.47%) had been advised to shield, a further 347,374 (26.41%) were classified
as moderate risk. Testing for COVID-19 was more common in the shielded (6.75%) and moderate (1.99%) than low (0.72%) risk categories. Referent to low-risk, the shielded group had higher risk of confirmed infection (RR 7.91, 95% 7.01-8.92), case-fatality (RR
5.19, 95% CI 4.12-6.53) and population mortality (RR 48.64, 95% 37.23-63.56). The moderate risk had intermediate risk of confirmed infection (RR 4.11, 95% CI 3.82-4.42) and population mortality (RR 26.10, 95% CI 20.89-32.60), but had comparable case-fatality
(RR 5.13, 95% CI 4.24-6.21) to the shielded, and accounted for a higher proportion of deaths (PAF 75.27% vs 13.38%). Age ≥70 years made the largest contribution to deaths (49.53%) and was associated with an 8-fold risk of infection, 7-fold case-fatality and
74-fold mortality. |
|
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Prioritising COVID-19 vaccination in changing social
and epidemiological landscapes |
Jentsch, Peter, Anand, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
We developed a coupled social-epidemiological model of SARS-CoV-2 transmission. Schools and workplaces are closed and
re-opened based on reported cases. We used evolutionary game theory and mobility data to model individual adherence to NPIs. We explored the impact of vaccinating 60+ year-olds first; <20 year-olds first; uniformly by age; and a novel contact-based strategy.
The last three strategies interrupt transmission while the first targets a vulnerable group. Vaccination rates ranged from 0.5% to 4.5% of the population per week, beginning in January or July 2021. Case notifications, NPI adherence, and lockdown periods undergo
successive waves during the simulated pandemic. Vaccination reduces median deaths by 32%-77% (22%-63%) for January (July) availability, depending on the scenario. Vaccinating 60+ year-olds first prevents more deaths (up to 8% more) than transmission-interrupting
strategies for January vaccine availability across most parameter regimes. In contrast, transmission-interrupting strategies prevent up to 33% more deaths than vaccinating 60+ year-olds first for July availability, due to higher levels of natural immunity
by that time. Sensitivity analysis supports the findings. |
|
Evidence for and level of herd immunity against SARS-CoV-2
infection: the ten-community study |
Jeremijenko, Andrew, Chemaitelly, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
Qatar experienced a large severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic that disproportionately
affected the craft and manual workers (CMWs) who constitute 60% of the population. This study aimed to investigate level of immunity in communities within this population as well as infection exposure required to achieve herd immunity. Study included 4,970
CMWs who were mostly men (95.0%) and <40 years of age (71.5%). Seropositivity ranged from 54.9% (95% CI: 50.2-59.4%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean seropositivity across all communities was 66.1% (95% CI: 61.5-70.6%).
PCR positivity ranged from 0.0% to 10.5% (95% CI: 7.4-14.8%) in the different CMW communities. Pooled mean PCR positivity was 3.9% (95% CI: 1.6-6.9%). Median cycle threshold (Ct) value was 34.0 (range: 15.8-37.4). The majority (79.5%) of PCR-positive individuals
had Ct value >30 indicative of earlier rather than recent infection. Infection positivity (antibody and/or PCR positive) ranged from 62.5% (95% CI: 58.3-66.7%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean infection positivity
was 69.5% (95% CI: 62.8-75.9%). Only five infections were ever severe and one was ever critical, an infection severity rate of 0.2% (95% CI: 0.1-0.4%). |
|
Jiandani, MP, Salagre, et al |
J Assoc Physicians India |
Healthcare Response | Réponse des soins de santé |
This retrospective study was undertaken to explore the physiotherapy practices that could be implemented in patients
admitted with COVID 19 in the ICU and its effect on mobility and oxygen requirement as an outcome. 278 record sheets (110 ICU and 168 SDU) were retrospectively analysed for demographics. 44.55% of patients improved with side lying position, 37.27% with prone
position and 10.91% with quarter prone position. 4.55% of patient maintained oxygenation in propped up sitting. 2.73% could not be positioned. Chest physiotherapy techniques applied were deep breathing, ACBT, paced breathing and diaphragmatic breathing. Deep
intercostal pressure on NIV along with vibrations was given to 12.72% of patients in the ICU. Group therapy sessions were conducted in SDU where 50.59% patients participated. ICU mobility score showed significant improvement on Wilcoxon Signed Ranks test status
on day 7 in the ICU (z=-5.99, p=0.00) and SDU (z= 7.676, p=0.00) compared to day 1. Descriptive analysis showed a definitive reduction in oxygen support requirement. |
|
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Resuming assisted reproduction services during COVID-19
Pandemic: An Indian experience |
Jirge, Padma Rekha, Patwardhan, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The purpose of the study was to assess the preparedness of assisted reproductive treatment (ART) clinics and staff
to resume services and patients reasons to initiate treatment and key performance indicators (KPIs) of ART labs during pandemic. One-third of the patients consulted through telemedicine accepted or were eligible to initiate treatment upon clinic resumption.
Lack of safe transport and financial constraints prevented majority from undergoing IVF, and only 9 percent delayed treatment due to fear of pandemic. With adequate training, staff compliance to meet new demands could be achieved within a week, but supply
of consumables was a major constraint. 52 cycles of IVF were performed including fresh cycles and frozen embryo transfers with satisfactory KPIs even during pandemic. Conscious sedation and analgesia during oocyte retrieval was associated with reduced procedure
time and no intervention for airway maintenance, compared to general anaesthesia. Self reported pain scores by patients ranged from nil to mild on a graphic rating scale. |
|
Resuming assisted reproduction services during COVID-19
Pandemic: An Indian experience |
Jirge, Padma Rekha, Patwardhan, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The purpose of the study was to assess the preparedness of assisted reproductive treatment (ART) clinics and staff
to resume services and patients reasons to initiate treatment and key performance indicators (KPIs) of ART labs during pandemic. One-third of the patients consulted through telemedicine accepted or were eligible to initiate treatment upon clinic resumption.
Lack of safe transport and financial constraints prevented majority from undergoing IVF, and only 9 percent delayed treatment due to fear of pandemic. With adequate training, staff compliance to meet new demands could be achieved within a week, but supply
of consumables was a major constraint. 52 cycles of IVF were performed including fresh cycles and frozen embryo transfers with satisfactory KPIs even during pandemic. Conscious sedation and analgesia during oocyte retrieval was associated with reduced procedure
time and no intervention for airway maintenance, compared to general anaesthesia. Self reported pain scores by patients ranged from nil to mild on a graphic rating scale. |
|
Cost-effectiveness of remdesivir and dexamethasone
for COVID-19 treatment in South Africa |
Jo, Youngji, Jamieson, et al |
medRxiv |
Economics | Économie |
We projected intensive care unit (ICU) needs and capacity from August 2020 to January 2021 using the South African
National COVID-19 Epi Model. We assessed cost-effectiveness of 1) administration of dexamethasone to ventilated patients and remdesivir to non-ventilated patients, 2) dexamethasone alone to both non-ventilated and ventilated patients, 3) remdesivir to non-ventilated
patients only, and 4) dexamethasone to ventilated patients only; all relative to a scenario of standard care. Remdesivir for non-ventilated patients and dexamethasone for ventilated patients was estimated to result in 1,111 deaths averted (assuming a 0-30%
efficacy of remdesivir) compared to standard care, and save $11.5 million. The result was driven by the efficacy of the drugs, and the reduction of ICU-time required for patients treated with remdesivir. The scenario of dexamethasone alone to ventilated and
non-ventilated patients requires additional $159,000 and averts 1,146 deaths, resulting in $139 per death averted, relative to standard care. |
|
Johnson, KaitlynE, Stoddard, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
we have used epidemiological modeling to explore the feasibility and consequences of school reopening in the face of
differing rates of COVID-19 prevalence and transmission. Our findings indicate that, regardless of the initial prevalence of the disease, and in the absence of systematic surveillance testing, most schools in the United States can expect to remain open for
20-60 days. At this point, one or more large disease clusters can be expected to be detected, forcing schools to close again. These disease clusters, in turn, can be expected to propagate through the community, with potentially hundreds to thousands of additional
cases resulting from each individual school cluster. |
|
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Excess Risk of COVID-19 to University Populations
Resulting from In-Person Sporting Events |
Johnson, StephanieS, Jackson, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
We explore the impact of having in-person sports on COVID-19 transmission on a college campus, specifically the excess
cases within the campus community can be anticipated. Events caused an increase in the number of cases among the campus community, ranging from a 25% increase in a scenario where the campus already had an uncontrolled COVID-19 outbreak and visitors had a low
prevalence of COVID-19 and mixed lightly with the campus community to an 822% increase where the campus had controlled their COVID-19 outbreak and visitors had both a high prevalence of COVID-19 and mixed heavily with the campus community. The model was insensitive
to parameter uncertainty, save for the duration a symptomatic individual was infectious. |
|
DOSING OF THROMBOPROPHYLAXIS AND MORTALITY IN CRITICALLY
ILL COVID-19 PATIENTS |
Jonmarker, Sandra, Hollenberg, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The purpose of the study was to evaluate the association of initial dosing strategy of thromboprophylaxis in critically
ill COVID-19 patients and the risk of death, thromboembolism, and bleeding. A total of 152 patients were included; 67 received low, 48 medium, and 37 high dose thromboprophylaxis. Baseline characteristics did not differ between groups. Mortality was lower
in high (13.5%) vs medium (25.0%) and low dose thromboprophylaxis (38.8%) groups, p≡0.02. The hazard ratio of death was 0.33 (95% confidence intervals 0.13 − 0.87) among those who received high dose, respectively 0.88 (95% confidence intervals 0.43 − 1.83)
among those who received medium dose, as compared with those who received low dose thromboprophylaxis. There were fewer thromboembolic events in the high (2.7%) vs medium (18.8%) and low dose thromboprophylaxis (17.9%) groups, p≡0.04, but no difference in
the proportion of bleeding events, p≡0.16. |
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High-throughput quantitation of SARS-CoV-2 antibodies
in a single-dilution homogeneous assay |
Kainulainen, MarkusH, Bergeron, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We developed a simpler and faster system that is highly automatable and achieves quantitation in a single-dilution
screening format with sensitivity and specificity comparable to those of ELISA. |
|
Kalippurayil Moozhipurath, Rahul |
medRxiv |
Epidemiology| Épidémiologie |
In this observational study, we outline the roles of 7 relevant weather factors including temperature, humidity, UVI,
precipitation, ozone, pollution (visibility) and cloud cover in COVID-19 deaths in Brazil. We control for all time-fixed and various time-varying region-specific factors confounding factors. We observe a significant negative association of COVID-19 daily deaths
growth rate in Brazil with weather factors - UVI, temperature, ozone and cloud cover. Specifically, a unit increase in UVI, maximum temperature, and ozone independently associate with 6.0 percentage points [p<0.001], 1.8 percentage points [p<0.01] and 0.3
percentage points [p<0. 1] decline in COVID-19 deaths growth rate. Further, a unit percentage increase in cloud cover associates with a decline of 0.148 percentage points [p<0.05] in COVID-19 deaths growth rate. Surprisingly, contrary to other studies, we
do not find evidence of any association between COVID-19 daily deaths growth rate and humidity, visibility and precipitation. |
|
|
Implications of Monsoon Season & UVB Radiation for
COVID-19 in India |
Kalippurayil Moozhipurath, Rahul, Kraft, et al |
medRxiv |
Epidemiology| Épidémiologie |
In this observational study, we empirically study the respective roles of monsoon season and UVB, whilst further exploring,
whether monsoon season negatively impacts the protective role of UVB in COVID-19 deaths in India. After controlling for various confounding factors, we observe that the monsoon season and a unit increase in UVI are separately associated with 12.8 percentage
points and 2.0 percentage points decline in growth rates of COVID-19 deaths in the long run. These associations translate into substantial relative changes. |
|
Face Masks, Public Policies and Slowing the Spread
of COVID-19: Evidence from Canada |
Karaivanov, Alexander, Lu, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
We estimate the impact of mask mandates and other non-pharmaceutical interventions (NPI) on COVID-19 case growth in
Canada, including regulations on businesses and gatherings, school closures, travel and self-isolation, and long-term care homes. We find that, in the first few weeks after implementation, mask mandates are associated with a reduction of 25 percent in the
weekly number of new COVID-19 cases. Additional analysis with province-level data provides corroborating evidence. Counterfactual policy simulations suggest that mandating indoor masks nationwide in early July could have reduced the weekly number of new cases
in Canada by 25 to 40 percent in mid-August, which translates into 700 to 1,100 fewer cases per week. |
|
Kase, Kerstin, Skrzat-Klapaczynska, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The aim of our study was to describe epidemiology and clinical characteristics of people living with HIV (PLWH) diagnosed
with COVID-19 reported form Central and Eastern European Countries. In total 34 cases were reported. The mean age of those patients was 42.7 years (IQR=35.8-48.5) and most of the patients were male (70.6% vs 29.4%). The mean CD4+ T-cell count prior COVID-19
diagnosis was 558 cells/mm3 (IQR=312-719) and HIV RNA viral load (VL) was undetectable in 18 of 34 (53%) cases, the data about most recent HIV RNA VL was not available in three cases (8,8%). Comorbidities were observed in 19 (55.9%) patients, mostly cardiovascular
disease (27,8%), and in 10 (29.4%) patients had coinfection, mostly chronic hepatitis C (87.5%). The clinical course of COVID-19 was asymptomatic in 4 (12%) cases, mild disease without hospitalization was reported in 11 (32%) cases. Stable patients with respiratory
and/or systemic symptoms have been documented in 14 (41%) cases; 5 (15%) patients were clinically unstable with respiratory failure. Full recovery was reported in 31 (91%) cases, two patients died. In one case the data was not available. |
|
|
Ke, Ruian, Zitzmann, et al |
medRxiv |
Clinical data| Données cliniques |
Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection in both h the upper respiratory tract (URT)
and the lower respiratory tract (LRT). We found that to explain the substantial fraction of transmissions occurring presymptomatically, the infectiousness of a person should depend on a saturating function of the viral load, making the logarithm of the URT
viral load a better surrogate of infectiousness than the viral load itself. Comparing the roles of target-cell limitation, the innate immune response, proliferation of target cells and spatial infection in the LRT, we found that spatial dissemination in the
lungs is likely to be an important process in sustaining the prolonged high viral loads |
|
|
Fitting to the UK COVID-19 outbreak, short-term forecasts
and estimating the reproductive number |
Keeling, MattJ, Dyson, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Here, focusing on the dynamics of the first-wave (March-June 2020), we present in some detail the inference scheme
employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired
parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. |
|
Automated Contact Tracing: a game of big numbers
in the time of COVID-19 |
Kim, Hyunju, Paul, et al |
medRxiv |
Public health interventions*| Interventions de santé publique |
In this work, we study the characteristics of voluntary and automated contact tracing and its effectiveness for mapping
the spread of a pandemic due to the spread of SARS-CoV-2. We highlight the infrastructure and social structures required for automated contact tracing to work. We display the vulnerabilities of the strategy to inadequate sampling of the population, which results
in the inability to sufficiently determine significant contact with infected individuals. Of crucial importance will be the participation of a significant fraction of the population for which we derive a minimum threshold. We conclude that relying largely
on automated contact tracing without population-wide participation to contain the spread of the SARS-CoV-2 pandemic can be counterproductive and allow the pandemic to spread unchecked. The simultaneous implementation of various mitigation methods along with
automated contact tracing is necessary for reaching an optimal solution to contain the pandemic. |
|
Privacy-Protecting, Reliable Response Data Discovery
Using COVID-19 Patient Observations |
Kim, Jihoon, Neumann, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
Using a privacy-protecting strategy, we launched a public Questions & Answers web portal (https://covid19questions.org)
with analyses of comorbidities, medications and laboratory tests using data from 202 hospitals (59,074 COVID-19 patients) in the USA and Germany. We find, for example, that 8.6% of hospitalizations in which the patient was not admitted to the ICU resulted
in the patient returning to the hospital within seven days from discharge and that, when adjusted for age, mortality for hospitalized patients was not significantly different by gender or ethnicity. |
|
Modelling the risk of SARS-CoV-2 infection through
PPE doffing in a hospital environment |
King, Marco-Felipe, Wilson, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Infection Prevention and Control/ Prévention
et contrôle des infections (IPAC/PCI) |
HCW surface contact sequences on a respiratory ward were modelled using a discrete-time Markov chin for: IV-drip care,
blood pressure monitoring and doctors' rounds. Accretion of viral RNA on gloves during care was modelled using a stochastic recurrence relation. The HCW then doffed PPE and contaminated themselves in a fraction of cases based on increasing case load. The risk
of infection from this exposure was quantified using a dose-response methodology. |
|
Kip, KevinE, Snyder, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We reviewed demographic and clinical profiles, along with measures of hospital-based clinical practice to identify
temporal changes in clinical practice that may have affected in-hospital outcomes of patients with COVID-19. In our large system, recently treated hospitalized COVID-19 patients had lower rates of in-hospital mechanical ventilation/mortality and shorter length
of hospital stay. Alongside of this was a change to early initiation of glucocorticoid therapy and anticoagulation. |
|
|
Klein, Hadar, Asseo, et al |
medRxiv |
Clinical data| Données cliniques |
Phone interviews and follow-ups were completed with 112 mild COVID-19 RT-PCR-positive adult patients, over a 6 week
period. More than one symptom at disease onset was experienced by ~70 of the patients. Over one third of patients experienced fever, dry cough, headache, or muscle ache as the first symptom. Each symptom can occur as first or later, though some are more likely
to appear as firsts, and typically more than one symptom occurs at disease onset. The severity of olfactory change is associated with its recovery time. |
|
|
Kouriba, Bourema, Duerr, et al |
medRxiv |
Epidemiology| Épidémiologie Coronavirology| Coronavirologie |
We have focused our efforts on generating the first Malian sequencing data available. Screening of 217 Malian patient
samples for the presence of SARS-CoV-2 resulted in 38 positive isolates from which 21 whole genome sequences were generated. Our analysis shows that both, the early A (19B) and the fast evolving B (20A/C) clade, are present in Mali indicating multiple and
independent introductions of the SARS-CoV-2 to the Sahel region. |
|
|
Kumar, Abhimanyu, Prasad, et al |
Sci Transl Med |
Clinical data| Données cliniques Therapeutics| Thérapeutique |
A recent in silico study found the therapeutic efficacy of Guduchi against SARS-CoV-2. Based on available evidence,
we conducted a feasibility study of the safety and efficacy of Guduchi Ghan Vati in asymptomatic patients with covid-19. A single-arm study with no control group and blinding was executed in Jodhpur, Rajasthan, India on 46 patients. In adult patients with
asymptomatic Covid-19, Gudhuchi Ghan Vati could be effective; by the end of D-7, 38 (95%) patients had viral load disappearance. Follow-up at D-14 showed that all participants tested negative. |
|
|
Kumar, BK, Faheem, et al |
J Biomol Struct Dyn |
Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
Pharmacophore based virtual screening of the selected natural product databases followed by Glide molecular docking
and dynamics studies against SARS-CoV-2 main protease was investigated to identify potential ligands that may act as inhibitors. The molecules SN00293542 and SN00382835 revealed the highest docking score of -14.57 and -12.42 kcal/mol, respectively, when compared
with the co-crystal ligands of PDB-6Y2F (O6K) and 6W63 (X77) of the SARS-CoV-2 M(pro). To further validate the interactions of top scored molecules SN00293542 and SN00382835, molecular dynamics study of 100 ns was carried out. This indicated that the protein-ligand
complex was stable throughout the simulation period, and minimal backbone fluctuations have ensued in the system. Post-MM-GBSA analysis of molecular dynamics data showed free binding energy-71.7004 +/- 7.98, -56.81+/- 7.54 kcal/mol, respectively. The computational
study identified several ligands that may act as potential inhibitors of SARS-CoV-2 M(pro). |
|
|
Kumar, Narendra, Hameed, et al |
medRxiv |
Epidemiology| Épidémiologie Transmission |
In this report, we describe the epidemiology of SARS-CoV-2 infection, specifically examining how the symptomatic persons
drove the transmission in the state of Karnataka, India, during the lockdown phase. Our findings indicate that both asymptomatic and symptomatic SARS-CoV-2 cases transmit the infection; however, the main driving force behind the spread of infection within
the state was significantly higher from symptomatic cases. |
|
|
Kurita, Junko, Sugawara, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We sought to quantify excess mortality in April using the National Institute of Infectious Diseases (NIID) model. We
applied the NIID model to deaths of all causes from 1987 up through June, 2020. Results show no significant excess mortality in March to June, 2020, when the COVID−19 outbreak affected Japan most. It might be important to continue to monitor excess mortality
of COVID-19 carefully after June 2020. |
|
|
Kuryntseva, Polina, Karamova, et al |
medRxiv |
Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
In the present study, a modified approach for detection of COVID-19 infection rate using wastewater analysis has been
developed. The minimum infection rate that can be detected using this approach is 0.01%. The approach developed was used to investigate wastewater from eleven sewage inspection chambers in the city of Kazan (Russia). It was demonstrated that the average infection
rate of people using these sewers was over 0.4% in July 2020. |
|
|
Larsson, SusannaC, Burgess, et al |
medRxiv |
Therapeutics| Thérapeutique |
We conducted a Mendelian randomization study investigating the effect of IL-6 signaling on susceptibility to COVID-19
and pneumonia. Our results showed that genetically proxied inhibition of IL-6 signaling was associated with reduced risk of COVID-19, but also with increased risk of pneumonia. Respiratory disease is a main feature of severe COVID-19, and the potential of
IL-6 signaling inhibitors to increase risk of pneumonia warrants vigilance and caution in their application to treat COVID-19. |
|
|
Lascarrou, Jean Baptiste, Colin, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
Performance concerns have recently emerged regarding RT-PCR testing, especially about its sensitivity. We hypothesized
that clinical, biological and radiological characteristics of patients with false negative first RT-PCR testing, despite final diagnosis of COVID19, might differ from patients with positive first RT PCR. Patients with suspected COVID19 and higher inflammatory
biological signs expected higher risk of false negative RT PCR testing. Strategy of serial RT PCR testings must be rigorously evaluated before adoption by clinicians. |
|
|
Laursen, Jannie, Petersen, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
The aim of the study is to contribute to the surveillance of the pandemic by bringing new knowledge about SARS-CoV-2
seropositivity among healthcare workers and evaluating whether certain job functions is associated with a higher risk of being infected, and to clarify if such association is mediated by the number of individuals that the employees meet during a workday. Our
study presents geographical variations in seroprevalence within the Falck organization and shows evidence that social interaction is one of the biggest risk factors for getting infected with SARS-CoV-2. |
|
|
Lazzeri, Massimo, Duga, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This is a case-control study on patients hospitalized for COVID-19 (cases), matched to beneficiaries of the Lombardy
Regional Health Service (controls), to determine whether men who received 5ARIs for benign prostatic hyperplasia (BPH) have a lower risk of hospitalization for COVID-19. the use of 5ARIs was less frequent among patients hospitalized for COVID-19 than among
controls, suggesting that men exposed to 5ARIs might be less vulnerable to severe COVID-19. |
|
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SARS-CoV-2 N-antigenemia: A new alternative to nucleic
acid amplification techniques |
Le Hingrat, Quentin, Visseaux, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We assessed the performances of a new ELISA microplate assay quantifying SARS-CoV-2 nucleocapsid antigen (N-antigen)
in serum or plasma. The specificity of the assay, determined on 63 non-COVID patients, was 98.4%; and Sensitivity was 132/142, 93.0%, within the first two weeks after symptoms onset. This is the first demonstration of the N-antigen antigenemia during COVID-19.
Its detection presented a robust sensitivity, especially within the first 14 days after symptoms onset and high nasopharyngeal viral loads. |
|
Lebedin, YuriS, Lyang, et al |
medRxiv |
Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
The article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results
of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia |
|
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Aerosol transmission of COVID-19 and infection risk
in indoor environments |
Lelieveld, Jos, Helleis, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission |
Here we present a simple, easy-to-use spreadsheet algorithm to estimate the infection risk for different indoor environments,
constrained by published data on human aerosol emissions, SARS-CoV-2 viral loads, infective dose and other parameters. We evaluate typical indoor settings such as an office, a classroom, a choir practice room and reception/party environments. |
|
Leon-Abarca, Juan, Memon, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We used the Mexican Open Registry of COVID-19 patients 11 to analyze anonymized records of those who had symptoms related
to COVID-19 to analyze the rates of SARS-CoV-2 infection, development of COVID-19 pneumonia, admission, intubation, Intensive Care Unit admission and mortality. Patients with diabetic nephropathy had nearly a twofold rate of COVID-19 pneumonia, a higher probability
of admission, a twofold probability of intubation and a higher chance of death once admitted compared to patients with chronic kidney disease alone. Also, both diseases had higher COVID-19 pneumonia rates, intubation rates and case-fatality rates compared
to the overall population. |
|
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Clinical evolution of COVID-19 during pregnancy at
different altitudes: a population-based study |
Leon-Abarca, Juan, Pena-Gallardo, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We analyzed the records of 326,586 non-pregnant women of reproductive age and 7,444 pregnant women with no other risk
factor who also had a SARS-CoV-2 RT-PCR result to estimate adjusted prevalence (aP) and adjusted prevalence ratios (aPR) of COVID-19 and its requirement of hospitalization, intubation, ICU admission and case-fatality rates. Pregnancy was independently associated
with a 15% higher probability of COVID-19 (aPR: 1.15), a 116% higher probability of its following admission (aPR: 2.169) and a 127% higher probability of ICU admission (aPR: 2.275). |
|
Empirical transmission advantage of the D614G mutant
strain of SARS-CoV-2 |
Leung, Kathy, Pei, et al |
medRxiv |
Transmission Coronavirology| Coronavirologie |
Using our previous epidemiological framework to analyze COVID-19 surveillance and sequence data, we estimated that
the G614 mutant is 31% (28-34%) more transmissible than the D614 wildtype. As such, interventions that were previously effective in containing or mitigating the D614 wildtype (e.g. in China, Vietnam, Thailand, etc.) might be less effective against the G614
mutant. |
|
Epidemiology and precision of SARS-CoV-2 detection
following lockdown and relaxation measures |
Leuzinger, Karoline, Gosert, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We aim to cross-validate manual and automated high-throughput (Roche-cobas6800-Target1/Target2) testing for SARS-CoV-2-RNA,
to describe detection rates following lockdown and relaxation, and to evaluate SARS-CoV-2-loads in different specimens. Concordant results were obtained in 1308 cases (97%) including 97 (9%) SARS-CoV-2-positives showing high quantitative correlations (Spearman
r>0.95; p<0.001) for all assays. Discordant samples (N=36) had significantly lower SARS-CoV-2-loads (p<0.001). |
|
Lexmond, AxelS, Nouwen, et al |
medRxiv |
Epidemiology| Épidémiologie |
For the 12 countries we studied, the hypothesis that these countries have reached herd immunity warrants serious consideration.
The Reed-Frost model, perhaps the simplest description for the evolution of cases in an epidemic, with only a few constant parameters, fits the observed case data remarkably well, and yields parameter values that are reasonable. The results suggest that between
51 and 80% of the population in these countries have been infected, and that between 0.05% and 2.50% of cases have been detected; values which are consistent with findings from serological and T-cell immunity studies. |
|
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Clinical Course And Risk Factors For In-hospital
Death In Critical COVID-19 In Wuhan, China |
Li, Fei, Cai, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study aimed to described the clinical outcomes and further explored risk factors of in-hospital death for COVID-19
classified as critical type. COVID-19 classified as critical type had a high prevalence of acute cardiac and kidney injury, which were associated with a higher risk of in-hospital mortality. |
|
Li, MatthewD, Arun, et al |
medRxiv |
Clinical data| Données cliniques Healthcare Response | Réponse des soins de santé |
We aim to improve and test the generalizability of a deep learning-based model for assessment of COVID-19 lung disease
severity on chest radiographs (CXRs) from different patient populations. Tuning the deep learning model with outpatient data improved model performance in two United States hospitalized patient datasets (r=0.88 and r=0.90, compared to baseline r=0.86). Model
performance was similar, though slightly lower, when tested on the United States outpatient and Brazil emergency department datasets (r=0.86 and r=0.85, respectively). |
|
|
Seroprevalence of immunoglobulin M and G antibodies
against SARS-CoV-2 in ophthalmic patients |
li, shengjie, qiu, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
We conducted a cross-sectional study assaying the IgG and IgM antibodies in 1331 individuals with ocular diseases by
using a magnetic chemiluminescence enzyme immunoassay kit, during the period from February 2020 to May 2020. In our study, the seroposivity in total ocular disease patients was 0.83% (11/1331). All the participants were reverse transcription polymerase chain
reaction negative for SARS-CoV-2 from throat swabs. |
|
Li, zhouxuan, Xu, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
We observed that no metrics showed significant evidence in mitigating the COVID-19 epidemic in FL and only a few metrics
showed evidence in reducing the number of new cases of COVID-19 in AZ, NY and TX. Our results showed that the majority of non-pharmaceutical interventions had a large effect on slowing the transmission and reducing deaths, and that health interventions were
still needed to contain COVID-19. |
|
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COVID-19 mortality rate in Russia: forecasts and
reality evaluation |
Lifshits, Marina, Neklyudova, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
The aim of the study is to analyze the factors affecting COVID-19 mortality rate in various countries, to predict direct
and indirect victims of the pandemic in the Russian Federation, and to estimate additional mortality during the pandemic based on the demographic data. It is determined that the number of additional deaths due to the coronavirus is approximately 31 thousand
people. The analysis revealed that the relatively low proportion of COVID in Russia is the result of a special approach to the cause of death determination. |
|
Linares, Manuel, Pérez Tanoira, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Evaluate the performances of the Panbio COVID-19 AG Rapid Test Device (Nasopharyngeal), a rapid immunochromatographic
test for the detection of SARS-CoV-2 antigen, in comparison to RT-qPCR. This assay seems to be an effective strategy for controlling the COVID-19 pandemic for the rapid identification and isolation of SARS-CoV-2 infected patients. |
|
|
Linssen, Joachim, Ermens, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The observed haemocytometric patterns formed the basis to develop a multi-haemocytometric-parameter prognostic score
to predict, during the first three days after presentation, which patients will recover without ventilation or deteriorate within a two-week timeframe, needing intensive care or with fatal outcome. |
|
|
Liu, Qi, Brookbank, et al |
medRxiv |
Transmission Infection Prevention and Control/ Prévention et contrôle des infections
(IPAC/PCI) |
Here, we report a novel bead transfer method for evaluating fomite transmission in common laboratory settings. We show
that this method meets several important criteria for quantitative test methods, including reasonableness, relevancy, resemblance, responsiveness, and repeatability, and therefore may be adaptable for standardization. |
|
|
Evaluation of China's Hubei Control Strategy for COVID-19 Epidemic: An
Observational Study |
Liu, Yu, Zheng, et al |
Research Square prepub |
Public health interventions*| Interventions de santé publique |
This study aimed to assess the response process and estimate time-varying effect of Hubei control strategy to provide
insights for intervention design and implementation. The analysis detected much higher but differential importation risk in Hubei. The response timing largely coincided with the importation risk in non-Hubei areas, but Hubei areas showed an opposite pattern.
A careful and comprehensive comparison showed that Hubei control strategy implemented interventions characterized by unprecedentedly strict and ‘monitored’ self-quarantine at home, while non-Hubei strategy included physical distancing measures to reduce contact
among individuals within or between populations. In contrast with non-Hubei control strategy, Hubei strategy showed a much higher, non-linear and gradually diminishing protective effect with at least 3 times fewer cases. |
|
Loisel, Patrice |
medRxiv |
Epidemiology| Épidémiologie |
We provide an explanation for the apparent discrepancy between the dynamic of the positive COVID-19 test rates and
of the numbers of COVID-19-related hospital and intensive care admissions and deaths in France. We highlight the existence of a latency period of around 5 weeks between the infections of young individual (generally asymptomatic) to older individuals that may
have a severe form of the disease and may be hospitalized. |
|
|
Long, Scott Wesley, Olsen, et al |
medRxiv |
Epidemiology| Épidémiologie Coronavirology| Coronavirologie |
We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas,
an ethnically diverse region with seven million residents. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected
with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. |
|
|
Lu, Tina, Reis, et al |
medRxiv |
Epidemiology| Épidémiologie Public Health response| Interventions de santé publique |
We sought to determine whether Internet search patterns can be useful for tracking COVID-19 spread, and whether these
data could also be useful in understanding the clinical progression of the disease in 32 countries across six continents. Increases in COVID-19 symptom-related searches preceded increases in reported COVID-19 cases and deaths by an average of 18.53 days (95%
confidence interval 15.98 to 21.08) and 22.16 days (20.33 to 23.99), respectively. |
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|
Lugo Goytia, Gustavo, Hernandez-Cardenas, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The purpose of this study was to describe the clinical manifestations, and outcomes in a COVID-19 cohort attended to
from March to May 2020 in our RICU. We found six independent factors associated with the mortality risk: delta lymphocyte count, delta ventilatory ratio, BMI, norepinephrine support, no AKI/AKI 1, and bacterial coinfection . |
|
|
Luo, Shengxue, Zhang, et al |
bioRxiv |
Vaccine Research| Recherche sur les vaccins Animal model | Modèle animal |
Here, we constructed two novel adenovirus vectored COVID-19 vaccine candidates on simian adenovirus serotype 23 (Sad23L)
and human adenovirus serotype 49 vectors (Ad49L) carrying the full-length gene of SARS-CoV-2 spike protein (S), designated Sad23L-nCoV-S and Ad49L-nCoV-S vaccines, respectively. The immunogenicity elicited by these two vaccine strains was individually evaluated
in mice. Furthermore, five rhesus macaques were intramuscularly injected with a dose of 5X10^9 PFU Sad23L-nCoV-S for prime vaccination, followed by boosting with 5X10^9 PFU of Ad49L-nCoV-S vaccine at a 4-week interval. Both mice and macaques tolerated well
the vaccine inoculation without detectable clinical and pathologic changes. In macaques, prime-boost vaccination regimen induced high titers of 10^3.16 S binding antibody (S-BAb), 10^2.75 RBD-BAb and 10^2.38 neutralizing antibody (NAb to pVNT) a week after
boosting injection, followed by sustained high levels. Robust IFN-γ; secreting T-cell response (712.6 SFCs/106 cells), IL-2 secreting T-cell response (334 SFCs/106 cells) and intracellular IFN-γ; expressing CD4+/CD8+ T cell response (0.39%/0.55%) to S peptides
were detected in the vaccinated macaques. The study concluded that prime-boost immunization with Sad23L-nCoV-S and Ad49L-nCoV-S vaccines can safely elicit strong immunity in animals in preparation of clinical phase 1/2 trials. |
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Characterizing COVID-19 Clinical Phenotypes and Associated
Comorbidities and Complication Profiles |
Lusczek, ElizabethR, Ingraham, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
Identify specific clinical phenotypes across COVID-19 patients (n=1022) and compare admission characteristics and outcomes.
Three clinical phenotypes were identified (I, II, III).When grouping comorbidities by organ system, patients with respiratory comorbidities were most commonly characterized by phenotype III (p=0.002), while patients with hematologic (p<0.001), renal (p<0.001),
and cardiac (p<0.001) comorbidities were most commonly characterized by phenotype I. |
|
Lye, Phatcharawan, Dunk, et al |
medRxiv |
Coronavirology| Coronavirologie Immunology | Immunologie |
Assessed pathways by which SARS-CoV-2 could access the placenta and contribute to fetal transmission. The data suggest
that in COVID19 positive pregnancies complicated by ChA, ACE2 positive immune cells have the potential to traffic SARS-CoV-2 virus to the placenta and increase the risk of vertical transmission to the placenta/fetus. |
|
|
Lytras, Theodore, Sypsa, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
Present an improved method to estimate Rt and its application to routine surveillance data from Greece. Mobility patterns
significantly affect Rt. Most of the reduction in COVID-19 transmissibility in Greece occurred already before the lockdown, likely as a result of decreased population mobility. Lower viral transmissibility in summer does not appear sufficient to counterbalance
the increased mobility due to tourism. |
|
|
Lyu, Mingdong, Hall, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Propose an enhanced SEIRD (Susceptible-Exposed-Infectious-Recovered-Death) model with time varying case fatality and
transmission rates for confirmed cases and deaths from COVID-19. |
|
|
Ma, Yunlong, Huang, et al |
medRxiv |
Immunology | Immunologie |
Results uncover 21q22.11 as a novel susceptibility locus for COVID-19, in which individuals with G alleles of rs9976829
have a higher probability of COVID-19 susceptibility than those with non-G alleles. |
|
|
Madera, Sharline, Crawford, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The role of children in the spread of the SARS-CoV2 coronavirus has become a matter of urgent debate as societies in
the US and abroad consider how to safely reopen schools. Small studies have suggested higher viral loads in young children. Here we present a multicenter investigation on over five thousand SARS-CoV-2 cases confirmed by real-time reverse transcription (RT)
PCR assay. Notably, we found no discernable difference in amount of viral nucleic acid among young children and adults. |
|
|
Mahajan, Shiwani, Srinivasan, et al |
medRxiv |
Epidemiology| Épidémiologie Public Health response| Interventions de santé publique |
Estimated the seroprevalence of SARS-CoV-2-specific IgG antibodies and the prevalence of symptomatic illness and self-reported
adherence to risk mitigation behaviors among on-Hispanic Black and Hispanic subpopulations in Connecticut, US. The weighted seroprevalence for the oversampled non-Hispanic Black and Hispanic populations was 6.4% (90% CI 0.9-11.9) and 19.9% (90% CI 13.2-26.6),
respectively. The majority of respondents at the state-level reported following risk mitigation behaviors: 73% avoided public places, 75% avoided gatherings of families or friends, and 97% wore a facemask, at least part of the time. |
|
|
Mahmud, Riaz, Patwari, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
The basic reproduction number R0 of novel coronavirus (SARS-CoV-2) in Bangladesh is estimated to be 2.66 [95% CI: 2.58-2.75],
optimized R0 is 2.78 [95% CI: 2.69-2.88] using generation time 5.20 with a standard deviation of 1.72 for Singapore. |
|
|
Malecki, Monika, Luesebrink, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the
PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. |
|
|
Maneck, Matthias, Guenster, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
Assess if the obligatory confinement (lockdown) had an effect on the number of appendectomies (during and after the
period of lockdown).The lockdown in Germany resulted in a decreased number of appendectomies. This affected mainly appendectomies in simple acute and non-acute appendicitis, but not complicated acute appendicitis. |
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Structural insights into decreased affinity of SARS-CoV-2 to ACE2 by steroids |
Mansouri, Alireza, Kowsar, et al |
Research Square prepub |
Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
In this study, we hypothesized that, as endogenous inhibitors, predominant female sex steroid hormones (P4 and E2)
may outperform T as the predominant male sex steroid hormone in reducing the affinity of coronavirus spike protein to ACE2. In addition, we attempted to understand the behavior of DEX in the presence of sex steroid hormones against coronavirus proteins interaction
with ACE2. To this aim, computational approaches were used to determine a detailed molecular-level mechanism for the interaction of coronavirus spike protein with ACE2 in the presence of sex steroid hormones. The findings of this study showed a very strong
interaction between steroid molecules and coronavirus spike protein and protease, which might lead to a change in coronavirus function. |
|
Predictors of Incident Viral Symptoms Ascertained
in the Era of Covid-19 |
Marcus, Gregory, Olgin, et al |
medRxiv |
Epidemiology| Épidémiologie |
Conducted a world-wide mobile application-based prospective cohort study to assess incident symptoms of viral infection,
defined as fevers and chills plus one other symptom previously shown to occur with SARS-CoV-2 infection. In pooled multivariable logistic regression models, female biological sex (odds ration [OR] 1.75, 95% CI 1.39-2.20, p<0.001), anemia (OR 1.45, 95% CI 1.16-1.81,
p=0.001), hypertension (OR 1.35, 95% CI 1.08-1.68, p=0.007), cigarette smoking in the last 30 days (OR 1.86, 95% CI 1.35-2.55, p<0.001), any viral symptoms among household members 6-12 days prior (OR 2.06, 95% CI 1.67-2.55, p<0.001), and the maximum number
of individuals the participant interacted with within 6 feet in the past 6-12 days (OR 1.15, 95% CI 1.06-1.25, p<0.001) were each associated with a higher risk of developing viral symptoms. Conversely, a higher subjective social status (OR 0.87, 95% CI 0.83-0.93,
p<0.001), at least weekly exercise (OR 0.57, 95% CI 0.47-0.70, p<0.001), and sanitizing one's phone (OR 0.79, 95% CI 0.63-0.99, p=0.037) were each associated with a lower risk of developing viral symptoms. |
|
Maripuu, Martin, Bendix, et al |
medRxiv |
Epidemiology| Épidémiologie Public Health Priorities| Priorités de santé publique |
Population-based study to assess whether individuals with severe mental disorder (SMD) had a higher risk of death associated
with a COVID-19 infection (COVID-19 associated death) than individuals without SMD. There were 130 (0.1%) COVID-19 associated deaths in the SMD group and 4945 (0.06%) in the control group, corresponding to an OR of 1.98 (CI 1.66-2.35; p < 0.001). The odds
were fourfold in the age group between 60 and 79 years. Cardiovascular diseases increased the odds by 50%. Individuals with SMD without any of the risk factors under study had three-folds odds of COVID-19 associated death. |
|
|
Marquez-Ipiña, Alan Roberto, Gonzalez-Gonzalez, et al |
medRxiv |
Coronavirology| Coronavirologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
Results demonstrate that ELISA-functional SARS-CoV-2 antigens can be produced in bacterial cultures, Peptide S-RBDN318-V510,
which contains the receptor binding domain of the SARS-CoV-2 spike protein is amenable to massive production and may represent a cost-effective alternative to the use of structurally more complex antigens in serological COVID-19 testing. |
|
|
Secondary traumatic stress and burnout in healthcare
workers during COVID-19 outbreak |
Marzetti, Francesca, Vagheggini, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
Assess the level of professional burnout and secondary traumatic stress, and identify potential risk or protective
factors among health care workers (HCWs) during the coronavirus disease 2019 (COVID-19) outbreak. A considerable proportion of HCWs had symptoms of secondary traumatic stress (41.3%), emotional exhaustion (56.0%), and depersonalization (48.9%). The prevalence
of secondary traumatic stress in frontline HCWs was 47.5% while in HCWs working in other units it was 30.3% (p<.023); additionally, the prevalence of the same outcome was 67.1% for the HCWs exposed to patients' death and 32.9% for those HCWs which were not
exposed to the same condition (p<.001). |
|
Massey, Ruth |
medRxiv |
Clinical data| Données cliniques |
The COVID-19 pandemic has brought with it the largest ever cohort of patients requiring mechanical ventilation. Here
we describe such a patient who developed a recurring ventilator-associated pneumonia caused by a strain of Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis recovered whole
genomes of the bacterium directly from samples, revealing the AMR genotype. While immunological analysis of longitudinally-collected blood samples revealed escalating levels of T-cell activation targeting both bacteria and virus, with evidence of bystander-activation,
a feature which may have contributed to the continuing inflammation and prolonged requirement for ventilation. |
|
|
Mathur, Rohini, Rentsch, et al |
medRxiv |
Epidemiology| Épidémiologie Public Health response| Interventions de santé publique |
Identify ethnic differences in the risk of COVID-19 infection, hospitalisation and mortality using a large general
population cohort in England. The study found evidence of substantial ethnic inequalities in the risk of testing positive for SARS-CoV-2, ICU admission, and mortality, which persisted after accounting for explanatory factors, including household size. |
|
|
Matzinger, Polly, Skinner, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique
Public Health response| Interventions de santé publique |
Plotted COVID-19 cases, hospitalizations and deaths, on a log2 Y axis and a linear date-based X axis, and analyzed
them using segmented regression. Data fit straight lines with correlation coefficients ranging from 92% - 99%, and that these lines broke at interesting intervals, revealing that school closings dropped infection rates in half, lockdowns dropped the rates
3 to 4 fold, and other actions (such as closing bars and mandating masks) brought the rates even further down. Hospitalizations and deaths paralleled cases, with lags of three to ten days. |
|
|
Efficacy of face-masks used in Uganda: a laboratory-based
inquiry during the COVID-19 pandemic |
Mboowa, Gerald, Semugenze, et al |
medRxiv |
Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI) |
Locally-made double layered cloth face-masks could serve as alternative face-masks especially for populations in low-
and middle- income settings like Uganda while allowing restricted use of surgical face-masks and other respirators like the KN95 to high-risk groups only. |
|
An expert judgment model to predict early stages
of the COVID-19 outbreak in the United States |
McAndrew, Thomas Charles, Reich, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
During early stages of the COVID-19 pandemic, forecasts provided actionable information about disease transmission
to public health decision-makers. Between February and May 2020, experts in infectious disease modeling made weekly predictions about the impact of the pandemic in the U.S. We aggregated these predictions into consensus predictions. In March and April 2020,
experts predicted that the number of COVID-19 related deaths in the U.S. by the end of 2020 would be in the range of 150,000 to 250,000, with scenarios of near 1m deaths considered plausible. The wide range of possible future outcomes underscored the uncertainty
surrounding the outbreak's trajectory. Experts' predictions of measurable short-term outcomes had varying levels of accuracy over the surveys but showed appropriate levels of uncertainty when aggregated. An expert consensus model can provide important insight
early on in an emerging global catastrophe. |
|
McAuley, HamishJC, Hadley, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
Evaluate the change in AECOPD treatment frequency during the first six weeks of lockdown in the UK compared with 2019
and assess changes in self-reported behaviour and well-being. Significantly more community treated exacerbations were observed in 2020 compared with 2019 (126 vs 99, p=0.026). The increase was as a result of multiple courses of treatment, with a similar proportion
of patients receiving at least one course (34.4% vs 33.8%). During 'lockdown' participants reported significantly increased anxiety, adherence to their preventative inhalers, and good adherence to shielding advice (all p<0.001). |
|
|
COVID-19 Mortality in Cancer Patients: A Report from
a Tertiary Cancer Centre in India |
Mehta, Anurag, Vasudevan, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This is the first study from India reporting the mortality, clinical associations, and risk factors for mortality in
SARS-CoV-2 infected cancer patients. The study shows that the frequency of COVID-19 in cancer patients is high, and the CFR is 7.6 times more than the national average. |
|
Anti-SARS-CoV-2 IgM and IgG antibodies in health
workers in Sergipe, Brazil |
Melo, Monica Santos De, Borges, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
Evaluate the seroprevalence of IgM and IgG for SARS-CoV-2 in health workers in Sergipe, Brazil. 471 health professionals
were tested. Of these, 28 workers (5.95%) tested positive for IgM and 64 (13.59%) tested positive for IgG. 9 workers (1.91%) tested positive for IgM and were also positive for IgG. |
|
Short-term Neuropsychiatric Outcomes and Quality
of Life in COVID-19 Survivors |
Mendez, Raul, Balanza-Martinez, et al |
medRxiv |
Public Health response| Interventions de santé publique Healthcare Response | Réponse
des soins de santé |
Evaluate neurocognitive function, psychiatric symptoms, and QoL in COVID-19 survivors shortly after hospital discharge.
Among survivors, the prevalence of moderately impaired immediate verbal memory and learning was 38%, delayed verbal memory (11.8%), verbal fluency (34.6%), and working memory (executive function) (6.1%), respectively. Moreover, 58.7% of patients had neurocognitive
impairment in at least one function. Rates of positive screening for anxiety were 29.6%, depression (26.8%), and post-traumatic stress disorder (25.1%) respectively. In addition, 39.1% of the patients had psychiatric morbidity. Low QoL for physical and mental
components was detected in 44.1% and 39.1% of patients, respectively. Delirium and stress-related symptoms increased approximately 4-fold the odds of developing neurocognitive impairment. Female gender and neurocognitive impairment diagnosis were related with
an increase of 2.5 and 4.56-fold odds respectively of psychiatric morbidity. Interpretation: Hospitalized COVID-19 survivors showed a high prevalence of neurocognitive impairment, psychiatric morbidity, and poor QoL in the short-term. It is uncertain if these
impacts persist over the long-term. |
|
Meng, L, Ma, et al |
J Dent Res |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This retrospective study investigated the risk of infection in health care workers, including oral health care workers
(OHCWs), due to the characteristics of dental practice. There were 22 females and 9 males, with a median age of 39 y. Although the severity of most cases of COVID-19 (93.5%) was mild or moderate, 1 case was severe, and another case was critical, resulting
in death. Fever was the main first symptom of COVID-19, followed by fatigue and myalgia. Most of the OHCWs routinely used PPE such as medical masks, gloves, caps, and work clothes while performing clinical work. N95 or KN95 masks were rarely available because
of the scarcity of PPE during the outbreak. Nineteen OHCWs reported a contact history, among whom 7 worked in a fever clinic, 5 reported contact with dental patients suspected of having COVID-19, and 7 reported contact with family members with COVID-19-related
symptoms at least 1 d earlier. Findings indicated that there were few clusters of COVID-19 in dental settings. |
|
|
Validation and clinical evaluation of a SARS-CoV-2
Surrogate Virus Neutralization Test (sVNT) |
Meyer, Benjamin, Reimerink, et al |
medRxiv |
Coronavirology| Coronavirologie Immunology | Immunologie |
A new surrogate virus neutralisation assay (sVNT) was described that uses the principle of an ELISA to measure the
neutralization capacity of anti-SARS-CoV-2 antibodies directed against the receptor binding domain. An independent evaluation of the robustness, specificity and sensitivity on an extensive panel of sera from 269 PCR-confirmed COVID-19 cases and 259 unmatched
samples collected before 2020 and compared it to cell-based neutralization assays. We found a high specificity of 99.2 (95%CI: 96.9-99.9) and overall sensitivity of 80.3 (95%CI: 74.9-84.8) for the sVNT. Clinical sensitivity increased between early (<14 days
post symptom onset or post diagnosis, dpos/dpd) and late sera (>14 dpos/dpd) from 75.0 (64.7-83.2) to 83.1 (76.5-88.1). Also, higher severity was associated with an increase in clinical sensitivity. Upon comparison with cell-based neutralisation assays we
determined an analytical sensitivity of 74.3 (56.4-86.9) and 98.2 (89.4-99.9) for titres ≥10 to <40 and ≥40 to <160, respectively. |
|
Michel, Wiebke, Farber, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding SARS-CoV-2 test performance. Of 76 persons,
39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 (17%) of these infections but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal
samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs. Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection. |
|
|
Correlation between universal BCG vaccination policy
and reduced mortality for COVID-19 |
Miller, Aaron, Reandelar, et al |
medRxiv |
Epidemiology| Épidémiologie Public Health response| Interventions de santé publique |
Propose that national differences in COVID-19 impact could be partially explained by different national policies with
respect to Bacillus Calmette-Guerin (BCG) vaccination. Countries without universal policies of BCG vaccination (Italy, the Netherlands, USA) have been more severely affected compared to countries with universal and long-standing BCG policies. The difference
cannot be accounted for by differences in disease onset, adoption of early social distancing policies, state of health services, nor income level. Reduced mortality suggests BCG vaccination could be a potential new tool in the fight against COVID-19. |
|
Mitarai, Osamu, Yanagi, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public Health
response| Interventions de santé publique |
Introduce the isolation control time parameter q and study its effect on this pandemic. Required isolation time for
a confirmed case to terminate the COVID-19 pandemic estimated by the proposed method is 3~8 days, achieved by widely performed testing. |
|
|
Mol, BenW, Karnon, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique
Economics | Économie |
Balance the costs and effects comparing a strict lockdown versus a flexible social distancing strategy for societies
affected by Coronavirus-19 Disease (COVID-19) using a cost-effectiveness analysis. Apply societal data and COVID-19 mortality rates from the public domain to compare strict lockdown strategy that has been followed by Denmark to flexible social distancing
policy as was applied by Sweden. In Sweden, the number of people who died with COVID-19 was 577 per million inhabitants, resulting in an estimated 6,350 life years lost per million inhabitants. In Denmark, where a strict lockdown strategy was installed for
months, the number of people dying with COVID-19 was on average 111 per million, resulting in an estimated 1,216 life years per million inhabitants lost. The incremental costs of strict lockdown to save one life year was US$ 137,285, and higher in most of
the sensitivity analyses |
|
|
Age groups that sustain resurging COVID-19 epidemics
in the United States |
Monod, Mélodie, Blenkinsop, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique Public Health response| Interventions de santé publique |
Considering dynamics for the United States, we analyse aggregated, age-specific mobility trends from more than 10 million
individuals and link these mechanistically to age-specific COVID-19 mortality data. Iink mobility to mortality via age-specific contact patterns and use this rich relationship to reconstruct accurate transmission dynamics. In areas with continued, community-wide
transmission, our transmission model predicts that re-opening kindergartens and elementary schools could facilitate spread and lead to additional COVID-19 attributable deaths over a 90-day period. These findings indicate that targeting interventions to adults
aged 20-49 are an important consideration in halting resurgent epidemics and preventing COVID-19-attributable deaths when kindergartens and elementary schools reopen. |
|
Moore, Ginny, Rickard, et al |
medRxiv |
Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI)
Healthcare Response | Réponse des soins de santé |
The presence of SARS-CoV-2 in the air and on environmental surfaces around hospitalized patients, with and without
respiratory symptoms, was investigated. SARS-CoV-2 RNA was detected in four of 55 air samples taken < 1 m from four different patients. In all cases, the concentration of viral RNA was low and ranged from < 10 to 460 genomic copies per m3 of air. Infectious
virus was not recovered from any of the PCR positive samples analysed. |
|
|
Modelling optimal vaccination strategy for SARS-CoV-2
in the UK |
Moore, Sam, Hill, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique Public Health response| Interventions de santé publique |
Consider the optimal targeting of vaccination within the UK, with the aim of minimising future deaths or quality adjusted
life year (QALY) losses. Analysis demonstrate for a range of assumptions on the action and efficacy of the vaccine, targeting older age groups first is optimal and can avoid a second wave if the vaccine prevents transmission as well as disease. |
|
Moussaoui, LS, Ofosu, et al |
Appl Psychol Health Well Being |
Public Health response| Interventions de santé publique |
In this paper, we report a survey on the adoption of the recommended protective behaviours before and during the epidemic.
We also assessed demographic correlates, and beliefs (towards COVID-19 and protective behaviours, towards SARS-CoV-2 transmission, social dilemma variables, and perceived external cues) of a representative sample of British residents. Results showed a marked
increase in the adoption of protective behaviour. We also identified targets for intervention in variables related to transmission of the virus and social dilemma-related beliefs. Sex differences in the adoption of protective measures, as well as differences
associated with the frequency of social contacts, were associated with differences in beliefs. |
|
|
Aerosol emission of child voices during speaking,
singing and shouting |
Muerbe, Dirk, Kriegel, et al |
medRxiv |
Transmission Infection Prevention and Control/ Prévention et contrôle des infections
(IPAC/PCI) |
Apply a laser particle counter in cleanroom conditions to show, that children emit fewer aerosols during singing than
what has been known so far for adults. The emission rates among children ranged from 16 P/s to 267 P/s for speaking, 141 P/s to 1240 P/s for singing, and 683 P/s to 4332 P/s for shouting. |
|
Fair allocation of potential COVID-19 vaccines using an optimization-based
strategy |
Munguía-López, Aurora del Carmen, Ponce-Ortega, et al |
Research Square prepub |
Public health interventions*| Interventions de santé publique |
This paper presents an optimization strategy for the allocation of COVID-19 vaccines, when they are available, through
different fairness schemes (social welfare, Nash, Rawlsian justice, and social welfare II scheme). The applicability of the proposed model is illustrated using the case study of Mexico, including the states of the country as stakeholders. We involve several
parameters to guide the allocation, such as the size, risk profiles, and fraction of vulnerable groups in the population. Furthermore, different scenarios of the availability of potential COVID-19 vaccines were evaluated. The social welfare approach is the
most commonly used scheme for the allocation of resources. |
|
Predictors of symptomatic laboratory-confirmed SARS-COV-2
reinfection |
Murillo-Zamora, Efren, Hernandez-Suarez, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
Objective: To identify factors predicting symptomatic laboratory-positive SARS-COV-2 reinfection. Method: We conducted
a nationwide retrospective cohort study and data from 99,993 confirmed cases of COVID-19 were analyzed. Results: The overall risk of reinfection (28 or more elapsed days between both episodes onset) was 0.21%, and older subjects and those with mild primary
disease were at reduced risk of reinfection. Healthcare workers and immunosuppressed or renal patients had at greater risk of SARS-COV-2 reinfection. Conclusions: If replicated in other populations, these results may be useful to prioritize efforts focusing
on the reduction of SARS-COV-2 spread and the related burden. |
|
Occupation and risk of severe COVID-19: prospective
cohort study of 120,075 UK Biobank participants |
Mutambudzi, Miriam, Niedzwiedz, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The objective of this study was to investigate severe COVID-19 risk by occupational group in England. Of 120,075
participants, 271 had severe COVID-19. Relative to non-essential workers, healthcare workers, social and education workers and other essential workers had higher risk of severe COVID-19. Compared to white non-essential workers, non-white non-essential workers
had a higher risk and non-white essential workers had the highest risk . |
|
Prospective comparison of saliva and nasopharyngeal
swab sampling for mass screening for COVID-19 |
nacher, mathieu, demar, et al |
medRxiv |
Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes |
We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. 162
had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples versus nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. |
|
Outcomes associated with SARS-CoV-2 viral clades
in COVID-19 |
Nakamichi, Kenji, Shen, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Coronavirology| Coronavirologie |
This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19
patients in a single medical system in Seattle, Washington. Full length SARS-CoV-2 sequence was obtained from 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide
variants were identified. Clustering methods demonstrated two major viral clades. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Major risk factors for hospitalization and death for either major clade of virus
include patient age and comorbid conditions. |
|
Narayanan, Sai, Ritchey, et al |
medRxiv |
Epidemiology| Épidémiologie Coronavirology| Coronavirologie |
In this study we sequenced SARS-CoV-2 from 5 clinical samples obtained in Oklahoma, USA during different time points
of pandemic presence in the state. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected such as G1167V
in S gene, A6269S and P3371S in ORF1ab, T28I in ORF7b, G96R in ORF8. The nearest neighbors to the genomes were found to be isolates reported from San Diego and Atlanta in USA and from Greece and Australia. |
|
|
Narison, Stephan, Maltezos, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
We scrutinize the evolution of Covid-19 in Madagascar by comparing results from three approaches (cubic polynomial,
semi-gaussian and gaussian-like models) which we use to provide an analytical form of the spread of the pandemic. We pursue this analysis until 12th September. We show the evolution of the per cent number of cured persons and the total number of deaths from
which we deduce some comments on the performance of medical cares. |
|
|
Naseef, HaniA, Al-Shami, et al |
Research Square prepub |
Public Health response| Interventions de santé publique |
This cross-sectional study aimed to assess knowledge, attitudes and practices toward COVID-19 among Birzeit University
students. A total of 665 students have completed the online questionnaire. The mean age was (20.55±3.069) years. Multivariate analysis revealed that males, students from health professions and scientific faculties and those with highly educated parents had
manifested a good knowledge level (GKL) about Covid -19. Regarding students’ practices, less negative practices were prompted by students from health professions faculty and the students living at the middle governorate of Palestine compared to north, south
and Jerusalem dwellers. With regards to the practices, the vast majority of the participants held a positive and very cautious practice towards the COVID-19 epidemic. |
|
|
Nassir, AngusA, Baptiste, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Our aims were to design primer-probe pairs for use in isothermal amplification of the S1, ORF3 and ORF8 regions of
the SARS-CoV2 virus, optimize the recombinase polymerase amplification (RPA) assay for the isothermal amplification of the named SARS-COV2 regions, detect amplification products on a lateral flow device, and perform a pilot field validation of RPA on RNA extracted
from nasopharyngeal swabs. The assay provides a faster and cheaper alternative to rRT-PCR with 100% sensitivity, 93% specificity, and positive and negative predictive agreements of 100% and 93% respectively. |
|
|
Natarajan, Harini, Crowley, et al |
medRxiv |
Therapeutics| Thérapeutique Immunology | Immunologie |
This study functionally and phenotypically profiled plasma from eligible convalescent donors. In addition to viral
neutralization, convalescent plasma contained antibodies capable of mediating such Fc-dependent functions as complement activation, phagocytosis and antibody-dependent cellular cytotoxicity against SARS-CoV-2. |
|
|
Newell, TyA |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
End-of-August updates for Covid-19 infection case predictions for 10 US States are compared to actual data. The US
as a whole and the 10 States investigated continue to follow periods of linear infection growth. August 31 predictions for four States (NY, WA, MI and MN) are within 10% of actual data. Predictions for four other States (GA, IL, CA, and OH) agree between 10
and 20% of actual data. Predictions for two States (FL and NC) are greater than 20% different from actual data. Systematic differences between predictions and actual data are related to the impact of the June-July summer surge, and human behavior reactions
(ie, increased face mask usage and distancing) to accelerated infection growth. Outdoor temperature effects and school re-opening effects are not apparent nor expected for August. |
|
|
Nicholson, ChristopherJ, Wooster, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The objective of this retrospective cohort study was to evaluate the risk factors associated with ventilation need
and mortality in patients hospitalized in Boston, Massachusetts. We found seven factors to be independently predictive for ventilation requirement (diabetes mellitus, dyspnea, alanine aminotransferase, troponin, C-reactive protein, neutrophil-lymphocyte ratio,
and lactate dehydrogenase), and 10 factors to be predictors of in-hospital mortality (age, sex, diabetes mellitus, chronic statin use, albumin, C-reactive protein, neutrophil-lymphocyte ratio, mean corpuscular volume, platelet count, and procalcitonin). Using
these factors, we constructed risk scores, which performed with C-statistics of at least 0.8 in our cohorts. Importantly, the chronic use of a statin was associated with protection against death due to COVID-19. |
|
|
Nicolelis, MiguelAL, Raimundo, et al |
medRxiv |
Epidemiology| Épidémiologie |
Here we show that four major factors likely accounted for the entire dynamics of COVID-19 in Brazil: Super-spreading
in Sao Paulo, major Brazilian federal highways, geographic distribution of the country's hospital intensive care unit beds, and the geographic distribution of dengue fever. This final factor was confirmed by the identification of significant negative correlations
between COVID-19's incidence, infection growth rate, and mortality to the percentage of people with antibody (IgM) levels for dengue fever in each of the country's states. This finding raises the possibility of an immunological cross-reactivity between DENV
serotypes and SARS-CoV-2, which may have important implications for immunization. |
|
|
Superspreaders provide essential clues for mitigation
of COVID-19 |
Nielsen, Bjarke Frost, Sneppen, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission
Public health interventions*| Interventions de santé publique |
Using a mathematical model, we show that superspreading represents an Achilles' heel of COVID-19, and drastically improves
the efficacy of mitigations which reduce the personal contact number, even when this is done without changing the average social contact time. |
|
The importance of saturating density dependence for
predicting SARS-CoV-2 resurgence |
Nightingale, Emily, Brady, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission |
SARS-CoV-2 associated mortality data from England show evidence for an increasing trend with population density until
a saturating level. Projections from a mathematical model that accounts for this observation deviate markedly from the current status quo for SARS-CoV-2 models which either assume linearity between density and transmission (30% of models) or no relationship
at all (70%). Respectively, these standard model structures over- and under-estimate the delay in infection resurgence following the release of lockdown. Identifying saturation points for given populations and including transmission terms that account for
this feature will improve model accuracy and utility for the current and future pandemics. |
|
Estimation of the fraction of COVID-19 infected people
in U.S. states and countries worldwide |
Noh, Jungsik, Danuser, et al |
medRxiv |
Epidemiology| Épidémiologie |
A machine learning framework was developed to estimate time courses of actual new COVID-19 cases and current infections
in 50 countries and 50 U.S. states from reported test results and deaths, as well as published epidemiological parameters. Severe under-reporting of cases was found to be universal. Our framework projects for countries like Belgium, Brazil, and the U.S. ~10%
of the population has been once infected. In the U.S. states like Louisiana, Georgia, and Florida, more than 4% of the population is estimated to be currently infected, as of September 3, 2020, while in New York the fraction is 0.12%. |
|
Disparities in COVID-19 Related Mortality in U.S.
Prisons and the General Population |
Nowotny, KathrynM, Cloud, et al |
medRxiv |
Epidemiology| Épidémiologie |
We provide an analysis of COVID-19 mortality data to assess the potential magnitude of COVID-19 among prison residents.
Data were pooled from Covid Prison Project and multiple publicly available national and state level sources. People in prison experienced a significantly higher mortality burden compared to the general population. |
|
Núñez, IsaacJ, Belaunzarán-Zamudio, et al |
medRxiv |
Epidemiology| Épidémiologie |
In this study, we aimed to provide corrected estimates of the number of cases among people that were tested for SARS-Cov-2
in Mexico by taking into account the probability of RT-PCR false negative tests results. Using open data, we estimated that among 1 343 730 people tested in Mexico since February 27th, there were 838 377 cases, compared with 604 376 considering only positive
tests. ICU admissions and deaths were around 16% and 9% higher than reported. Thus, we show that accounting for the sensitivity of SARS-Cov-2 RT-PCR diagnostic tests is a simple way to improve estimations for the true number of COVID-19 cases in tested people,
particularly in high-prevalence populations. |
|
|
Potentials of constrained sliding mode control as
an intervention guide to manage COVID19 spread |
Nuñez, Sebastian, Inthamoussou, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
This work evaluates the potential of using sliding mode reference conditioning (SMRC) techniques as a guide for non-pharmaceutical
interventions and population confinement to control the COVID-19 pandemic. This technique can be used to compute day by day the contact rate reduction requirement in order to limit the intense care units occupancy to a given threshold. Simulations are performed
using the well-known SEIR model fitted to the Argentinian case to demonstrate what this control strategy suggests, while the effect of realistic period transitions between different confinement levels are also considered. |
|
Nuzum, Eleanor, Martin, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact
on mental healthcare for both services themselves and the people accessing those services. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes
daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. |
|
|
Ogbe, Ane, Kronsteiner, et al |
medRxiv |
Immunology | Immunologie |
We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative
subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens were found in those who had been infected by SARS-CoV-2 but
were rare in pre-pandemic and unexposed seronegative subjects. Over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. |
|
|
Osborne, MS, Bentley, et al |
J Laryngol Otol |
Healthcare Response | Réponse des soins de santé |
This prospective case series studied the impact of coronavirus disease 2019 on urgent referrals to secondary care otolaryngology.
There was a total of 133 referrals. Referral rates fell by 93 per cent over seven weeks, from a mean of 5.4 to 0.4 per day. Reductions were seen in referrals from both primary care (89 per cent) and the accident and emergency department (93 per cent). Presentations
of otitis externa and epistaxis fell by 83 per cent, and presentations of glandular fever, tonsillitis and peritonsillar abscess fell by 67 per cent. |
|
|
CLINICAL AND DEMOGRAPHIC CHARACTERISTICS OF COVID-19
PATIENTS IN LAGOS, NIGERIA: A DESCRIPTIVE STUDY |
Otuonye, Ngozi Mirabel, Olumade, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This case series study was designed to provide a description of the clinical and demographic characteristics of COVID-19
patients in Nigeria. A total of 154 COVID-19 patients were included in this study, with a mean age of 46.16. Most of the patients survived (mortality rate of 2.6%), and were symptomatic (89.6%). There were more males (74.7%) than females, and the most common
symptoms were fever, breathing difficulty, dry cough and malaise. Co-morbidities were also present in almost half of the study participants (49.4%). |
|
Ouadfeul, Sid-Ali |
medRxiv |
Epidemiology| Épidémiologie |
Here, the multifractal behavior of the SARS-CoV-2 COVID-19 pandemic daily and death cases is investigated through the
so-called Wavelet Transform Modulus Maxima lines (WTMM) method, data available via the World Health Organization (WHO) dashboard of Algeria, Russia, USA and Italy are analyzed. The obtained results show the multifractal behavior of the COVID-19 pandemic data
with different spectra of singularities. |
|
|
COVID-19 and human milk: SARS-CoV-2, antibodies,
and neutralizing capacity |
Pace, RyanM, Williams, et al |
medRxiv |
Transmission Immunology | Immunologie |
This study was designed to evaluate if SARS-CoV-2 RNA can be detected in milk and on the breast of infected women,
concentrations of milk-borne anti-SARS-CoV-2 antibodies, and the capacity of milk to neutralize SARS-CoV-2 infectivity. Our data do not support maternal-to-child transmission of SARS-CoV-2 via milk; however, risk of transmission via breast skin should be further
evaluated. Milk produced by infected mothers was a source of anti-SARS-CoV-2 IgA and IgG and neutralizes SARS-CoV-2 activity. These results support recommendations to continue breastfeeding during mild-to-moderate maternal COVID-19 illness. |
|
The quantitative landscape of the neutralizing antibody
response to SARS-CoV-2 |
Padmanabhan, Pranesh, Desikan, et al |
medRxiv |
Therapeutics| Thérapeutique Immunology | Immunologie |
Here, we analysed reported in vitro dose-response curves (DRCs) of >70 neutralizing antibodies (NAbs) and estimated
corresponding 50% inhibitory concentrations, slope parameters, and instantaneous inhibitory potentials (IIPs), presenting a comprehensive quantitative landscape of NAb responses to SARS-CoV-2. NAbs with high IIPs are likely to be potent. The landscapeoffers
a facile tool for benchmarking NAbs and would aid the development of NAb-based therapies for SARS-CoV-2 infection. |
|
Pairo-Castineira, Erola, Clohisey, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits,
we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19. Here we report the results of a genome-wide association study (GWAS) in 2244 critically-ill Covid-19 patients from 208 UK intensive care units.
Our results identify robust genetic signals relating to key host antiviral defence mechanisms, and mediators of inflammatory organ damage in Covid-19. |
|
|
Panovska-Griffiths, Jasmina, Kerr, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
Here we assess the potential importance of mandatory masks in the parts of community and in secondary schools in the
UK. We show that, assuming current test-trace-isolate levels, adoption of masks in secondary schools in addition to community settings can reduce the size of a second wave, but will not prevent it; more testing of symptomatic people, tracing and isolating
of their contacts is also needed. |
|
|
COVID-19 in Portugal: predictability of hospitalization,
ICU and respiratory-assistance needs |
Patricio, Andre, Costa, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Clinical
data| Données cliniques |
This work ascertains the predictability of medical needs (as hospitalization, respiratory support, and admission to
intensive care units) and the survivability of individuals testing SARS-CoV-2 positive considering a cohort with all infected individuals in Portugal as per June 30, 2020. A thorough optimization of state-of-the-art predictors is undertaken to assess the ability
to anticipate medical needs and infection outcomes using demographic and comorbidity variables, as well as onset date of symptoms, test and hospitalization. |
|
Pepkowitz, SamuelH, Hobel, et al |
Research Square prepub |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We hypothesized that vitamin D deficiency existing prior to SARS-CoV-2 infection could contribute to patients developing
severe pulmonary compromise as a result of dysfunctional hyperinflammation. Serum vitamin D concentrations of patients experiencing such severe COVID-19 manifestations that they required ICU care at any point of their hospitalization were compared to serum
vitamin D concentrations of patients achieving discharge without the need for any ICU care. Having serum vitamin D < 20 ng/mL was significantly associated with increased COVID-19 severity, p=0.001. It is conjectured that population groups know to have low
serum vitamin D should be prospectively screened for deficiency and if found emergently treated. |
|
|
Peto, Leon, Rodger, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
LamPORE is a novel diagnostic platform for the detection of SARS-CoV-2 RNA. We evaluated the performance of LamPORE
against RT-PCR using RNA extracted from spiked respiratory samples and from stored nose and throat swabs collected at two UK hospitals. LamPORE has a similar performance to RT-PCR for the diagnosis of SARS-CoV-2 infection in symptomatic patients, and offers
a promising approach to high-throughput testing. |
|
|
Petrocchi, Serena, Iannello, et al |
Research Square prepub |
Public Health response| Interventions de santé publique |
The study was conducted in Italy during the mandatory lockdown for the COVID-19 pandemic on 240 individuals (age range
18-76). COVID-19 exposure was positively associated with worry about COVID-19 and health-related information seeking; risk aversion was positively associated with health-related information seeking and perceived utility of the lockdown to contain the spread
of the virus. Worry and health-related information seeking were positively associated with distress, while the perceived utility of the lockdown was negatively associated with distress. Intolerance for ambiguity was directly linked to distress with a positive
sign. |
|
|
Accessioning and automation compatible anterior nares
swab design |
Pettit, Mary, Boswell, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We have designed an injection molded polypropylene anterior nares swab, the RHINOstick, with a screw cap integrated
into the swab handle that is compatible with fully automated sample accessioning and processing. SARS-CoV-2 is stable on dry RHINOstick swabs for at least 3 days, even at 42°C, and elution can be achieved with small volumes. The swab and barcoded tube set
can be produced, sterilized, and packaged at < 2 USD per unit and can easily be adopted by large research institutes to increase throughput and dramatically reduce the cost of a standard SARS-CoV-2 detection pipeline. |
|
Analyzing How Changes in the Health Status of Healthcare
Workers Affects Epidemic Outcomes |
Phadke, Ishan, McKee, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Healthcare
Response | Réponse des soins de santé |
As more healthcare workers get infected, fewer are available to provide care for others, and the overall quality of
care available to infected individuals declines. To examine this issue, we explicitly model declining quality of care in four differential equation-based SIR-type models with vaccination. We show that explicitly modelling healthcare workers and accounting
for declining quality of care significantly alters model-predicted disease outcomes, specifically case counts and mortality. Models neglecting the decline of quality of care resulting from infection of HCWs may significantly under-estimate cases and mortality. |
|
The impact of digital contact tracing on the SARS-CoV-2
pandemic - a comprehensive modelling study |
Pollmann, TinaR, Pollmann, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
Digital contact tracing (DCT) uses tools such as cell-phone applications to improve tracing speed and reach. We model
the impact of DCT on the spread of the virus for a large epidemiological parameter space. We also model DCT in combination with random testing (RT) and social distancing (SD). At least 60% of the population would have to use the DCT system for its effect to
become significant. On its own, DCT cannot bring the reproductive number below 1 unless nearly the entire population uses the DCT system and follows quarantining and testing protocols strictly. |
|
Pompeo, Carolina, Ferreira Junior, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The objective was to analyze the evolution of confirmed cases of COVID-19 in the first four months of the pandemic
in Mato Grosso do Sul, a state in the Center-West region of Brazil, as well as the factors related to the prevalence of deaths. There was a predominance of women among the cases, and of men in terms of deaths. The presence of comorbidities was statistically
related to mortality, particularly lung disease and diabetes, and the mean age of the deaths was 67.7 years. |
|
|
De Novo Discovery of High Affinity Peptide Binders
for the SARS-CoV-2 Spike Protein |
Pomplun, Sebastian, Jbara, et al |
bioRxiv |
Coronavirology| Coronavirologie |
This study used affinity selection-mass spectrometry for the rapid discovery of synthetic high affinity peptide binders
for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. From library screening with 800 million synthetic peptides, we identified three sequences with nanomolar affinities (dissociation constants of 80 to 970 nM) for RBD and selectivity over
human serum proteins. Picomolar RBD concentrations in biological matrix could be detected using the biotinylated lead peptide in ELISA format. These peptides might associate with the SARS-CoV-2-spike-RBD at a site unrelated to ACE2 binding, making them potential
orthogonal reagents for sandwich immunoassays. |
|
Prats-Uribe, Albert, Sena, et al |
medRxiv |
Clinical data| Données cliniques |
We characterized the utilization of medicines as prescribed in routine practice amongst patients hospitalized for COVID-19
in South Korea, China, Spain, and the USA. Multiple medicines were used in the first months of COVID-19 pandemic, with substantial geographic and temporal variation. Hydroxychloroquine, azithromycin, lopinavir-ritonavir, and umifenovir (in China only) were
the most prescribed repurposed medicines. Antithrombotics, antibiotics, H2 receptor antagonists and corticosteroids were often used as adjunctive treatments. |
|
|
INFERRED RESOLUTION THROUGH HERD IMMMUNITY OF FIRST
COVID-19 WAVE IN MANAUS, BRAZILIAN AMAZON |
Prowse, Thomas, Purcell, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission
Immunology | Immunologie |
To avoid early information bias, we used detailed age and gender stratified death certificate and hospitalisation data
to evaluate the epidemic's trajectory and infer the cause of its decline using a stochastic model. Our results are consistent with heterogenous transmission reducing over time due to the development of herd immunity. Relative to a baseline model that assumed
homogenous mixing across Manaus, a model that permitted a small, self-isolated population fraction raised the estimated herd-immunity threshold from 28% to 30% and reduced the final attack rate from 86% to 65%. |
|
A comparison of five epidemiological models for
transmission of SARS-CoV-2 in India |
Purkayastha, Soumik, Bhattacharyya, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission |
We compare five epidemiological transmission models for forecasting and assessing the course of the pandemic. The five
models were: a baseline model, an extended SIR (eSIR) model, two extended SEIR (SAPHIRE and SEIR-fansy) models, and a semi-mechanistic Bayesian hierarchical model (ICM). While the estimation of the reproduction number is relatively robust across the models,
the prediction of daily active number of cases does show variation across models. The largest variability across models is observed in predicting the “total” number of infections including reported and unreported cases. |
|
Rabbani, Md Golam, Akter, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The aim of this study was to assess the KAP of Bangladeshi people towards Covid-19 and determinants of those KAPs.
We conducted a cross-sectional survey of 492 Bangladeshi people aged above 18 years from May 7 to 29, 2020 throughout the country. Almost three fourths of the respondents went outside home during the lockdown period. The study found that good knowledge and
attitude were associated with better practice of COVID-19 health measures. |
|
|
Radfar, Seyed Ramin, De Jong, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
One week after the announcement of the COVID-19 as a pandemic, in a global survey, 177 addiction medicine professionals
described COVID-19-related health responses in their own 77 countries in terms of SUD treatment and harm reduction services. Respondents from over 88% of countries reported that core medical and psychiatric care for SUDs had continued; however, only 56% of
countries reported having had any business continuity plan, and 37.5% of countries reported shortages of methadone or buprenorphine supplies. Participants reported that SUD treatment and harm reduction services had been significantly impacted globally early
during the COVID-19 pandemic. |
|
|
COVID-19 epidemic severity is associated with timing
of non-pharmaceutical interventions |
Ragonnet-Cronin, Manon, Boyd, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique
Coronavirology| Coronavirologie |
SARS-CoV-2 genetic sequences can be analyzed to provide an estimate of both the time of epidemic origin and the rate
of early epidemic growth in different settings. Carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates
were cross-referenced with dates of the most stringent interventions in each location as well as the number of cumulative COVID-19 deaths following maximum intervention. The time elapsed between epidemic origin and maximum intervention is strongly associated
with different measures of epidemic severity and explains 46% of variance in numbers infected at time of maximum intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity
and mortality during the period of study. |
|
Raham, TareefF |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
To examine influence of BCG status and TB prevalence on variances among countries which report new multisystem inflammatory
syndrome in children (MIS-C). Included all countries which report MIS-C till 23/6/2020, number of cases for each 10 million inhabitants was examined among 3 categories of countries classified according to BCG program status. TB prevalence, MIS-C no. / 10 million
(M) population and Covid- 19 deaths/M are taken as markers. BCG vaccinations and high TB prevalence are found to be associated with decrease MIS-C no. and COVID-19 deaths. Findings might explain variances in MIS-C incidence and in COVID-19 mortality among
countries worldwide. |
|
|
Rajasingham, Radha, Bangdiwala, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique RCT |
Investigated whether hydroxychloroquine could prevent SARS CoV-2 in healthcare workers at high-risk of exposure. Conducted
a randomized, double-blind, placebo-controlled clinical trial of healthcare workers with ongoing exposure to persons with Covid-19, including those working in emergency departments, intensive care units, Covid-19 hospital wards, and first responders. Enrolled
1483 healthcare workers, of which 79% reported performing aerosol-generating procedures. For once weekly hydroxychloroquine prophylaxis, the hazard ratio was 0.72 (95%CI 0.44 to 1.16; P=0.18) and for twice weekly was 0.74 (95%CI 0.46 to 1.19; P=0.22) as compared
with placebo. Pre-exposure prophylaxis with hydroxychloroquine once or twice weekly did not significantly reduce laboratory-confirmed Covid-19 or Covid-19-compatible illness among healthcare workers. |
|
|
Broad SARS-CoV-2 cell tropism and immunopathology
in lung tissues from fatal COVID-19 |
Ramos da Silva, Suzane, Ju, et al |
medRxiv |
Coronavirology| Coronavirologie Immunology | Immunologie |
This study analyzed the expression of SARS-CoV-2 S1 and NC proteins in postmortem lung tissues from five severe COVID-19
patients with various degrees of lung damage. Performed multicolor staining for viral proteins, and lineage cell markers to identify SARS-CoV-2 tropism and to define the lung pathobiology in postmortem tissues from five patients with fatal SARS-CoV-2 infections.
The lung parenchyma showed severe DAD with thromboemboli in all cases. SARS-CoV-2 infection was found in an extensive range of cells including alveolar epithelial type II/pneumocyte type II (AT2) cells (HT2-280), ciliated cells (tyr-α-tubulin), goblet cells
(MUC5AC), club-like cells (MUC5B) and endothelial cells (CD31 and CD34). Greater than 90% of infiltrating immune cells were positive for viral proteins including macrophages and monocytes (CD68 and CD163), neutrophils (ELA-2), natural killer (NK) cells (CD56),
B-cells (CD19 and CD20), and T-cells (CD3ε). In lung tissues from severely affected COVID-19 patients, there is evidence for broad SARS-CoV-2 cell tropisms, activation of immune cells, and clearance of immunosuppressive cells, which could contribute to severe
tissue damage, thromboemboli, excess inflammation and compromised adaptive immune responses. |
|
FeverIQ - A Privacy-Preserving COVID-19 Symptom Tracker
with 3.6 Million Reports |
Ranjan, Ankit, Li, et al |
medRxiv |
Clinical data| Données cliniques Public health interventions*| Interventions de santé
publique Healthcare Response | Réponse des soins de santé |
Population-scale COVID-19 management benefits from timely and honest information from billions of people. Here, we
provide a first report on the FeverIQ symptom tracker, a global effort to collect symptom and test data which has received more than 3.6 million submissions. Unlike other trackers, FeverIQ uses secure multiparty computation (SMC) to cryptographically guarantee
user privacy while providing insights to scientists and public health efforts. We performed basic integrity checks of the FeverIQ dataset, such as by comparing it to other publicly released data. We then trained a linear classifier on diagnosis scores which
were computed securely, without unprotected symptom data ever leaving a user's phone or computer. FeverIQ is currently the world's largest application of SMC in a health context, demonstrating the practicality of privacy-preserving analytics for population-scale
digital health interventions. |
|
Rao, Sudha, Gavali, et al |
Research Square prepub |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study describes the clinical characteristics and outcome of children admitted, with SARS-CoV-2 infection, to a
paediatric hospital in Mumbai. 123 (71M) tested SARS-CoV-2-positive by RT-PCR with median age of presentation of 3 years IQR 0.7– 6 years]. 47 (38%) had co-morbidities and were more severely affected (p = 0.0146). MIS-C/ KD was common in Group I. Thirty nine
(31.7 %) needed intensive care. Fourteen (11.4%) died. Male sex, respiratory manifestation, pulseox saturation <94% at admission, need for ventilation, inotrope, hospital stay of <10 days were independent mortality predictors. Regression analysis revealed
oxygen saturation <94% at admission (OR 35.9, 95% CI 1.5-856) and hospital stay <10 days (OR 9.1, 95% CI 1.04 -99.1) as predictors of mortality. |
|
|
A low-cost, rapidly scalable, emergency use ventilator
for the COVID-19 crisis |
Raymond, SamuelJ, Wesolowski, et al |
medRxiv |
Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI)
Healthcare Response | Réponse des soins de santé |
The present work introduces a low-cost, ventilator designed and built in accordance with the Emergence Use guidance
provided by the US Food and Drug Administration (FDA) wherein an external gas supply feeds into the ventilator and time limited flow interruption guarantees tidal volume. The goal of this device is to allow a patient to be treated by a single ventilator platform,
capable of supporting the various treatment paradigms during a potential COVID-19 related hospitalization. This proof-of-concept provides support for this cost-effective, readily mass-produced ventilator that can be used to support patients when the demand
for ventilators outstrips supply in hospital settings worldwide. |
|
A Sew-Free Origami Mask for Improvised Respiratory
Protection |
Realmuto, Jonathan, Kleinman, et al |
medRxiv |
Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI)
Healthcare Response | Réponse des soins de santé |
We describe a fabrication technique that makes use of a folding procedure (origami) to transform a filtration material
into a mask. These origami masks can be fabricated by non-experts at minimal cost and effort, provide adequate filtration efficiencies, and are easily scaled to different facial sizes. Using a mannequin fit test simulator, we demonstrate that these masks can
provide optimal filtration efficiency and ease of breathing with minimal leak- age. Because this mask provides greater comfort compared to commercial alternatives, it is likely to promote greater mask wearing tolerance and acceptance. |
|
Sex differences in innate anti-viral immune responses
to respiratory viruses |
Regis, Eteri, Fontanella, et al |
medRxiv |
Immunology | Immunologie |
We hypothesised that innate immune responses may be deficient in males relative to females. To test this we stimulated
peripheral blood mononuclear cells (PBMCs) from participants in a population-based birth cohort with three respiratory viruses (rhinoviruses-RV-A16 and RV-A1, and respiratory syncytial virus-RSV) and two viral mimics (R848 and CpG-A, to mimic responses to
SARS-CoV-2). Responses in males were greater than those in females in only one of 35 cytokine-stimulus pairs investigated. Impaired innate anti-viral immunity in males likely results in high morbidity and mortality from respiratory viruses including COVID-19. |
|
Remaeus, K, Savchenko, et al |
Acta Obstet Gynecol Scand |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study described the clinical characteristics in 67 SARS-CoV-2 positive women and their 68 neonates, and reported
short-term maternal and neonate outcomes. The mean age was 32 years, 40% were nulliparous, and 61% were overweight or obese. Further, 15% had diabetes and 21% a hypertensive disease. 70% of the women had a vaginal birth. Preterm delivery occurred in 19% of
the women. The preterm deliveries were mostly medically indicated, including two women who were delivered preterm due to severe coronavirus disease 19 (COVID-19) illness, corresponding to 15% of the preterm births. Four women (6%) were admitted to intensive
care unit postpartum. Three neonates were PCR-positive for SARS-CoV-2 after birth. |
|
|
Inflammatory leptomeningeal cytokines mediate delayed
COVID-19 encephalopathy |
Remsik, Jan, Wilcox, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
This study shows that a particularly vulnerable population with neurologic manifestations of COVID-19 harbor an influx
of inflammatory cytokines within the cerebrospinal fluid in the absence of viral neuro-invasion. The majority of these inflammatory mediators are driven by type 2 interferon and are known to induce neuronal injury in other disease models. Levels of matrix
metalloproteinase-10 within the spinal fluid correlate with the degree of neurologic dysfunction. Furthermore, this neuroinflammatory process persists weeks following convalescence from the acute respiratory infection. These prolonged neurologic sequelae following
a systemic cytokine release syndrome lead to long-term neurocognitive dysfunction with a wide range of phenotypes. |
|
Performance characteristics of the VIDAS® SARS-COV-2
IgM and IgG serological assays |
Renard, Nathalie, Daniel, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We describe here the analytical and clinical performance of VIDAS® SARS-CoV-2 IgM and VIDAS® SARS-CoV-2 IgG, two CE-marked,
EUA-authorized, automated, qualitative assays for the detection of SARS-CoV-2-specific IgM and IgG, respectively. Both assays showed high within-run and within-laboratory precision (coefficients of variation < 11.0%) and very low cross-reactivity towards sera
of patients with a past common coronavirus or respiratory virus infection. Altogether, the VIDAS® SARS-CoV-2 IgM and IgG assays are highly specific and sensitive serological tests suitable for the reliable monitoring of past SARS-CoV-2 infections and for
seroepidemiology investigations. |
|
T cell anergy in COVID-19 reflects virus persistence
and poor outcomes |
Renner, Kerstin, Mueller, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
We applied novel approaches to analyze T cell reactivity and showed that T anergy is already present in non-ventilated
COVID-19 patients, very pronounced in ventilated patients, strongly associated with virus persistence and reversible with clinical recovery. T cell activation was measured by downstream effects on responder cells like basophils, plasmacytoid dendritic cells,
monocytes and neutrophils in whole blood and proved to be much more meaningful than classical readouts with PBMCs. Monocytes responded stronger in males than females and IL-2 partially reversed T cell anergy. Downstream markers of T cell anergy were also found
in fresh blood samples of critically ill patients with severe T cell anergy. Based on our data we were able to develop a score to predict fatal outcomes and to identify patients that may benefit from strategies to overcome T cell anergy. |
|
Reyes, Leila, Sanchez-Garcia, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
With emerging evidence of a dysregulated innate immune response in COVID-19, we undertook a functional proteomic survey
of circulating neutrophil populations, comparing patients with COVID-19 ARDS, non-COVID-19 ARDS, moderate COVID-19, and healthy controls. We observe that expansion of the circulating neutrophil compartment and the presence of activated low and normal density
mature and immature neutrophil populations occurs in both COVID-19 and non-COVID-19 ARDS. Importantly, activation of components of the neutrophil type I IFN responses is specific to infection with SARS-CoV-2 and linked to metabolic rewiring. Together this
work highlights how differential activation of circulating neutrophil populations may contribute to the pathogenesis of ARDS, identifying processes that are specific to COVID-19 ARDS. |
|
|
Rezel-Potts, Emma, Douiri, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
To evaluate antihypertensive medications and COVID-19 diagnosis and mortality, accounting for healthcare seeking behaviour.
A population-based case control study with additional cohort analysis. Primary care patients from the UK Clinical Practice Research Datalink (CPRD). 16 866 patients with COVID-19 events in the CPRD from 29th January to June 25th 2020 and 70 137 matched controls.
We explored associations between COVID-19 diagnosis and prescriptions for angiotensin converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs), beta-blockers (B), calcium-channel blockers (C), thiazide diuretics (D) and other antihypertensive
drugs (O). Results: In covariate adjusted analyses, ACEIs were associated with lower odds of COVID-19 diagnosis (0.82, 95% confidence interval 0.77 to 0.88) as were ARBs, 0.87 (0.80 to 0.95) with little attenuation from adjustment for consultation frequency.
Associations were sensitive to adjustment for confounding and healthcare seeking, but there was no evidence that antihypertensive therapy is associated with increased risk of COVID-19 diagnosis or mortality; most classes of antihypertensive therapy showed
negative associations with COVID-19 diagnosis. |
|
|
COVeAGE-DB: A database of age-structured COVID-19
cases and deaths |
Riffe, Tim, Acosta, et al |
medRxiv |
Epidemiology| Épidémiologie Surveillance |
COVerAGE-DB is an open access database including cumulative counts of confirmed COVID-19 cases, deaths, and tests by
age and sex. Cumulative counts of COVID-19 cases, deaths, and tests are recorded daily (when possible) since January 2020. An international team, composed of more than 60 researchers, contributed to the collection of data and metadata in COVerAGE-DB from
governmental institutions, as well as to the design and implementation of the data processing and validation pipeline. |
|
Riley, Bridget, Packer, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
This study aims to determin if the lockdown period was associated with differences in the case-mix of non-COVID acute
medical admissions compared with the previous year. Retrospective data were collected for 1st to 30th April 2019 and 1st to 30th April 2020 from University Hospitals Birmingham NHS Foundation Trust. The total number of acute medical admissions fell comparing
April 2019 (n=2409) to April 2020 (n=1682). As a proportion of total admissions, those aged under 45 years decreased, while those aged 46 and over did not change. In this large, single-centre study, there was a change in hospitalised case-mix when comparing
April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain
and non-cardiac chest pain) especially among younger adults. |
|
|
Rios, Christopher, Ling, et al |
medRxiv |
Public Health response| Interventions de santé publique |
This study aims to comprehensively examined the underlying health system weaknesses contributing to the deleterious
health outcomes. A qualitative case study was conducted to assess the ability of the UPR health system to provide patient care in response to Hurricane Maria. An established five key resilience framework and inductive analysis was used to identify factors
that affected health system resilience. Hurricane Maria exposed weaknesses in the Puerto Rican health system, notably the lack of awareness about the limited capacity of backup generators, poor patient care coordination, and interruption of medical care for
patients with chronic conditions. As in other countries, the current COVID epidemic is taxing the capacity of the Puerto Rico health system, which could increase the likelihood of another health system collapse should another hurricane hit the island. Therefore,
a resilience framework is a useful tool to help health systems identify areas of improvement in preparation for possible natural disasters. |
|
|
Risanger, Simon, Singh, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public Health response| Interventions
de santé publique |
Using a facility location optimization model and willingness-to-travel estimates from US National Household Travel
Survey data, we find that if COVID-19 testing became available in all US pharmacies, an estimated 94% of the US population would be willing to travel to obtain a test, if warranted. If only 1,000 pharmacies in the US are selected to provide testing, judicious
selection, using our optimization model, provides estimated access to 29 million more people than selecting pharmacies simply based on population density. COVID-19 testing through pharmacies can improve access across the US. Even if only few pharmacies offer
testing, judicious selection of specific sites can simplify logistics and improve access. |
|
|
Excess Mortality in the United States During the
First Three Months of the COVID-19 Pandemic |
Rivera, Roberto, Rosenbaum, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
This study estimates excess all-cause, pneumonia, and influenza mortality during the COVID-19 pandemic using the September
11, 2020 release of weekly mortality data from the United States (U.S.) Mortality Surveillance System (MSS) from September 27, 2015 to May 9, 2020. Significant excess pneumonia deaths were also found for all locations and we estimated hundreds of excess influenza
deaths in New York. We find that official COVID-19 mortality substantially understates actual mortality, excess deaths cannot be explained entirely by official COVID-19 death counts. Mortality reporting lags appeared to worsen during the pandemic, when timeliness
in surveillance systems was most crucial for improving pandemic response. |
|
Rizan, Chantelle, Reed, et al |
medRxiv |
Public Health response| Interventions de santé publique |
Use of Personal Protective Equipment (PPE) has been central to controlling spread of SARS-CoV2. This study aims to
quantify the environmental impact of this, and to model strategies for its reduction. Life cycle assessment was used to determine environmental impacts of PPE supplied to health and social care in England during the first six months of the COVID-19 pandemic.
The base scenario assumed all products were single-use, air freighted, and disposed via clinical waste. The carbon footprint of PPE supplied during the study period totalled 158,838 tonnes CO2e, with greatest contributions from gloves, aprons, face shields,
and Type IIR surgical masks. The environmental impact of PPE could be reduced through shipping supplies or domestic manufacture, rationalising glove use, using reusables where possible, and optimising waste management |
|
|
Rodriguez, Alexander, Tabassum, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In this paper, we present DeepCOVID, an operational deep learning framework designed for real-time COVID-19 forecasting.
DeepCOVID works well with sparse data and can handle noisy heterogeneous data signals by propagating the uncertainty from the data in a principled manner resulting in meaningful uncertainties in the forecast. The framework also consists of modules for both
real-time and retrospective exploratory analysis to enable interpretation of the forecasts. Results from real-time predictions (featured on the CDC website and FiveThirtyEight.com) since April 2020 indicates that our approach is competitive among the methods
in the COVID-19 Forecast Hub, especially for short-term predictions. |
|
|
Roimi, Michael, Gutman, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Healthcare Response | Réponse des soins
de santé |
Retrospective nationwide cohort study following the day-by-day clinical status of all hospitalized COVID-19 patients
in Israel from March 1st to May 2nd, 2020. The model predicts the patient's entire disease course in terms of clinical states, from which we derive the patient's hospital length-of-stay, length-of-stay in critical state, the risk of in-hospital mortality,
and total and critical care hospital-bed utilization. During the study period, 2,703 confirmed COVID-19 patients were hospitalized in Israel. The per-day MAEs for total and critical-care hospital- bed utilization, were 4.72 ± 1.07 and 1.68 ± 0.40 respectively;
the AUROCs for prediction of the probabilities of critical illness and in-hospital mortality were 0.88 ± 0.04 and 0.96 ± 0.04, respectively. The model enables evaluating the impact of various patient influx scenarios on hospital utilization and planning ahead
of hospital resource allocation. |
|
|
Romero-Cristobal, Mario |
Research Square prepub |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We aimed to explore the association of pre-admission liver fibrosis indexes with the prognosis of critically ill COVID-19
patients. Methods Observational study in 214 patients with COVID-19 consecutively admitted to the ICU. Pre-admission liver fibrosis indexes were calculated. In-hospital mortality and predictive factors were explored with Kaplan-Meier and Cox regression analysis.
Results Sixteen patients (7.48%) had previously recognized chronic liver disease. Fibrosis indexes were higher in non-survivors but no differences were found in liver biochemistry parameters. Patients with any degree of fibrosis either by Forns or FIB-4 had
a higher mortality, which increased according to the severity of fibrosis |
|
|
The Immune-Buffer COVID-19 Exit Strategy that Protects
the Elderly |
Rom-Kedar, Vered, Yaniv, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
With the increasing spread of the virus, there is growing fraction of the general population that may be immune to
COVID-19, following infection. This immunised cohort can be uncovered via large-scale screening for the SARS-CoV-2 (Corona) virus and/or its antibodies. We propose that this immune cohort be deployed as a buffer between the general population and the population
most at risk from the disease. Here we show that under a broad range of realistic scenarios deploying such an immunized buffer between the general population and the population at risk may lead to a dramatic reduction in the number of deaths from the disease.
This provides an impetus for: screening for the SARS-CoV-2 virus and/or its antibodies on the largest scale possible, and organizing at the family, community, national and international levels to protect vulnerable populations by deploying immunized buffers
between them and the general population wherever possible. |
|
High-Quality Masks Can Reduce Infections and Deaths
in the US |
Rosenstrom, Erik, Oruc Aglar, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
Objectives: To evaluate the effectiveness of widespread adoption of masks or face coverings to reduce community transmission
of the SARS-CoV-2 virus that causes Covid-19. Methods: We employed an agent-based stochastic network simulation model, where Covid-19 progresses across census tracts according to a variant of SEIR. We considered a mask order that was initiated 3.5 months after
the first confirmed Covid-19 case. We evaluated scenarios where wearing a mask reduces transmission and susceptibility by 50% or 80%; an individual wears a mask with a probability of 0%, 20%, 40%, 60%, 80%, or 100%. Results: If 60% of the population wears
masks that are 50% effective, this decreases the cumulative infection attack rate (CAR) by 25%, the peak prevalence by 51%, and the population mortality by 25%. If 100% of people wear masks (or 60% wear masks that are 80% effective), this decreases the CAR
by 38%, the peak prevalence by 67%, and the population mortality by 40%. Conclusions: After community transmission is present, masks can significantly reduce infections. |
|
Rovetta, Alessandro, Castaldo, et al |
medRxiv |
Epidemiology| Épidémiologie |
This study investigated significant correlations between COVID-19 cases and demographic, geographical, and environmental
statistics of each Italian region from February 26 to August 12, 2020. We further investigated the link between the spread of SARS-CoV-2 and particulate matter (PM) 2.5 and 10 concentrations before the lockdown in Lombardy. All demographic data were obtained
from the AdminStat Italia website, and geographic data were from the Il Meteo website. We used Pearson's coefficients to correlate the quantities that followed a normal distribution, and Spearman's coefficient to correlate quantities that did not follow a
normal distribution.We found significant strong correlations between COVID-19 cases and population number in 60.0% of the regions. We also found a significant strong correlation between the spread of SARS-CoV-2 in the various regions and their latitude, and
with the historical averages (last 30 years) of their minimum temperatures. Since SARS-CoV-2 is correlated with historical minimum temperatures and PM10 and 2.5, health authorities are urged to monitor pollution levels and to invest in precautions for the
arrival of autumn. |
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Roy, Avishek, Behera, et al |
medRxiv |
Clinical data| Données cliniques Healthcare Response | Réponse des soins de santé |
Prone position ventilation has been shown to decrease mortality and improve oxygenation in ARDS patients. In this prospective
observational study, data of n=20 consecutive laboratory confirmed SARS- CoV-2 patients with severe ARDS as per Berlin definition was included. Data of 20 patients analyzed with a median (Interquartile range, IQR) age of 56 (45.5- 67) y and median (IQR) P/F
ratio of 56 (54- 66) with a median (IQR) PEEP of 12 (12- 14) before initiation of prone position. There was a significant decrease in plateau airway pressure (p<0.0001), peak airway pressure (p<0.0001) and driving pressure(p<0.0001) and increase in static
compliance (p=0.001), P/F ratio (p<0.0001), PaO2 (p=0.0002)and SpO2 (p=0.0004) at 4h and 16h since initiation of prone session and also after return of supine position. Prone position in SARS- CoV-2 infected severe ARDS patients is associated with improvement
in lung compliance and oxygenation in two- third of the patients and persisted in half of the patients. |
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Rubio-Rivas, Manuel, Corbella, et al |
medRxiv |
Clinical data| Données cliniques Coronavirology| Coronavirologie |
This study aims to identify different clinical phenotypes in COVID-19 pneumonia using cluster analysis and to assess
the prognostic impact among identified clusters in such patients. Cluster analysis including 11 phenotypic variables was performed in a large cohort of 12,066 COVID-19 patients, collected and followed-up from March 1, to July 31, 2020, from the nationwide
Spanish SEMI-COVID-19 Registry. The present study identified 4 phenotypic clusters in patients with COVID-19 pneumonia, which predicted the in-hospital prognosis of clinical outcomes. |
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Ruiz-Quinonez, Jesus, Guzman-Priego, et al |
medRxiv |
Clinical data| Données cliniques |
The aim of this study was to evaluate demographic features, clinical characteristics, and the pharmacological treatment
of individuals who died by COVID-19 in the south of Mexico. We performed an observational study including 185 deceased individuals with confirmed diagnosis of COVID-19. Data were retrieved from medical records. Present comorbidities were diabetes (60.63%),
hypertension (59.57%) and obesity (43.61%). The main drugs used were azithromycin (60.6%), hydroxychloroquine (53.0%) and oseltamivir (27.3%). Mexican individuals who died of COVID-19 had shorter hospital stays, higher frequency of shortness of breath, and
higher prevalence of diabetes compared with individuals from other countries. Also, there was a high frequency of off-label use of drugs for their treatment. |
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Runfola, M, Fantola, et al |
Obes Surg |
Healthcare Response | Réponse des soins de santé |
This paper is aimed to evaluate the impact of tele-consulting technology in a single bariatric center. MATERIALS AND
METHODS: Our outpatient clinic reorganized the service from on-site to long-distance video consultations. All patients received a satisfaction questionnaire. The main goals were to evaluate patient compliance and to assess patient satisfaction. RESULTS: Of
the 33 booked patients who were offered a teleconsultation, 19 (57.6%) participated in the video-call. No significant differences were found between participants and non-participants in terms of age and gender ratio. Urban area residents were 57.9% of the
participants versus 42.8% of the non-participants group. Of the participants, 52.6% completed the survey reporting levels of satisfaction ranging from high to very high. CONCLUSION: Telemedicine has been advocated as a useful tool to relieve pressure on the
overwhelmed Health Systems during the COVID-19 pandemic. |
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Reconstructing the early global dynamics of under-ascertained
COVID-19 cases and infections |
Russell, TimothyW, Golding, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases that
were reported in 210 countries and territories, given those countries had experienced more than ten deaths. Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries
which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country's
population infected with SARS-CoV-2 worldwide is generally low. |
|
S G, Amrutha, Sharma, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
we substantiate the implementation of the instantaneous reproduction number (Rins) method over the conventional method
to estimate Rt viz case reproduction number (Rcase), by unmasking the real-time estimation ability of both methodologies using credible datasets. We employed the daily incidence dataset of COVID-19 for India and high incidence states to estimate Rins and Rcase.
Although, both the Rins and Rcase for the selected states were higher during the lockdown phases (March 25 - June 1, 2020) and subsequently stabilizes co-equally during the unlock phase (June 1- August 23, 2020), Rins demonstrated variations in accordance
with the interventions while Rcase remained generalized and under- & overestimated. A larger difference in Rins and Rcase estimates were also observed for states that are conducting high testing. |
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Covid-19 Cases in India: A Visual Exploratory Data
Analysis Model |
S, Jayesh, Sreedharan, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In this paper, an exploratory data analysis of Covid-19 cases in India is carried out. Data namely number of cases,
testing done, Case Fatality ratio, Number of deaths, change in visits stringency index and measures taken by the government is used for modelling and visual exploratory data analysis. |
|
Sadoff, Jerry, Le Gars, et al |
medRxiv |
Clinical data| Données cliniques Vaccine Research| Recherche sur les vaccins RCT |
We designed a multi-center phase 1/2a randomized, double-blinded, placebo-controlled clinical study to assesses the
safety, reactogenicity and immunogenicity of Ad26.COV2.S, a non-replicating adenovirus 26 based vector expressing the stabilized pre-fusion spike (S) protein of SARS-CoV-2. Vaccine elicited S specific antibody levels were measured by ELISA and neutralizing
titers were measured in a wild-type virus neutralization assay (wtVNA). CD4+ T-helper (Th)1 and Th2, and CD8+ immune responses were assessed by intracellular cytokine staining (ICS). We here report interim analyses after the first dose of blinded safety data
from cohorts 1a, 1b and 3 and group unblinded immunogenicity data from cohort 1a and 3. In cohorts 1 and 3 solicited local adverse events were observed in 58% and 27% of participants, respectively. Solicited systemic adverse events were reported in 64% and
36% of participants, respectively. Fevers occurred in both cohorts 1 and 3 in 19% (5% grade 3) and 4% (0% grade 3), respectively, were mostly mild or moderate, and resolved within 1 to 2 days after vaccination. The safety profile and immunogenicity after only
a single dose are supportive for further clinical development of Ad26.COV2.S at a dose level of 5x1010 vp, as a potentially protective vaccine against COVID-19. |
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Saeedi, Nazli, rafat, et al |
medRxiv |
Transmission |
We assessed the effect of animal origin foods consumption on the pandemic of COVID-19. For this purpose, we studied
the relationship among 20 food supply as independent variables, and the parameter of Total Cases as dependent variable. Here we show a relationship between a group of animal origin foods and total cases. Regression, Bayes, and Lasso results showed that eggs
and fresh water fish have positive coefficient. So, among the transmission ways of COVID_19, the role of foodborne transmission should be more significant than previously thought. The possibility of animal origin foodborne transmission should be taken into
more consideration. The perspective is to expand the surveillance of SARS-Cov-2 during the food production chain. In conclusion, the results of the present study indicate that one important vehicle for SARS-Cov2 may be some of animal origin foods. |
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Saha, Ayan, Ahsan, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
his study aimed to analyse the epidemiological and clinical characteristics of critical COVID-19 cases and investigate
risk factors including comorbidities and age in relation with the clinical aftermath of COVID-19 in critical cases in Bangladesh. In this retrospective study, epidemiological and clinical characteristics, complications, laboratory results, and clinical management
of the patients were studied from data obtained from 168 individuals diagnosed with an advanced prognosis of COVID-19 admitted in two hospitals in Bangladesh. Individuals in the study sample contracted COVID-19 through community transmission. 56.5% (n = 95)
cases died in intensive care units (ICU) during the study period. Susceptibility to developing critical illness due to COVID-19 was found more in comorbid males. These atypical patients require more clinical attention from the prospect of controlling mortality
rate in Bangladesh. |
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First quarter chronicle of COVID-19: an attempt to
measure governments response |
Sahin, Sule, Boado-Penas, et al |
medRxiv |
Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique |
The crisis caused by COVID-19 revealed the global unpreparedness for handling the impact of a pandemic. In this paper,
we present a first quarter chronicle of COVID- 19 in Hubei China, Italy and Spain, specifically their infection speed, death and fatality rates. By fitting distributions to these rates, we look for the effectiveness of government measures during the pandemic
through a number of statistical approaches. |
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An Application of Logistic Formula to Deaths by COVID-19
in Japan |
Saito, Takesi |
medRxiv |
Epidemiology| Épidémiologie |
A logistic formula in biology is applied to analyze deaths by COVID-19 for both of the first and the second waves in
Japan. We then discuss ends of both waves and their mortality ratios. The meaning of population N in an epidemic is discussed. |
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Environmental and climatic impact on the infection
and mortality of SARS-CoV-2 in Peru |
Samillan, VictorJ, Flores-Leon, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
In this study, we explored the relationship between the cumulative number of infections and mortality cases with climate
(temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, NDVI, PM2.5 and NO2 concentration), and population density in Peru. Using the data from confirmed cases of infection from 1287 districts and confirmed
cases of mortality in 479 districts, we used Spearman's correlations to assess the correlation between environmental and climatic factors with cumulative infection cases, cumulative mortality and case-fatality rate. We also explored district cases by the ecozones
of coast, sierra, high montane forest and lowland rainforest. Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green cover are influential factors in the distribution of infection and mortality
of SARS-CoV-2 in Peru. The case-fatality rate was weakly associated with elevation. Our results also strongly suggest that exposure to poor air quality is a significant factor in the mortality of individuals with SARS-CoV-2 below the age of 30. |
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Sandmann, Frank, Davies, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique Economics | Économie |
We explored the health and economic value of introducing SARS-CoV-2 immunisation alongside physical distancing scenarios
in the UK. We used an age-structured dynamic-transmission and economic model to explore different scenarios of immunisation programmes over ten years. Findings Without vaccination and physical distancing, we estimated 147.9 million COVID-19 cases (95% uncertainty
interval: 48.5 million, 198.7 million) and 2.8 million (770,000, 4.2 million) deaths in the UK over ten years. Vaccination with 75% vaccine effectiveness and 10-year protection may stop community transmission entirely for several years, whereas SARS-CoV-2
becomes endemic without highly effective vaccines. Introducing vaccination compared to no vaccination leads to economic gains (positive net monetary value) of 0.37 billion to +1.33 billion across all physical distancing and vaccine effectiveness scenarios
from the healthcare perspective, but net monetary values of physical distancing scenarios may be negative from societal perspective if the daily national economy losses are persistent and large. |
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Development of equine antisera with high neutralizing activity against
SARS-CoV-2 |
Sapkal, Gajanan, Yadav, et al |
Research Square prepub |
Therapeutics| Thérapeutique Immunology | Immunologie |
The study reports the development and evaluation of equine hyper immune globulin raised against inactivated SARS-CoV-2
virus. Post immunization neutralization titres of the equines demonstrated high neutralizing antibodies. To minimize the adverse effects, the immunoglobulins were digested with pepsin, and purified to obtain the F(ab’)2 fragments. The average nAb titre of
the purified bulk was 22,927 and correlated with high IgG binding efficiency in ELISA. The quality control assessments of the different batches proved to have consistent nAb titres. The study provides evidence of the potential of generating highly purified
F(ab’)2 from equines against SARS-CoV-2 that can demonstrate consistent and high neutralization activity. |
|
Savage, David, Fisher, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission
Healthcare Response | Réponse des soins de santé |
Our aim is to investigate the potential effect of COVID-19 on transmission, ICU resources and mortality in northwestern
Ontario. This study was conducted in northwestern Ontario which has a population of 230,000. A set of differential equations were used to represent a modified Susceptible-Infectious-Recovered (SIR) model with urban and rural hospital resources. Sensitivity
analyses were used to investigate the effect of poorer health status (i.e., increased hospital admission, ICU admission, and mortality) and overcrowding in the rural population as compared to the urban population. An increased contact rate and worse health
status in the rural population will likely increase the required ICU resources and mortality as compared to the urban population. Rural populations will likely be affected disproportionately more than urban populations. |
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An optimal control policy for COVID-19 pandemic until
a vaccine deployment |
Sayarshad, HamidR |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique Economics | Économie |
In order to provide an effective strategy, here we propose a control strategy model. Our model assesses the trade-off
between social performance and limited medical resources by determining individuals' propensities. The proposed strategy also helps decision makers to find optimal lockdown and exit strategy for each region. Moreover, the financial loss is minimized. |
|
Scarduelli, Cleante, Inglese, et al |
Research Square prepub |
Clinical data| Données cliniques |
Our retrospective study reports the incidence of pulmonary embolism (PE) in patients with COVID-19 and severe respiratory
failure (SRF) treated with intermediate to full-dose enoxaparin. Ninety-two patients (71 males, 21 females; mean age 58 ± 11 years) with COVID-19 pneumonia and SRF were admitted to our RICU. Twenty-two patients underwent CTPA (24%), with PEs detected in 11
(12%). Mean PaO2/FiO2 and mean D-dimer levels did not significantly differ between patients with or without PE. Eleven patients (12%) died in the hospital, with a mean age of 70 ± 11 years for deceased patients and 56 ± 11 years for surviving patients (p <
0.0001). PE was diagnosed in 12% of patients despite intermediate to full-dose enoxaparin treatment. However the incidence of PE in our patients was lower than that previously reported. We hypothesize that this reduced PE incidence may have been secondary
to the higher than prophylactic enoxaparin dose that was used. |
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Schizas, N, Michailidis, et al |
Am J Case Rep |
Clinical data| Données cliniques |
BACKGROUND The worldwide spread of the severe acute respiratory syndrome-coronavirus-2 (SARS-COV-2) has created unprecedented
situations for healthcare professionals and healthcare systems. Although infection with this virus is considered the main health problem currently, other diseases are still prevalent. CASE REPORT This report describes a 59-year-old man who presented with symptoms
of dyspnea and fever that were attributed to Covid-19 infection. His clinical condition deteriorated and further examinations revealed a subjacent severe aortic regurgitation due to acute infective endocarditis. Surgical treatment was successful. CONCLUSIONS
The results of diagnostic tests for Covid-19 should be re-evaluated whenever there are clinical mismatches or doubts, as false-positive Covid-19 test results can occur. Clinical interpretation should not be determined exclusively by the Covid-19 pandemic.
This case report highlights the importance of using validated and approved serological and molecular testing to detect infection with SARS-CoV-2, and to repeat tests when there is doubt about presenting symptoms. |
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Schneider, MatthiasM, Emmenegger, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
Using Microfluidic Antibody Affinity Profiling (MAAP), we determined the aggregate affinities and concentrations of
anti-SARS-CoV-2 antibodies in plasma samples of 42 seropositive individuals, 23 of whom were confirmed to be SARS-CoV-2. We found that dissociation constants (Kd) of anti-RBD antibodies spanned more than two orders of magnitude from 80 pM to 25 nM, despite
having similar antibody concentrations. Individual patients showed progressively higher antibody concentrations but constant Kd values, suggesting that affinities did not mature over time. 33 sera showed affinities higher than that of the CoV2 spike for its
ACE2 receptor. Accordingly, addition of seropositive plasma to pre-formed spike-ACE2 receptor complexes led to their dissociation. Finally, we observed that the RBD of HKU1, OC43, and SARS-CoV coronaviruses, but not unrelated control proteins, were able to
compete substantially with the RBD of SARS-CoV-2 in solution. Therefore, the affinity of total plasma immunoglobulins to SARS-CoV-2 is an indicator of the quality of the immune response to SARS-CoV-2, and may help select the most efficacious samples for therapeutic
plasmapheresis. |
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Seaman, Shaun, Samartsidis, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In this article, we estimate the number of deaths per day in each of five age strata within seven English regions.
We use a Bayesian hierarchical model that involves a submodel for the number of deaths per day and a submodel for the reporting delay distribution. This model accounts for reporting-day effects and longer-term changes over time in the delay distribution. We
show how the model can be fitted in a computationally efficient way when the delay distribution is same in multiple strata, e.g. over a wide range of ages. |
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Seneviratne, Chaminda Jayampath, Balan, et al |
medRxiv |
Clinical data| Données cliniques Infection Prevention and Control/ Prévention et contrôle
des infections (IPAC/PCI) RCT |
In this randomised control trial, the efficacy of three commercial mouth-rinse viz. povidone-iodine (PI), chlorhexidine
gluconate (CHX) and cetylpyridinium chloride (CPC), in reducing the salivary SARS-CoV-2 viral load in COVID-19 positive patients were compared with water. A total of 36 COVID-19 positive patients were recruited, of which 16 patients were randomly assigned
to four groups: PI group (n=4), CHX group (n=6), CPC group (n=4) and water as control group (n=2). Saliva samples were collected from all patients at baseline and at 5 min, 3 h and 6 h post-application of mouth-rinses/water. The samples were subjected to SARS-CoV-2
RT-PCR analysis. The fold change of Ct values were significantly increased in CPC group at 5 minutes and 6 h time points (p<0.05), while it showed significant increase at 6 h timepoint for PI group (p<0.01). Within the limitation of the current study, it can
be concluded that use of CPC and PI formulated commercial mouth-rinses, with its sustained effect on reducing salivary SARS-CoV-2 level, may be useful as a pre-procedural rinse to help reduce the transmission of COVID-19. |
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COVID-19 epidemic modelling and the effect of public
health interventions in India- SEIQHRF model |
Sengupta, Pooja, Ganguli, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique |
In the present study we will fit the SEIQHRF compartment model to COVID19 outbreak data for India and use simulations
to explore the impact of lockdown on the epidemic and perform a what -if analysis for strategies for imposition and relaxation of the lockdown. It has been projected that around two month span is required to arrest the epidemic with the present strategy
of lock-down and social distancing that includes phased withdrawal of such measures depending upon the identified hot spots. |
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Urban rail transport and SARS-CoV-2 infections: an
ecological study in Lisbon Metropolitan Area |
Severo, Milton, Ribeiro, et al |
medRxiv |
Epidemiology| Épidémiologie |
This study was conducted to investigate whether proximity to railway stations, a proxy for utilization, was associated
with higher rates of SARS-CoV-2 infection across small-areas of Lisbon Metropolitan Area. We used a Geographic Information System to estimate proximity to railway stations from the six railway lines operating in the area. Between May 2 and July 5, 2020, there
were a total of 17,168 SARS-CoV-2 infections in the Lisbon Metropolitan Area, with wide disparities between parishes. Globally, parishes near one of the railway lines (Sintra) presented significantly higher SARS-CoV-2 infection rates (RR=1.42, 95%CI 1.16,
1.75) compared to those parishes located far away from railway stations, while the opposite happened for parishes near other railway lines (Sado/Fertagus), whose infection rates were significantly lower than those observed in parishes located far away from
railway stations (RR=0.66, 95%CI 0.50, 0.87). The associations varied according to the stage of the epidemic and according to mitigation measures in place. Regression results also revealed an increasing influence of socioeconomic deprivation on SARS-CoV-2
infections. We found no consistent association between proximity to railway stations and SARS-CoV-2 infection rates in the most affected metropolitan area of the country. |
|
Shapiro, MarkB, Karim, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
We propose a simple method for estimating the time-varying infection rate and reproduction number R_t using a sliding
window approach applied to a Susceptible-Infectious-Removed model. The infection rate is estimated using the reported cases for a seven-day window to obtain continuous estimation of R_t. We demonstrate that the proposed adaptive SIR (aSIR) model can quickly
adapt to an increase in the number of tests and associated increase in the reported cases of infections. Our results also suggest that intensive testing may be one of the effective methods of reducing R_t. The aSIR model was applied to data at the state and
county levels. |
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Inferior Wall Myocardial Infarction in Severe COVID-19 Infection: A Case Report |
Sheikh, AB, Shekhar, et al |
Am J Case Rep |
Clinical data| Données cliniques |
We present the case of a 56-year-old man with cardiovascular risk factors including coronary artery disease, hypertension,
ischemic cardiomyopathy, and hyperlipidemia, who had COVID-19-induced pneumonia complicated with acute respiratory distress syndrome. He subsequently developed myocardial infarction during his hospitalization at our facility. |
|
Shi, SM, Bakaev, et al |
J Am Med Dir Assoc |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This retrospective cohort study aimed to describe clinical characteristics and risk factors associated with COVID-19
in long-stay nursing home residents. Overall 146 of 389 (37.5%) long-stay residents tested positive for COVID-19. At the time of positive test, 66 of 146 (45.5%) residents were asymptomatic. In the subsequent illness course, the most common symptom was anorexia
(70.8%), followed by delirium (57.6%). During follow-up, 44 (30.1%) of residents with COVID-19 died. Mortality increased with frailty (16.7% in pre-frail, 22.2% in moderately frail, and 50.0% in frail; P < .001). The proportion of residents infected with COVID-19
varied across the long-term care units (range: 0%‒90.5%). In adjusted models, male sex (RR 1.80, 95% CI 1.07, 3.05), bowel incontinence (RR 1.97, 95% CI 1.10, 3.52), and staff residence remained significant predictors of COVID-19. For every 10% increase in
the proportion of staff living in a high prevalence community, the risk of testing positive increased by 6% (95% CI 1.04, 1.08). |
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Comparative Effectiveness of Famotidine in Hospitalized
COVID-19 Patients |
Shoaibi, Azza, Fortin, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique |
We compared the incidence of COVID-19 outcomes among hospitalized famotidine users vs. proton pump inhibitors (PPIs)
users, hydroxychloroquine users or famotidine non-users separately. We constructed a retrospective cohort study using data from COVID-19 Premier Hospital electronic health records. Famotidine, PPI and hydroxychloroquine exposure groups were defined as patients
dispensed any medication containing one of the three drugs on the day of admission. Time-at-risk was defined based on the intention-to-treat principle starting 1 day after admission to 30 days after admission. For each study comparison group, we fit a propensity
score (PS) model through large-scale regularized logistic regression. We identified 2193 users of PPI, 5950 users of the hydroxychloroquine, 1816 users of famotidine and 26,820 non-famotidine users. After PS stratification, the hazard ratios for death were
as follows: famotidine vs no famotidine HR 1.03 (0.89-1.18); vs PPIs: HR 1.14 (0.94-1.39); vs hydroxychloroquine:1.03 (0.85-1.24). Similar results were observed for the risk of death or intensive services use. We found no evidence of a reduced risk of COVID-19
outcomes among hospitalized COVID-19 patients who used famotidine compared to those who did not or compared to PPI or hydroxychloroquine users. |
|
Simadibrata, Daniel Martin, Calvin, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
In this study, we investigated whether NLR levels on admission could predict the severity and mortality of COVID-19
patients. The risk of bias was assessed using the Newcastle Ottawa Scale (NOS). A meta-analysis was performed to determine the overall standardized mean difference (SMD) in NLR values and the pooled risk ratio (RR) for severity and mortality with the 95% Confidence
Interval (95%CI). Meta-regression analysis was done to identify potential confounders. A total of 38 articles, including 5699 patients with severity outcomes and 6033 patients with mortality outcomes, were included. The meta-analysis showed that severe and
non-survivors of COVID-19 had higher on-admission NLR levels than non-severe and survivors (SMD 0.88; 95%CI 0.72-1.04; I2=75% and 1.68; 95%CI 0.98-2.39; I2=99%, respectively). Regardless of the different NLR cut-off values, the pooled mortality RR in patients
with elevated vs. normal NLR levels was 2.75 (95%CI 0.97-7.72). Meta-regression analysis showed that the association between NLR levels on admission and COVID-19 severity and mortality was unaffected by age (p=0.236; p=0.213, respectively). High NLR levels
on admission were associated with severe COVID-19 and mortality. |
|
|
Simeone, Roberto |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
In a previous paper a simplified SEIR model applied to COVID-19 cases detected in Italy, including the lockdown period,
has shown a good fitting to the time evolution of the disease during the observed period. In this paper that model is applied to the initial data available for Italy in order to forecast, in a qualitative way, the time evolution of the disease spreading. The
values obtained are to be considered indicative. The same model has been applied both to the data relating to Italy and to some italian regions generally finding good qualitative results. The only tuning parameter in the model is the 'incubation period'. In
this modelization the tuning parameter, together with the calculated growth rate of the exponential curve used to approximate the early stage data, are in strong relationship with the compartments' transfer rates. The relationships between the parameters simplify
modeling by allowing a rough (not supported by statistical considerations) forecast of the time evolution, starting from the first period of growth of the diffusion. |
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|
Singh, NaveenK, Ray, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Significant barriers to the diagnosis of latent and acute SARS-CoV-2 infection continue to hamper population-based
screening efforts required to contain the COVID-19 pandemic in the absence of effective antiviral therapeutics or vaccines. We report an aptamer-based SARS-CoV-2 salivary antigen assay employing only low-cost reagents ($3.20/test) and an off-the-shelf glucometer.
The test was engineered around a glucometer as it is quantitative, easy to use, and the most prevalent piece of diagnostic equipment globally making the test highly scalable with an infrastructure that is already in place. Furthermore, many glucometers connect
to smartphones providing an opportunity to integrate with contract tracing apps, medical providers, and electronic medical records. In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads - as
benchmarked by RT-qPCR - within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). We propose that this approach
can provide an inexpensive, rapid, and accurate diagnostic for distributed screening of SARS-CoV-2 infection at scale. |
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Time Series Analysis of COVID-19 Data to Study the Effect of Lockdown and
Unlock in India |
Singh, Saswat, Chowdhury, et al |
Research Square prepub |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health
interventions*| Interventions de santé publique |
The study investigated prediction forecasts using the ARIMA model on the COVID-19 data on the lockdown period and the
unlock period. In this work, we have considered not only the no of positive COVID cases but also considered the number of tests carried out. The time-series data sample was collected till June 2020 and the prediction and analysis are done for August 2020.
The model developed and the forecasted results align very closely with the actual no of cases and we have drawn some important inferences through experimentation. |
|
Siska, PeterJ, Singer, et al |
medRxiv |
Immunology | Immunologie |
Coronavirus disease 2019 (COVID-19) is driven by dysregulated immune responses yet the role of immunometabolism in
COVID-19 pathogenesis remains unclear. By investigating 47 patients with confirmed SARS-CoV-2 infection and 16 uninfected controls, we found an immunometabolic dysregulation specific for patients with progressed disease that was reversible in the recovery
phase. Specifically, T cells and monocytes exhibited increased mitochondrial mass, accumulated intracellular ROS and these changes were accompanied by disrupted mitochondrial architecture. Basigin (CD147), but not established markers of T cell activation,
was up-regulated on T cells from progressed COVID-19 patients and correlated with ROS accumulation, reflected in the transcriptome. During recovery, basigin and ROS decreased to match the uninfected controls. In vitro analyses confirmed the correlation and
showed a down-regulation of ROS by dexamethasone treatment. Our findings provide evidence of a basigin-related and reversible immunometabolic dysregulation in COVID-19. |
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Smith, LouiseE, Potts, et al |
medRxiv |
Public Health response| Interventions de santé publique |
Time series of cross-sectional online surveys were used to investigate rates of adherence to the UKs test, trace and
isolate system over time. Data were collected between 2 March and 5 August 2020 and included 42,127 responses from 31,787 people living in the UK, aged 16 years or over (21 survey waves, n≈2,000 per wave). Only 48.9% of participants (95% CI 48.2% to 49.7%)
identified key symptoms of COVID-19. Self-reported adherence to test, trace and isolate behaviours was low (self-isolation 18.2%, 95% CI 16.4% to 19.9%; requesting an antigen test 11.9%, 95% CI 10.1% to 13.8%; intention to share details of close contacts 76.1%,
95% CI 75.4% to 76.8%; quarantining 10.9%, 95% CI 7.8% to 13.9%) and largely stable over time. By contrast, intention to adhere to protective measures was much higher. Non-adherence was associated with: men, younger age groups, having a dependent child in
the household, lower socio-economic grade, greater hardship during the pandemic, and working in a key sector. Conclusions: Practical support and financial reimbursement is likely to improve adherence. Targeting messaging and policies to men, younger age groups,
and key workers may also be necessary. |
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So, MikeKP, Chu, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
This study proposes a network analysis to assess global pandemic risk by linking 164 countries in pandemic networks,
where links between countries were specified by the level of 'co-movement' of newly confirmed COVID-19 cases. More countries showing increase in the COVID-19 cases simultaneously will signal the pandemic prevalent over the world. The network density, clustering
coefficients, and assortativity in the pandemic networks provide early warning signals of the pandemic in late February 2020. We propose a preparedness pandemic risk score for prediction and a severity risk score for pandemic control. The preparedness risk
score contributed by countries in Asia is between 25% to 50% most of the time after February and America contributes close to 50% recently. The high preparedness risk contribution implies the importance of travel restrictions between those countries. The severity
risk score of America is greater than 50% after May and even exceeds 75% in July, signifying that the control of COVID-19 is still worrying in America. We can keep track of the pandemic situation in each country using an online dashboard to update the pandemic
risk scores and contributions. |
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Immune dysfunction following COVID-19, especially in severe patients |
Song, CY, Xu, et al |
Sci Rep |
Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie |
This study investigated the clinical features of COVID-19 and identified the risk factors associated with its progression.
Thirty-seven healthy people and 79 confirmed patients, which include 48 severe patients and 31 mild patients, were recruited. COVID-19 patients presented with dysregulated immune response (decreased T, B, and NK cells and increased inflammatory cytokines).
Also, they were found to have increased levels of white blood cell, neutrophil count, and D-dimer in severe cases. Moreover, lymphocyte, CD4(+) T cell, CD8(+) T cell, NK cell, and B cell counts were lower in the severe group. Multivariate logistic regression
analysis showed that CD4(+) cell count, neutrophil-to-lymphocyte ratio (NLR) and D-dimer were risk factors for severe cases. Both CT score and clinical pulmonary infection score (CPIS) were associated with disease severity. |
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Souza, Fernanda Sumika Hojo, Hojo-Souza, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This data-driven study was based on the Brazilian Ministry of Health Database (SIVEP-Gripe, 2020) regarding notified
cases of hospitalized COVID-19 patients during the period from February 26 to August 10, 2020. The hospitalization rate was higher for male gender (56.56%) and for older age patients of both sexes. Overall, the mortality rate was quite high (41.28%) among
hospitalized patients, especially those over 60 years of age. Most prevalent symptoms were cough, dyspnoea, fever, low oxygen saturation and respiratory distress. Heart disease, diabetes, obesity, kidney disease, neurological disease, and pneumopathy were
the most prevalent comorbidities. A high prevalence of hospitalized COVID-19 patients with heart disease (65.7%) and diabetes (53.55%) and with a high mortality rate of around 50% was observed. The ICU admission rate was 39.37% and of these 62.4% died. 24.4%
of patients required invasive mechanical ventilation (IMV), with high mortality among them (82.98%). The main mortality risk predictors were older age and IMV requirement. In addition, socioeconomic conditions have been shown to significantly influence the
disease outcome, regardless of age and comorbidities. Our study provides a comprehensive overview of the hospitalized Brazilian COVID-19 patients profile and the mortality risk factors. |
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Spada, Alessia, Tucci, et al |
Research Square prepub |
Epidemiology| Épidémiologie |
This study analyzed the relation between Covid-19, population density, and climate. A theoretical path diagram was
hypothesized and tested using Structural Equation Modeling (SEM) for the evaluation of causal assumptions. The results of the analysis showed that both climate and population density significantly influence the spread of Covid-19 (p<0.001 and p<0.01, respectively).
Overall, climate outweighs population density (b-incidence=0.18, b-prevalence=0.11 versus b-incidence=0.04, b-prevalence=0.05). Among the climatic factors, irradiation plays the most relevant role, with a factor-loading of -0.77, followed by temperature (-0.56),
humidity (0.52), precipitation (0.44), and pressure (0.073); for all p<0.001. An interesting outcome was the value of residual variance (ε-incidence=0.97, ε-prevalence=0.98) suggesting that other factors influence the transmission of the infection. |
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Spick, MattP, Longman, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
The COVID-19 pandemic has led to an urgent and unprecedented demand for testing - both for diagnosis and prognosis.
Here we explore the potential for using sebum, collected via swabbing of a patient's skin, as a novel sampling matrix to fulfil these requirements. In this pilot study, sebum samples were collected from 67 hospitalised patients (30 PCR positive and 37 PCR
negative). Lipidomics analysis was carried out using liquid chromatography mass spectrometry. Total fatty acid derivative levels were found to be depressed in COVID-19 positive participants, indicative of dyslipidemia. Orthogonal Partial Least Squares-Discriminant
Analysis (OPLS-DA) modelling showed promising separation of COVID-19 positive and negative participants when comorbidities and medication were controlled for. Given that sebum sampling is rapid and non-invasive, this work may offer the potential for diagnostic
and prognostic testing for COVID-19. |
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Spinelli, M, Lionetti, et al |
Fam Process |
Public Health response| Interventions de santé publique |
The present study explored risk factors associated with parenting stress and implications for children's emotion regulation
in families with different socioeconomic risks. Household chaos predicted higher levels of parenting stress, which, in turn, was associated with less effective emotion regulation in children through the mediating role of parental involvement. More stressed
parents were less involved in their children's activities, decreasing children's effective emotion regulation. Only for SES no-risk families, the lockdown constraints increased parenting stress. For SES at-risk families, the impact of parenting stress and
involvement on children regulation strategies was stronger, with a protective role played by parental involvement on children's negativity not evident for SES no-risk families. Dealing with the lockdown is a stressful experience for parents who have to balance
personal life, work, and children upbringing, without other help. |
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Stewart, Robert, Martin, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
This study sought to provide an early description of mental health service activity before and after national implementation
of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i)
inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison,
home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily
numbers of deaths increased by 61.8%. |
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Stowe, Julia, Tessier, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study investigates the interaction between influenza and COVID-19 during the latter part of the 2019-20 influenza
season in England. Individuals tested for influenza and SARS-CoV-2 were extracted from national surveillance systems between 20/01/2020 and 25/04/2020. The risk of testing positive for SARS-CoV-2 was 68% lower among influenza positive cases, suggesting possible
pathogenic competition between the two viruses. Patients with a coinfection had a risk of death of 5.92 (95% CI, 3.21-10.91) times greater than among those with neither influenza nor SARS-CoV-2 suggesting possible synergistic effects in coinfected individuals.
The odds of ventilator use or death and ICU admission or death was greatest among coinfection patients showing strong evidence of an interaction effect compared to SARS-CoV-2/influenza acting independently. Cocirculation of these viruses could have a significant
impact on morbidity, mortality and health service demand. Testing for influenza alongside SARS-CoV-2 and maximising influenza vaccine uptake should be prioritised to mitigate these risks. |
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Strausz, Satu, Kiiskinen, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
To examine whether the risk for contracting COVID-19 is elevated among obstructive sleep apnoea (OSA) patients a registry
based retrospective case-control study using Finnish nationwide health registries and the FinnGen Study cohort was performed. Information regarding OSA diagnosis and COVID-19 infection was extracted from the FinnGen study (N=260,405) with a total of 305 patients
who had a recorded PCR-validated COVID-19 infection including 26 (8.5%) individuals who were also OSA patients. Severe COVID-19 (N=83, 27.2%) was defined as an infection requiring hospitalization. Among the hospitalized individuals there were 16 (19.3%) with
OSA diagnosis. We show that OSA is a risk factor for COVID-19 hospitalization independent from age, sex, body mass index (BMI), hypertension, diabetes, coronary heart disease (CHD), asthma and chronic obstructive pulmonary disease (COPD), (p-unadjusted=1.04x10^-4,
OR-adjusted=5.24 95%CI 1.33 to 23.43], p-adjusted=0.022). OSA was not associated with the risk of contracting COVID-19 (p=0.49). While an OSA patients risk of contracting COVID-19 is the same as non-OSA individuals, the OSA patients have a five-fold risk to
be hospitalized when affected by COVID-19 than non-OSA individuals. |
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Are "fibrosis-like" strips on chest CT in patients with COVID-19 pneumonia
true fibrosis? |
Sun, Qiulian, Xu, et al |
Research Square prepub |
Clinical data| Données cliniques |
This study investigated the evolution and characteristics of "fibrosis-like" strips on chest CT in patients with COVID-19
pneumonia. The study included 36 patients (20 males and 16 females) diagnosed with mild or common COVID-19; "fibrosis-like" strips were observed in 29 patients (80.6%) on the first chest CT scan, and "fibrosis-like" strips were observed in 7 patients (19.4%)
on the second chest CT scan, Repeated chest CT during the course of treatment showed that all patients with "fibrosis-like" strips had varying degrees of absorption. Follow-up chest CT after treatment showed that "fibrosis-like" strips in 15 patients completely
disappeared in both lungs, and "fibrosis-like" strips completely disappeared in unilateral lung of 8 cases. |
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Szocska, Miklos Karoly, Pollner, et al |
medRxiv |
Public Health response| Interventions de santé publique |
We describe a collaboration with all 3 major domestic telecommunication companies in Hungary to use aggregated anonymous
mobile phone usage data to calculate two indices for assessing the effect of movement restrictions: a "mobility-index" and a "stay-at-home (or resting) index". The strengths and weaknesses of this approach are compared with the smartphone-based, COVID-19 Community
Mobility Reports from Google. Especially in populations where uptake of smartphones is modest, this method has certain advantages over app-based solutions, with greater population coverage, but it is not an alternative to smartphone-based solutions used for
contact tracing and quarantine monitoring. We believe that this method can easily be adapted by other countries. |
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Tan, EdinaYQ, Wee, et al |
medRxiv |
Public Health response| Interventions de santé publique |
During a crisis, the messaging platform WhatsApp allows crisis-related information to be disseminated quickly. Although
case studies have documented how WhatsApp has shaped crisis outcomes in both beneficial and harmful ways, little is known about: (i) how crisis-related content is spread; (ii) characteristics of users based on usage patterns; or (iii) how usage patterns link
to well-being. During the coronavirus disease 2019 (COVID-19) crisis, this study used the experience sampling method to track the daily WhatsApp usage of 151 adults throughout one week (capturing a total of 924 days of crisis-related communication). Each day,
participants reported the extent to which they had received, forwarded, or discussed COVID-19- related content. During the week-long monitoring, most participants (94.7%) reported at least one COVID-19 related use of WhatsApp. Those who engaged with more COVID-19
content in personal chats were more likely to report having COVID-19 thoughts throughout the day. We further observed that around 1 in 10 individuals (14%) were chronic users who received and shared forwarded COVID-19 messages at a high volume; this group
may represent everyday "super spreaders" of crisis-related content. Together, these findings provide an empirical base for policy makers to manage risk communication during large-scale crises. |
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Tan, Seow Yen, Tey, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We conducted a diagnostic accuracy study where subjects with a confirmed diagnosis of COVID-19 (n=401) and healthy
volunteers (n=100) were asked to self-swab from their oropharynx and mid-turbinate (OPMT), and self-collect saliva. The results of these samples were compared to an OPMT performed by a healthcare workers (HCW) in the same patient at the same session. In subjects
confirmed to have COVID-19, the detection rates of the HCW-swab, self-swab, saliva, and combined self-swab plus saliva samples were 82.8%, 75.1%, 74.3% and 86.5% respectively. All samples obtained from healthy volunteers were tested negative. Compared to HCW-swab,
the detection rates of a self-swab sample and saliva sample were inferior by 8.7% (95% CI: 2.4% to 15.0%, p=0.006) and 9.5% (95% CI: 3.1% to 15.8%, p=0.003) respectively. The combined detection rate of self-swab and saliva had a higher detection rate of 2.7%
(95% CI: -2.6% to 8.0%, p=0.321). The negative correctness of both the self-swab and saliva testing was 100% (95% CI 96.4% to 100%). Our study provides evidence that detection rates of self-collected OPMT swab and saliva samples were inferior to a HCW swab,
but they could still be useful testing tools in the appropriate clinical settings. |
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Thorne, Sophie, Bhopal, et al |
medRxiv |
Public Health response| Interventions de santé publique |
Childrens attendances in paediatric emergency departments have fallen precipitously in North East England and elsewhere
in recent months. We analysed data from 3 hospitals to understand which children were not being brought during the COVID-19 lockdown. In our population there is no evidence of a disproportionate impact on children belonging to vulnerable sociodemographic groups
and no obvious change in illness acuity among those children still attending. However we noted a marked reduction in infectious disease presentations which might reflect one positive impact of enhanced social distancing on child health. More granular data
describing the collateral damage of the COVID-19 pandemic to childrens clinical services are needed to plan for the mitigation of its continuing effects. |
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Tian, Ting, Tan, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique |
We proposed an epidemic model and applied it to evaluate the real-time risk of epidemic for the states of New York,
New Jersey, and Connecticut. We used California as the benchmark state because California began a phased reopening on May 8, 2020. The dates on which the estimated numbers of unidentified infectious individuals per 100,000 for states of New York, New Jersey,
and Connecticut were close to those in California on May 8, 2020, were June 1, 22, and 22, 2020, respectively. By the practice in California, New York, New Jersey, and Connecticut might consider reopening their business. Meanwhile, according to our simulation
models, to prevent the resurgence of infections after reopening the economy, it would be crucial to maintain sufficient measures to limit the social distance after the resumption of businesses. This precaution turned out to be critical as the situation in
California quickly deteriorated after our analysis was completed and its interventions after the reopening of business were not as effective as those in New York, New Jersey, and Connecticut. |
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Tran, Viet-Thi, Mahevas, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique |
To assess the effectiveness of corticosteroids on outcomes of patients with mild COVID-19 pneumonia. We used routine
care data from 51 hospitals in France and Luxembourg to assess the effectiveness of corticosteroids at 0.8 mg/kg/day eq. prednisone (CTC group) vs standard of care (no-CTC group) among patients ≤ 80 years old with COVID-19 pneumonia requiring oxygen without
mechanical ventilation. The primary outcome was intubation or death at Day 28.. Results Among the 891 patients included in the analysis, 203 were assigned to the CTC group. At day 28, corticosteroids did not reduce the rate of the primary outcome (wHR 0.92,
95% CI 0.61 to 1.39) nor the cumulative death rate (wHR 1.03, 95% CI 0.54 to 1.98). Corticosteroids significantly reduced the rate of the primary outcome for patients requiring oxygen ≥ at 3L/min (wHR 0.50, 95% CI 0.30 to 0.85) or C-Reactive Protein (CRP)
≥ 100mg/L (wHR 0.44, 95%CI 0.23 to 0.85).We found no association between the use of corticosteroids and intubation or death in the broad population of patients ≤80 years old with COVID-19 hospitalized in non-ICU settings. However, the treatment was beneficial
for patients with ≥ 3L/min oxygen or CRP ≥ 100mg/L at baseline. |
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Epidemiology of COVID-19 vs. Influenza: Differential
Failure of COVID-19 Mitigation among Hispanics |
Trick, WilliamE, Badri, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
We evaluated patients hospitalized at Cook County Health, the safety-net health system for the Chicago metropolitan
area. Among self-identified hospitalized Hispanic patients, we compared those with influenza (2019-2020 influenza season) to COVID-19 infection during March 16, 2020 through May 11, 2020. Relative to non-Hispanic blacks and whites, COVID-19 rapidly increased
among Hispanics during promotion of social-distancing policies. Whereas non-Hispanic blacks were more likely to be hospitalized for influenza, Hispanic patients predominated among COVID-19 infections (40% relative increase compared to influenza). In the comparative
analysis of influenza and COVID-19, Hispanic patients with COVID-19 were more likely to reside in census tracts with higher proportions of residents with the following characteristics: Hispanic; no high school diploma; non-US citizen; limited English speaking
ability; employed in manufacturing or construction; and, overcrowding. By multivariable analysis, Hispanic patients hospitalized with COVID-19 compared to those with influenza were more likely to be male (adjusted OR=1.8; 95% CI 1.1 to 2.9) or obese (aOR=2.5;
95% CI 1.5 to 4.2), and to reside in a census tract with ≥40% of residents without a high-school diploma (aOR=2.5; 95% CI 1.3 to 4.8). The rapid and disproportionate increase in COVID-19 hospitalizations among Hispanics after the shelter-in-place mandate indicates
that public health strategies were inadequate in protecting this population. In particular, those residing in neighborhoods with lower levels of educational attainment. |
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Trivedi, Ashutosh, Sreenivas, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions
de santé publique |
Data-centric models of COVID-19 have been tried, but have certain limitations. In this work, we propose an agent-based
model of the epidemic in a confined space of agents representing humans. An extension to the SEIR model allows us to consider the difference between the appearance (black-box view) of the spread of disease, and the real situation (glass-box view). Our model
allows for simulations of lockdowns, social distancing, personal hygiene, quarantine, and hospitalization, with further considerations of different parameters such as the extent to which hygiene and social distancing are observed in a population. Our results
give qualitative indications of the effects of various policies and parameters; for instance, that lockdowns by themselves are extremely unlikely to bring an end to an epidemic and may indeed make things worse, that social distancing matters more than personal
hygiene, and that the growth of infection comes down significantly for moderately high levels of social distancing and hygiene, even in the absence of herd immunity. |
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Delayed viral clearance and exacerbated airway hyperinflammation
in hypertensive COVID-19 patients |
Trump, Saskia, Lukassen, et al |
medRxiv |
Clinical data| Données cliniques Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
In COVID-19, hypertension and cardiovascular diseases have emerged as major risk factors for critical disease progression.
Concurrently, the impact of the main anti-hypertensive therapies, angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARB), on COVID-19 severity is controversially discussed. By combining clinical data, single-cell sequencing
data of airway samples and in vitro experiments, we assessed the cellular and pathophysiological changes in COVID-19 driven by cardiovascular disease and its treatment options. Anti-hypertensive ACEi or ARB therapy, was not associated with an altered expression
of SARS-CoV-2 entry receptor ACE2 in nasopharyngeal epithelial cells and thus presumably does not change susceptibility for SARS-CoV-2 infection. However, we observed a more critical progress in COVID-19 patients with hypertension associated with a distinct
inflammatory predisposition of immune cells. While ACEi treatment was associated with dampened COVID-19-related hyperinflammation and intrinsic anti-viral responses, under ARB treatment enhanced epithelial-immune cell interactions were observed. Macrophages
and neutrophils of COVID-19 patients with hypertension and cardiovascular comorbidities, in particular under ARB treatment, exhibited higher expression of CCL3, CCL4, and its receptor CCR1, which associated with critical COVID-19 progression. Overall, these
results provide a potential explanation for the adverse COVID-19 course in patients with cardiovascular disease, i.e. an augmented immune response in critical cells for the disease course, and might suggest a beneficial effect of clinical ACEi treatment in
hypertensive COVID-patients. |
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SARS-CoV-2 antibody seroprevalence in Tbilisi, the
capital city of country of Georgia |
Tsertsvadze, Tengiz, Gatserelia, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
We conducted a survey to estimate SARS-CoV-2 IgG antibody seroprevalence among adult residents of capital city of Tbilisi,
Georgia (adult population: 859,328). Participants were recruited through respondent driven sampling during May 18-27, 2020. Among 1,068 adults recruited, 176 (16.5%) reported symptoms indicative of SARS-CoV-2 infection occurring in previous three months. Nine
persons tested positive for IgG: crude seroprevalence: 0.84%, (95% CI: 0.33%-1.59%), weighted seroprevalence: 0.94% (95% CI: 0.37%-1.95%), weighted and adjusted for test accuracy: 1.02% (95% CI: 0.38%-2.18%). The seroprevalence estimates translate into 7,200
to 8,800 infections among adult residents of Tbilisi, which is at least 20 times higher than the number of confirmed cases. Conclusions: Low seroprevalence confirms that Georgia successfully contained spread of SARS-CoV-2 during the first wave of pandemic.
Findings also suggest that undocumented cases due to asymptomatic or very mild disease account for majority of infections. |
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Tubiana, Sarah, Burdet, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Healthcare Response |
Réponse des soins de santé |
We conducted a prospective cohort in HCWs who had a high-risk exposure to SARS-CoV-2-infected subject without PPE.
Daily symptoms were self-reported for 30 days, nasopharyngeal swabs for SARS-CoV-2 RT-PCR were performed at inclusion and at days 3, 5, 7 and 12, SARS-CoV-2 serology was assessed at inclusion and at day 30. Between February 5th and May 30th, 2020, 154 HCWs
were enrolled within 14 days following one high-risk exposure to either a hospital patient (70/154; 46.1%) and/or a colleague (95/154; 62.5%). At day 30, 25.0% had a confirmed infection (37/148; 95%CI, 18.4%; 32.9%), and 43.9% (65/148; 95%CI, 35.9%; 52.3%)
had a confirmed or possible infection. Factors independently associated with confirmed or possible SARS-CoV-2 infection were being a pharmacist or administrative assistant rather than being from medical staff (adjusted OR (aOR)=3.8, CI95%=1.3;11.2, p=0.01),
and exposure to a SARS-CoV-2-infected patient rather than exposure to a SARS-CoV-2-infected colleague (aOR=2.6, CI95%=1.2;5.9, p=0.02). Among the 26 HCWs with a SARS-CoV-2-positive nasopharyngeal swab, 7 (26.9%) had no symptom at the time of the RT-PCR positivity. |
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Tyson, B, Erdodi, et al |
Int J Neurosci |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
The study investigated the occurrence of neurologic symptoms with a focus on altered mental status in a sample of
deaths due to COVID-19. Sixty-one patients (86%) demonstrated neurologic symptoms at hospital admission. Altered mental status was seen in 47 patients (66%) and represented the most common neurologic symptom. Seven patients (10%) were comatose at hospital
admission and 5 (7%) presented with altered mental status without respiratory symptoms. Three patients had seizures and two had strokes. Hypertension (61%), cardiovascular disease (59%), and dementia (49%) were the most common comorbidities associated with
death due to COVID-19 in this sample. |
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Variation in SARS-CoV-2 seroprevalence in school-children
across districts, schools and classes |
Ulyte, Agne, Radtke, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie |
To determine the variation in SARS-CoV-2 seroprevalence in school children across districts, schools, grades, and classes,
and the relationship of SARS-CoV-2 seroprevalence with self-reported symptoms we performed a cross-sectional analysis of baseline measurements of a longitudinal cohort study (Ciao Corona) from June-July 2020. 55 randomly selected schools and classes stratified
by district in the canton of Zurich, Switzerland (1.5 million inhabitants) participated, including children, aged 6-16 years old, attending grades 1-2, 4-5 and 7-8. Overall seroprevalence was 2.8 % (95% CI 1.6-4.1%), ranging from 1.0% to 4.5% across districts.
Seroprevalence was 3.8% (1.9-6.1%) in grades 1-2, 2.5% (1.1-4.2%) in grades 4-5, and 1.5% (0.5-3.0%) in grades 7-8. At least one case was present in 36/55 tested schools and in 43/128 classes with ≥50% participation rate and ≥5 children tested. 73% of children
reported COVID-19 compatible symptoms since January 2020, but none were reported more frequently in seropositive compared to seronegative children. Seroprevalence of children was very similar to seroprevalence of randomly selected adults in the same region
in June-July 2020, measured with the same Corona Immunitas test, combining IgG and IgA (3.1%, 95% CI 1.4-5.4%, versus 3.3%, 95% CI 1.4-5.5%). Seroprevalence was inversely related to age and revealed a dark figure of around 90 when compared to 0.03% confirmed
PCR+ cases in children in the same area by end of June. We did not find clustering of SARS-CoV-2 seropositive cases in schools so far, but the follow-up of this school-based study will shed more light on transmission within and outside schools. |
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Valdivia, Arantxa, Torres, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
We evaluated the performance of two commercially-available lateral flow immunochromatographic assays (LFIC) (Wondfo
SARS-CoV-2 Antibody test and the INNOVITA 2019-nCoV Ab test) in comparison with a SARS-CoV-2 neutralization pseudotyped assay for COVID-19 diagnosis in hospitalized patients, and investigate whether the intensity of the test band in LFIC associates with neutralizing
antibody (NtAb) titers. Ninety sera were included from 51 patients with moderate to severe COVID-19. A green fluorescent protein (GFP) reporter-based pseudotyped neutralization assay (vesicular stomatitis virus coated with SARS-CoV-2 spike protein) was used.
Test line intensity was scored using a 4-level scale (0 to 3+). Overall sensitivity of LFIC assays was 91.1% for the Wondfo SARS-CoV-2 Antibody test, 72.2% for the INNOVITA 2019-nCoV IgG, 85.6% for the INNOVITA 2019-nCoV IgM and 92.2% for the NtAb assay. Sensitivity
increased for all assays in sera collected beyond day 14 after symptoms onset (93.9%, 79.6%,93.9% and 93.9%, respectively). Reactivities equal to or more intense than the positive control line (≥2+) in the Wondfo assay had a negative predictive value of 100%
and a positive predictive value of 96.4% for high NtAb50 titers (≥1/160). Our findings support the use of LFIC assays evaluated herein, particularly the Wondfo test, for COVID-19 diagnosis. We also find evidence that these rapid immunoassays can be used to
predict high SARS-CoV-2-S NtAb50 titers. |
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Valka, Fabian, Schuler, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Transmission |
Rt plays a key role in the development of the COVID-19 pandemic. The methods used for building an interactive website
for the visualization of the time-varying reproduction number Rt and a novel way to visualize the time delay from infection to estimation overlayed with the Rt estimate are described and analyzed with regards to the influence of parameters chosen and compared
to published estimates for Austria. Visualizing the time delays enables the interactive exploration of suspected changes in transmission and their effect on the Rt estimate. |
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van den Besselaar, Judith Henriette, Sikkema, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques Public health interventions*|
Interventions de santé publique Healthcare Response | Réponse des soins de santé |
Observational study in a 185-bed nursing home with two consecutive testing strategies: testing of symptomatic cases
only, and weekly facility-wide testing of staff and residents regardless of symptoms. Nasopharyngeal and oropharyngeal testing with RT-PCR for SARs-CoV-2 was conducted with a standardized symptom assessment. Positive samples with a cycle threshold (CT) value
below 32 were selected for sequencing. 185 residents and 244 staff participated. Sequencing identified one cluster. In the symptom-based test strategy period 3/39 residents were presymptomatic versus 38/74 residents in the period of weekly facility-wide testing
(p-value<0.001). In total, 51/59 (91.1%) of SARS-CoV-2 positive staff was symptomatic, with no difference between both testing strategies (p-value 0.763). Loss of smell and taste, sore throat, headache or myalga was hardly reported in residents compared to
staff (p-value <0.001). Median Ct-value of presymptomatic residents was 21.3, which did not differ from symptomatic (20.8) or asymptomatic (20.5) residents (p-value 0.624). The frequency of a/presymptomatic residents compared to staff suggests that a/presymptomatic
residents could be unrecognized symptomatic cases. However, symptomatic and presymptomatic/unrecognized symptomatic residents both have the same potential for viral shedding. The high prevalence symptomatic staff found in facility-wide testing suggests that
staff has difficulty attributing their symptoms to possible SARS-CoV-2 infection. Weekly testing was an effective strategy for early identification of SARS-Cov-2 cases, resulting in fast isolation and mitigation of this outbreak. |
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Van Wyk de Vries, MaximillianS, Rambabu, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie |
We create an agent-based epidemiology model based on both COVID-19 clinical and epidemiological data and geographic
data. We first model 35 scenarios with varying natural disaster timing and duration for a COVID-19 outbreak in a theoretical region. We then evaluate the potential effect of an eruption of Vesuvius volcano on the spread of COVID-19 in Campania, Italy. Our
objective is to determine if the occurrence of a natural disaster during the COVID-19 pandemic is likely to increase infection cases and disease related fatalities. In a majority of cases, the occurrence of a natural disaster increases the number of disease
related fatalities. When the natural disaster occurs at the beginning of the outbreak within a given region, there is little to no increase in the progression of disease spread. However, the occurrence of a natural disaster close to the peak of infections
may increase the number of fatalities by more than five-fold. In a theoretical test case, for a natural disaster that occurred fifty days after first infection case, the median increase in fatalities is 2%, 59%, and 180% for a 2, 14, and 31-day long natural
disaster respectively, when compared to the no natural disaster scenario. We propose that the compound risk from natural disasters is greatest in the case of already widespread disease outbreak. The key risk factors for increase in spread of infection and
disease related fatalities are the timing of the natural disaster relative to the peak in infections and the duration of the natural disaster. |
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Varlamov, DmitriyA, Blagodatskikh, et al |
PLoS Biol |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
To aid in the development of diagnostic kits for rapid and sensitive detection of the virus, we evaluated a combination
of polymerase chain reaction (PCR) and isothermal nucleic acid amplification techniques. Here, we compared conventional PCR and loop-mediated isothermal amplification (LAMP) methods with hybrid techniques such as polymerase chain displacement reaction (PCDR)
and a newly developed PCR-LAMP method. We found that the hybrid methods demonstrated higher sensitivity and assay reaction rates than those of the classic LAMP and PCR techniques and can be used to for SARS-CoV-2 detection. The proposed methods based on the
modern hybrid amplification techniques markedly improve virus detection and, therefore, can be extremely useful in the development of new diagnostic kits. |
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Seroprevalence of Antibodies to SARS-CoV-2 in US
Blood Donors |
Vassallo, RalphR, Bravo, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
We report the seroprevalence of total immunoglobulin directed against the S1 spike protein of SARS-CoV-2 in US blood
donors. Unique non-CCP donor sera from June 1-July 31, 2020 were tested with the Ortho VITROS Anti-SARS-CoV-2 total immunoglobulin assay (positive: signal-to-cutoff (S/C) =>1). Unique donors (n=252,882) showed an overall seroprevalence of 1.83% in June (1.37%)
and July (2.26%), with the highest prevalence in northern New Jersey (7.3%). In a subset of donors with demographic information (n=189,565), higher odds of antibody reactivity were associated with non-Hispanic Native American/Alaskan (NH-NAA/A) and Black (NH-B),
and Hispanic (H) race/ethnicity, age 18-64, middle school or lesser education, blood Group A, and never or non-recent donor status. In positive donors (n=2,831), antibody signal was associated with male sex, race/ethnicity (NH-NAA/A, NH-B and H) and geographic
location. Seroprevalence remains low in US blood donors but varies significantly by region. Temporal trends in reactivity may be used to gauge the effectiveness of public health measures. Before generalizing these data from healthy donors to the general population
however, rates must be corrected for false positive test results among low prevalence test subjects and adjusted to match the wider demography. |
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Coding Complete Genome Sequences of Twenty-three
SARS-CoV-2 Strains Isolated in the Philippines |
Velasco, JohnS, Chinnawirotpisan, et al |
medRxiv |
Coronavirology| Coronavirologie |
Here, we report the coding complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)
strains from the Philippines. Sequences were obtained from nasopharyngeal and oropharyngeal swabs from COVID-19 positive patients. Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes. |
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Velazquez, Anjelina, Bustria, et al |
medRxiv |
Epidemiology| Épidémiologie |
During the SARS-CoV-2 outbreak that caused the coronavirus pandemic it is important now more than ever that scientists
and public health officials work side-by-side and use their available resources to track patient information from those that have been affected by the novel coronavirus. The ability to track the disease helps identify possible trends and patterns that can
be used by public health officials to make more informed decisions. Tracking data like this may be the key to helping states and countries safely re-open. However, when analyzing large collections of data there is the occurrence of confounding factors such
as biases in patient sampling. In this project, a massive collection of COVID-19 data was analyzed, and explored potential biases in patient sampling were explored. |
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Vella, Laura, Giles, et al |
medRxiv |
Clinical data| Données cliniques Immunology | Immunologie |
Pediatric COVID-19 following SARS-CoV-2 infection is associated with fewer hospitalizations and often milder disease
than in adults. A subset of children, however, present with Multisystem Inflammatory Syndrome in Children (MIS-C) that can lead to vascular complications and shock, but rarely death. The immune features of MIS-C compared to pediatric COVID-19 or adult disease
remain poorly understood. We analyzed peripheral blood immune responses in hospitalized SARS-CoV-2 infected pediatric patients (pediatric COVID-19) and patients with MIS-C. MIS-C patients had patterns of T cell-biased lymphopenia and T cell activation similar
to severely ill adults, and all patients with MIS-C had SARS-CoV-2 spike-specific antibodies at admission. A distinct feature of MIS-C patients was robust activation of vascular patrolling CX3CR1+ CD8 T cells that correlated with use of vasoactive medication.
Finally, whereas pediatric COVID-19 patients with acute respiratory distress syndrome (ARDS) had sustained immune activation, MIS-C patients displayed clinical improvement over time, concomitant with decreasing immune activation. Thus, non-MIS-C versus MIS-C
SARS-CoV-2 associated illnesses are characterized by divergent immune signatures that are temporally distinct and implicate CD8 T cells in clinical presentation and trajectory of MIS-C. |
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Veyrenche, Nicolas, Bollore, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
The implementation of rapid diagnostic tests (RDTs) may enhance the efficiency of SARS-CoV-2 testing, as RDTs are widely
accessible and easy to use. The aim of this study was to evaluate the performance of a diagnosis strategy based on a combination of antigen and IgM/IgG serological RDTs. Plasma and nasopharyngeal samples were collected between 14 March and 11 April 2020 at
hospital admission from 45 patients with RT-PCR confirmed COVID-19 and 20 negative controls. SARS-CoV-2 antigen (Ag) was assessed in nasopharyngeal swabs using the Coris Respi-Strip. For IgM/IgG detection, SureScreen Diagnostics and Szybio Biotech RDTs were
used in addition to laboratory assays (Abbott Alinity i SARS-CoV-2 IgG and Theradiag COVID-19 IgM ELISA). Using the Ag RDT, 13 out of 45 (29.0%) specimens tested positive, the sensitivity was 87.0% for Cycle Threshold (CT) values ≤ 25 and 0% for CT values
> 25. IgG detection was associated with high CT values and the amount of time after the onset of symptoms. The profile of isolated IgM on RDTs was more frequently observed during the first and second week after the onset of symptoms. The combination of Ag
and IgM/IgG RDTs enabled the detection of up to 84.0% of COVID-19 confirmed cases at hospital admission. Antigen and antibody-based RDTs showed suboptimal performances when used alone. However when used in combination, they are able to identify most COVID-19
patients admitted in an emergency department. |
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Villalobos Dintrans, Pablo, Castillo, et al |
medRxiv |
Epidemiology| Épidémiologie |
Chile has been heavily affected by the COVID-19 pandemic. This article analyzes the association of different groups
of factors-demographic, health-related, and socioeconomic-on COVID-19-related outcomes. Using the municipalities of the Metropolitan Region the study looks at the role of time dynamics, space and place in cases and deaths during a 100-days period. Results
show that common and idiosyncratic elements that explain the prevalence and dynamics of infections and mortality, with an important role of social determinants of health, particularly multidimensional poverty index and use of public transportation, in explaining
differences in outcomes. The article contributes to the understanding of the determinants of COVID-19 outcomes in a specific region, but also highlights the need to consider time-space dynamics and social determinants as key in the analysis. The results are
specially relevant for similar research in unequal settings. |
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Villarreal, Alcibiades, Rangel, et al |
medRxiv |
Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection
d'agents pathogènes Immunology | Immunologie |
Authors aimed first to evaluate a lateral flow assay ability to identify specific IgM and IgG antibodies against SARS-CoV-2
and second, to report the seroprevalence of these antibodies among health care workers and healthy volunteer blood donors in Panama. We found an overall antibody seroprevalence of 11.6% (95% CI 8.5-15.8%) among both health care workers and healthy blood donors.
Findings suggest this lateral flow assay could contribute significantly to implementing seroprevalence testing in locations with active community transmission of SARS-CoV-2. |
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SalivaDirect: A simplified and flexible platform
to enhance SARS-CoV-2 testing capacity |
Vogels, ChantalBF, Watkins, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Authors developed SalivaDirect, which received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration
on August 15th, 2020, to resolve the current bottlenecks of COVID-19 testing. SalivaDirect is a flexible and inexpensive ($1.21-$4.39/sample in reagent costs) option to help improve SARS-CoV-2 testing capacity. |
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Wallentin, L, Lindbäck, et al |
Eur Heart J |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study explored the associations between higher plasma level of soluble ACE2 (sACE2) and clinical factors, cardiovascular
biomarkers, and genetic variability. Plasma and DNA samples were obtained from two international cohorts of elderly patients with atrial fibrillation (n = 3999 and n = 1088) and the sACE2 protein level was measured. Higher levels of sACE2 were statistically
significantly associated with male sex, cardiovascular disease, diabetes, and older age. The sACE2 level was most strongly associated with the levels of high-sensitive cardiac troponin T (hs-cTnT), N-terminal probrain natriuretic peptide (NT-proBNP), growth
differentiation factor 15 (GDF-15). When adjusting for these biomarkers, only male sex remained associated with sACE2. We found no statistically significant genetic regulation of the sACE2 level. |
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Virtual screening for functional foods against the main protease of SARS-CoV-2 |
Wang, J, Zhang, et al |
J Food Biochem |
Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
Here, 10,870 ligands were employed and screened by the molecular docking, which involved 12 kinds of functional foods
(carbohydrates, fatty acids, phospholipids, vitamin, β-sitosterol, flavonoids, nordihydroguaiaretic acid, curcumin, nootkatone, β-pinene, tincturoid, betulinic acid, and their isomers/analogs/derivatives). Then, 60 ligands were obtained with the good docking
affinity. Most of them belong to quercetrin and its isomers/analogs/derivatives, which also showed the highest affinity for the main protease of SARS-CoV-2. The dynamic simulation indicated that quercetrin-protease and quercetrin-analog-protease showed the
excellent stability. Compared with reported docking results, quercetrin should be the best inhibitor for the main protease of SARS-CoV-2. Considering the green and white tea are rich in quercetrin and its isomers/analogs/derivatives, tea and relative beverages
may become a good option to regulate our metabolism and help us to overcome this special time. |
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Wang, Jing Gennie, Liu, et al |
medRxiv |
Clinical data| Données cliniques Healthcare Response | Réponse des soins de santé |
The objective of this study was to describe outcomes with high-flow oxygen delivered through nasal cannula (HFNC) and
non-invasive positive pressure ventilation (NIPPV) in COVID-19 AHRF and identify individual factors associated with failure. A significant proportion of patients receiving non-invasive respiratory modalities for COVID-19 AHRF achieved successful discharge
without requiring ETI, with lower success rates among those with cardiovascular disease or more severe hypoxia. |
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Wang, Tingyan, Smith, et al |
medRxiv |
Clinical data| Données cliniques |
Authors discuss COVID-19 and how it has been associated with deranged liver biochemistry in studies from China, Italy
and the USA. In this UK population, liver biochemistry is commonly deranged in patients with COVID-19 but only baseline low albumin and a rising alkaline phosphatase over time are prognostic markers for death. |
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Wang, X, Liu, et al |
J Clin Endocrinol Metab |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
This study looked at the impacts of type 2 diabetes mellitus (T2DM) on disease severity, therapeutic effect, and mortality
of patients with COVID-19. A total of 663 patients with COVID-19 were included, while 67 patients with T2DM accounted for 10.1% of the total. Compared with patients with COVID-19 without T2DM, those with T2DM were older (aged 66 years vs 57 years; P < 0.001)
and had a male predominance (62.7% vs 37.3%; P = 0.019) and higher prevalence of cardiovascular diseases (61.2% vs 20.6%; P < 0.001) and urinary diseases (9% vs 2.5%; P = 0.014). Patients with T2DM were prone to developing severe (58.2% vs 46.3%; P = 0.002)
and critical COVID-19 (20.9% vs 13.4%; P = 0.002) and having poor therapeutic effect (76.1% vs 60.4%; P = 0.017). But there was no obvious difference in the mortality between patients with COVID-19 with and without T2DM (4.5% vs 3.7%; P = 0.732). Multivariate
logistic regression analysis identified that T2DM was associated with poor therapeutic effect in patients with COVID-19 (OR 2.99; 95% CI], 1.07-8.66; P = 0.04). Moreover, having a severe and critical COVID-19 condition and decreased lymphocytes were independent
risk factors associated with poor therapeutic effect in patients with COVID-19 with T2DM. |
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Wang, Xiaoli, Gao, et al |
medRxiv |
Epidemiology| Épidémiologie Immunology | Immunologie |
Authors evaluate the seroprevalence of COVID-19 in Beijing. The seroprevalence of COVID-19 in Beijing was estimated
< 0.17%. The seroprevalence of COVID-19 was low in April suggesting that community-wide spread was prevented in Beijing. |
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PMC7505633; Which states and cities protect residents from water shutoffs in the
COVID-19 pandemic? |
Warner, ME, Zhang, et al |
Util Policy |
Public Health response| Interventions de santé publique |
Many U.S. states and cities have imposed water disconnection moratoriums during the COVID-19 pandemic. Using logistic
and Cox Proportional-Hazards models, we assess factors that differentiate which governments imposed moratoriums. States, which have economic regulation of private water utilities, were more likely to impose moratoriums, and those with higher COVID-19 case
rates imposed moratoriums earlier. States with unified Republican Control and cities with more 2016 Trump voters were less likely to impose moratoriums on water disconnection. Cities in states without statewide moratoriums, were more likely to impose moratoriums
if they had higher income, more minority residents, and more income inequality. |
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Early detection of seasonality and second waves prediction
in the COVID-19 pandemic |
Watanabe, Marcio |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission |
In this study, authors use statistical methods to show how to detect the presence of seasonality in a pandemic at the
beginning of the seasonal period and that seasonality strongly affects SARS-coV-2 transmission. These predictions provide critical information for public health officials to plan their actions to combat the new coronavirus disease and to identify and measure
seasonal effects in a future pandemic. |
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Watson, Andrew, Haraldsdottir, et al |
medRxiv |
Epidemiology| Épidémiologie |
The purpose of this study was to determine the case and incidence rates of COVID-19 among youth soccer players and
evaluate the relationship with background COVID-19 risk and phase of return to play. The incidence of COVID-19 among youth soccer athletes is relatively low when compared to the background incidence among children in the United States and the local general
population. No relationship was identified between club COVID-19 incidence and phase of return to soccer. Youth soccer clubs universally report implementing a number of risk reduction procedures. |
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Clinical criteria for COVID-19-associated hyperinflammatory syndrome: a cohort
study |
Webb, BrandonJ, Peltan, et al |
The Lancet Rheumatology |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
BackgroundA subset of patients with COVID-19 develops a hyperinflammatory syndrome that has similarities with other
hyperinflammatory disorders. However, clinical criteria specifically to define COVID-19-associated hyperinflammatory syndrome (cHIS) have not been established. We aimed to develop and validate diagnostic criteria for cHIS in a cohort of inpatients with COVID-19. |
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The Use of Psychoactive Substances in the Context
of the Covid-19 Pandemic in Brazil |
Weber, Cesar Augusto Trinta, Monteiro, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The objective of this study was to investigate the use of psychoactive substances in the context of the Covid-19 pandemic
in Brazil. For a better understanding of the pattern use of psychoactive substances during the Covid-19 pandemic and the adverse effects on human behavior and mental disorders, careful longitudinal studies must be developed, due to the great interest in the
knowledge of adaptive responses when people's lives are at risk. |
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Wei, L, Wen, et al |
J Chem Inf Model |
Coronavirology| Coronavirologie Therapeutics| Thérapeutique |
This article presents a new protocol, called Cov_FB3D, which involves the in silico assembly of potential novel covalent
inhibitors by identifying the active fragments in the covalently binding site of the target protein. An in-depth test of this protocol against the crystal structures of 15 covalent complexes consisting of BTK inhibitors, KRAS inhibitors, EGFR inhibitors,
EphB1 inhibitors, MAGL inhibitors, and MAPK inhibitors revealed that most of these inhibitors could be de novo reproduced from the fragments by Cov_FB3D. The binding modes of most generated reference poses could accurately reproduce the known binding mode
of most of the reference covalent adduct in the binding site (RMSD ≤ 2 Å). In particular, most of these inhibitors were ranked in the top 2%, using the BA-SAMP strategy. Notably, the novel human ALDOA inhibitor (T1) with potent inhibitory activity (0.34 ±
0.03 μM) and greater synthetic accessibility was successfully de novo designed by this protocol. The positive results confirm the abilities of Cov_FB3D protocol. |
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Williams, Lynn, Rollins, et al |
medRxiv |
Public Health response| Interventions de santé publique |
Authors report on the social patterning of self-reported positive changes experienced during COVID-19 national lockdown
in Scotland. Findings begin to illuminate the complexity of the unanticipated effects of national lockdown and will be used to support future intervention development work sharing lessons learned from lockdown to increase positive health change amongst those
who may benefit |
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Willingham, StephenB, Criner, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique Immunology | Immunologie |
Authors report on CPI-006, a humanized FcγR binding-deficient IgG1 anti-CD73 antibody that blocks CD73 enzymatic activity
and directly activates CD73+ B cells, inducing differentiation into plasmablasts, immunoglobulin class switching, and antibody secretion independent of adenosine. The preliminary results suggest that CPI-006 activates B cells and may enhance and prolong anti-SARS-CoV-2
antibody responses in patients with COVID-19. |
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Wilson, AmandaM, Aviles, et al |
medRxiv |
Modelling/ prediction| Modélisation/prédiction Transmission |
Authors model uncertainty in the shape and orientation of an exhaled virus-containing plume and in inhalation parameters,
and measure uncertainty in distance as a function of Bluetooth attenuation. They capture a 10-fold range of risk using 6 infectiousness values, 11-fold range using 3 Bluetooth attenuation bins, ~6-fold range from exposure duration given the 30 minute duration
cap imposed by the Google/Apple v1.1, and ~11-fold between the beginning and end of 14 day quarantine. |
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Wilson, ClaireA, Dalton-Locke, et al |
medRxiv |
Public Health response| Interventions de santé publique Healthcare Response | Réponse
des soins de santé |
The aim of this study was to explore staff perceptions of the impact of the COVID-19 pandemic on mental health service
delivery and outcomes for women who were pregnant or in the first year after birth (perinatal women). Safeguarding and other risk assessment procedures must remain robust in spite of modifications made to service delivery during pandemics. |
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Wisniewski, Oskar, Kozak, et al |
medRxiv |
Epidemiology| Épidémiologie |
In this work authors analyze the impact of weather factors such as temperature, relative humidity, wind speed and ground
level ozone concentration on the number of COVID-19 cases in Warsaw, Poland. The obtained results show an inverse correlation between ground level ozone concentration and the daily number of COVID-19 cases. |
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Wondimu, Wondimagegn, Ejigu, et al |
Research Square prepub |
Public Health response| Interventions de santé publique |
This cross-sectional study assessed the COVID-19 prevention practices in three zones of Southwest Ethiopia. In this
study, 803 participants participated. About two-thirds (64.7%) of the respondents had a history of going to crowded places, while only 30.3% of the participants had a history of wearing a mask when leaving home. Two-thirds of the respondents had a history
of maintaining their distance at 2 meters (64.4%) and washing their hands with soap and water or using alcohol-based hand sanitizers (64.8%). Generally, less than two-thirds (59.4%) of study participants had a good practice of COVID-19 prevention methods.
Urban residence, good knowledge, positive attitude, intention to seek care, and perceived mortality were positively associated with good practice. |
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Wong, KennethCY, So, et al |
medRxiv |
Epidemiology| Épidémiologie Clinical data| Données cliniques |
Authors built machine learning (ML) models to predict the risk of developing severe or fatal infections from COVID-19,
and to evaluate the major risk factors involved. The top five contributing factors for severity were age, waist-hip ratio (WHR), HbA1c, number of drugs taken and gamma-glutamyl transferase levels. For prediction of mortality, the top features were age, systolic
blood pressure, waist circumference (WC), urea and WHR. |
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Wood, Rachael, Thomson, et al |
medRxiv |
Epidemiology| Épidémiologie Transmission |
Authors examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalization
with COVID-19, and/or testing positive for COVID-19 infection of any severity (any case of Covid-19). Increased household exposure to young children was associated with an attenuated risk of testing positive for SARS-CoV-2 and appeared to also be associated
with an attenuated risk of COVID-19 disease severe enough to require hospitalisation. |
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Wrobel, AntoniG, Benton, et al |
Research Square prepub |
Coronavirology| Coronavirologie |
Coronaviruses of bats and pangolins are implicated in the origin and evolution of the pandemic SARS-CoV-2. We show
that Spikes from Pangolin-CoVs, closely related to SARS-CoV-2, bind strongly to human and pangolin ACE2 receptors. We also report Cryo-EM structure of Pangolin-CoV S and show it adopts a fully-closed conformation and that, aside from the Receptor-Binding Domain,
it resembles the spike of a bat coronavirus RaTG13 more than that of SARS-CoV-2. |
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Shortages of Staff in Nursing Homes During the COVID-19 Pandemic: What are the
Driving Factors? |
Xu, H, Intrator, et al |
J Am Med Dir Assoc |
Healthcare Response | Réponse des soins de santé |
This study examines the prevalence and factors associated with shortages of NH staff during the COVID-19 pandemic.
Of the 11,920 NHs, 15.9%, 18.4%, 2.5%, and 9.8% reported shortages of licensed nurse staff, nurse aides, clinical staff, and other staff, respectively. Georgia and Minnesota reported the highest rates of shortages in licensed nurse and nurse aides (both >25%).
Multivariate regressions suggest that shortages in licensed nurses and nurse aides were more likely in NHs having any resident with COVID-19 (adjusted odds ratio AOR] = 1.44, 1.60, respectively) and any staff with COVID-19 (AOR = 1.37, 1.34, respectively).
Having 1-week supply of PPE was associated with lower probability of staff shortages. NHs with a higher proportion of Medicare residents were less likely to experience shortages |
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Xun, Helen, Shallal, et al |
medRxiv |
Healthcare Response | Réponse des soins de santé |
Authors utilized cost-effective, on-demand 3D printing (3DP) technology to produce critical components for a novel
ventilator multiplexer system, Vent-Lock, to split one ventilator or anesthesia gas machine between two patients. Studies underscore that while possible, ventilator multiplexing is a complicated synergy between machine settings, circuit modification, and patient
monitoring. |
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Yadav, Suryakant, Yadav, et al |
medRxiv |
Epidemiology| Épidémiologie |
This study aims to analyze the growth rates of the daily confirmed cases in India and to provide an expected count
of the peak of daily confirmed cases. This study based on moments of the distribution of the daily confirmed cases of COVID-19 disease unravels the uncertainty about the peak and curvature of COVID-19 disease. |
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Limited specificity of serologic tests for SARS-CoV-2
antibody detection, Benin, Western Africa |
Yadouleton, Anges, Sander, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Testing 68 RT-PCR-confirmed COVID-19 cases and controls from Benin, Western Africa with commercially available SARS-CoV-2
antibody ELISAs revealed up to 25% false-positive results, likely due to unspecific antibody responses elicited by acute malaria. Serologic tests must be carefully evaluated to robustly assess SARS-CoV-2 spread and immunity in tropical regions. |
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The assessment of the serum levels of TWEAK and prostaglandin F2? in COVID - 19 |
YalÇin Kehrİbar, D, CİhangİroĞlu, et al |
Turk J Med Sci |
Clinical data| Données cliniques |
This study investigated the possible roles of tumor necrosis factor-like weak inducer of apoptosis (TWEAK) / Fn14 pathway
and leukotrienes (LT) in uncontrolled immune response that occurs in severe acute respiratory syndrome coronavirus 2 (SARS - CoV - 2). Compared with the healthy control group, TWEAK, LTE4, and PGF2? levels were higher in the group of SARS - CoV - 2 infection
without lung involvement. In the group of SARS - CoV - 2 infection with lung involvement, age, fibrinogen, sedimentation, C - reactive protein and ferritin, TWEAK, LTE4, and PGF2? levels were higher, and lymphocyte levels were lower compared with the asymptomatic
group. |
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Yan, Huadong, Valdes, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique |
This study aimed to investigate whether specific medications used in the treatment chronic diseases affected either
the development and/ or severity of COVID-19 in a cohort of 610 COVID-19 cases and 48,667 population-based controls from Zheijang, China. Drugs used in the treatment of hypertension and diabetes influence the risk of development of COVID-19, but, not its severity. |
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Impact of stopping therapy during the SARS-CoV-2
pandemic in persons with lymphoma |
Yang, Shenmiao, Dong, et al |
medRxiv |
Public Health response| Interventions de santé publique |
Authors discuss the impact of COVID-19 on medical care for persons with cancer. During the SARS-CoV-2 pandemic lymphoma
patients and their caregivers had significantly higher incidence of anxiety compared with normals. Lymphoma respondents reported better health-related quality-of-life (HRQoL) compared with pre-pandemic controls. |
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Yildirim, Fatma, Yildiz Gulhan, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
In this study, authors aimed to report the features of the patients that were diagnosed and treated as possible COVID-19
cases whose multiple nasopharyngeal swab samples were negative by RT-PCR but serological IgM/IgG antibody against SARS-CoV-2 were detected by rapid antibody test. The study demonstrated the feasibility of COVID-19 diagnosis based on rapid antibody test in
the cases of patients whose RT-PCR samples were negative. |
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Young, Stephen, Taylor, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
In this article, two studies were completed to determine clinical performance of the BD Veritor System for Rapid Detection
of SARS-CoV-2 antigen (Veritor), a chromatographic immunoassay that detects the SARS-CoV-2 nucleocapsid antigen as a point-of-care test. Veritor met FDA-EUA acceptance criteria for SARS-CoV-2 antigen testing for the 0-5 and 0-6 DSO ranges. Veritor and Sofia
2 showed a high degree of agreement for SARS-CoV-2 detection. |
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Yu, Wenhua, Xu, et al |
medRxiv |
Epidemiology| Épidémiologie |
Authors aimed to assess whether the association between cold temperature and all-cause mortality in the pandemic period
has changed compared to non-COVID-19 period (2015-2019) in Italy. The findings suggest that the COVID-19 pandemic enhanced the risk of cold temperature on mortality in Italy, particularly among the elderly people. |
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Yuen, Rachel, Steiner, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
To measure lower quantities of SARS-CoV-2 IgM, IgG, and IgA with higher resolution than existing assays, authors developed
a new ELISA protocol with a distinct plate washing procedure and timed plate development via use of a standard curve. They propose that this improved ELISA protocol, which is straightforward to perform, low cost, and uses readily available commercial reagents,
is a useful tool to elucidate new information about SARS-CoV-2 infection and has promising implications for improved detection of all analytes measurable by this platform. |
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Clinical Thrombosis Rate was not Increased in a Cohort
of Cancer Patients with COVID-19 |
Zavras, PhaedonD, Kabarriti, et al |
medRxiv |
Clinical data| Données cliniques |
Authors aimed to assess whether COVID-19 further increased the risk of TE events in a cancer population who tested
positive for COVID-19 at Montefiore Medical Center, Bronx, NY. Findings support the need for larger studies in the COVID-19+ cancer population. |
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A Multi-center Study of COVID-19 with Multivariate
Prognostic Analysis |
Zeng, Wen, Feng, et al |
medRxiv |
Clinical data| Données cliniques Therapeutics| Thérapeutique |
Authors compared the clinical characteristics, laboratory findings, CT images, and treatment of COVID-19 patients from
two different cities in China. Early isolation, early diagnosis, and early initiation of management can slow down the progression and spread ofCOVID-19. |
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Monocyte volumetric parameters and lymph index are increased in SARS-CoV-2 infection |
Zeng, X, Xing, et al |
Int J Lab Hematol |
Clinical data| Données cliniques |
In this retrospective case‐control study, clinical data of 155 patients including contact history, initial symptoms,
routine hematology measurement, chest computed tomography (CT), and RT‐PCR analysis were reviewed and collected from February 14 to February 29, 2020, in The Wuhan Union Hospital, Wuhan China. The mean monocyte volume (MMV), monocyte distribution width (MDW),
mean lymphocyte volume (LV), lymphocyte distribution width (LV‐SD), and lymph index were significantly increased in COVID‐19 patients compared to those in the controls. No significant differences in neutrophil volumetric parameters or WBC between the patients
and the controls were observed. |
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Genomic characterization and phylogenetic evolution of the SARS-CoV-2 |
Zhang, RH, Ai, et al |
Acta Virol |
Coronavirology| Coronavirologie |
This study reports the genomic characterization and phylogenetic evolution of SARS-CoV-2. The genome sequences of SARS-CoV-2
were very similar, showing 99.6-100% sequence identity. Notably, SARS-CoV-2 was closely related (with 88% identity) to bat-SARS-like coronavirus, but was more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic tree of the complete viral
genome showed that the virus clustered with bat SARS-like coronavirus. The results of the similarity between SARS-CoV-2 and related viruses did not identify any potential genomic recombination events. Therefore, it seems like that the SARS-CoV-2 might be originally
hosted by bats, and might have been transmitted to humans via intermediate hosts of currently unknown wild animal(s). |
|
Zhang, Tingting, Robin, et al |
medRxiv |
Public health interventions*| Interventions de santé publique |
Authors aimed to rapidly evaluate the impact and effectiveness of advice to travelers communication materials for passengers
in the early stages of the pandemic. The study provides fresh insights into the importance of taking greater account of diverse information sources and of the need for public assurance in creating public health information materials to address global health
threats. |
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Zhao, Linlu, Ismail, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The objective of this study was to establish a preliminary expert stakeholder perspective on the relative importance
of pandemic immunisation strategies for different COVID-19 pandemic scenarios at the time of initial COVID-19 vaccine availability. The findings of this study provide a timely, preliminary Canadian expert perspective on priority COVID-19 pandemic immunisation
strategies to guide early public health planning for an eventual COVID-19 immunisation program. |
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SCOAT-Net: A Novel Network for Segmenting COVID-19
Lung Opacification from CT Images |
Zhao, Shixuan, Li, et al |
medRxiv |
Clinical data| Données cliniques |
Authors proposed a novel spatial and channel-wise coarse-to-fine attention network (CAT-Net) inspired by the biological
vision mechanism, which is for the segmentation of COVID-19 lung opacification from CT Images. Experiments show that the proposed CAT-Net achieves better results compared to state-of-the-art image segmentation networks. |
|
Zhou, Haiwei, Liu, et al |
medRxiv |
Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes |
Authors performed a collaborative study to estimate the NAT-detectable units as viral genomic equivalent quantity (GEQ)
of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a
unified solution for assay development, quality control, and regulatory surveillance. |
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Zhu, Hongjun, Huang, et al |
medRxiv |
Epidemiology| Épidémiologie |
It is well known that the transmissibility can be measured by reproduction number. For this reason, the large amount
of research focuses on the estimations of reproduction number of COVID-19. However, these previous results are controversial and even misleading. To alleviate this problem, Liu et al advised to use averaging technique. Unfortunately, the fluctuant consequence
principally arises from data error or model limitations rather than stochastic noise, where the averaging technique doesn't work well. |
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Zhu, Siyi, Gao, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The objective of this study was to estimate the prevalence of disability and anxiety in Covid-19 survivors at discharge
from hospital and analyze relative risk by exposures. A significant proportion of Covid-19 survivors had disability and anxiety at discharge from hospital. Health systems need to be prepared for an additional burden resulting from rehabilitation needs of
Covid-19 survivors. |
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Testing, Testing: What SARS-CoV-2 testing services
do adults in the United States actually want? |
Zimba, Rebecca, Kulkarni, et al |
medRxiv |
Public Health response| Interventions de santé publique |
The objective of this study was to determine important drivers of decisions to obtain a SARS-CoV-2 test in the context
of increasing community transmission. An online survey, embedded in an existing cohort study, was conducted during July 30 - September 8, 2020. Testing strategies that offer both PCR and serology with non-invasive methods and rapid turnaround time would likely
have the most uptake and engagement among residents in communities with increasing community transmission of SARS-CoV-2. |
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Ahmadi, ZH, Mousavizadeh, et al |
J Card Surg |
Review Literature| Revue de littérature |
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Arslan, BA, Timucin, et al |
Acta Virol |
Review Literature| Revue de littérature |
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Axfors, Cathrine, Schmitt, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: systematically identified published and unpublished RCTs by September 14, 2020 (ClinicalTrials.gov, WHO International
Clinical Trials Registry Platform, PubMed, Cochrane COVID-19 registry).We found no benefit of hydroxychloroquine or chloroquine on the survival of COVID-19 patients. |
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Comorbidities and Susceptibility to COVID-19: A Generalized
Gene Set Meta-Analysis Approach |
Beckman, MicaelaF, Igba, et al |
medRxiv |
Review Literature| Revue de littérature |
MA |
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Bilezikian, JP, Bikle, et al |
Eur J Endocrinol |
Review Literature| Revue de littérature |
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Boozari, M, Hosseinzadeh, et al |
Phytother Res |
Review Literature| Revue de littérature |
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Byambasuren, Oyungerel, Cardona, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: searched PubMed, Embase, Cochrane COVID-19 trials, and Europe PMC (which covers pre-print platforms such as
MedRxiv) from January 2019 to 20 Jul 2020. Our estimates of the prevalence of asymptomatic COVID-19 cases and asymptomatic transmission rates are lower than many highly publicized studies, but still sufficient to warrant policy attention. Further robust epidemiological
evidence is urgently needed, including in sub-populations such as children, to better understand the importance of asymptomatic cases for driving spread of the pandemic. |
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Cabarkapa, S, Nadjidai, et al |
Brain Behav Immun Health |
Review Literature| Revue de littérature |
Rapid SR: searched three electronic databases (PubMed, MEDLINE and CINAHL), dating back to 2002 until the 21st of
August 2020.Psychological implications are largely negative and require greater attention to be mitigated, potentially through the involvement of psychologists, raised awareness and better education. The current knowledge of therapeutic interventions suggests
they could be beneficial but more long-term follow-up is needed. |
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Scoping Review Supporting decision-making on allocation
of ICU beds and ventilators in pandemics |
Cardona, Magnolia, Dobler, et al |
medRxiv |
Review Literature| Revue de littérature |
ScR: searched the databases Medline and Embase on 1st May 2020 for English language articles published since 1st January
2002. Prognostic indicators and other decision tools presented here can be combined to create locally-relevant triage algorithms for clinical services and policy makers deciding about allocation of ICU beds and ventilators during a pandemic. Community awareness
of the triage protocol is recommended to build trust and alleviate anxiety among the public.
|
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Chatterjee, S, Anton, et al |
J Card Surg |
Review Literature| Revue de littérature |
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Model-based and model-free characterization of epidemic
outbreaks |
Dehning, Jonas, Spitzner, et al |
medRxiv |
Review Literature| Revue de littérature |
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Del Riccio, Marco, Lorini, et al |
medRxiv |
Review Literature| Revue de littérature |
SR: search was performed on 31 August, 2020, by interrogating the MEDLINE, Embase and medRxiv. None of the studies
that were reviewed (n=12) found a significant increase in the risk of infection or in the illness severity or lethality, while some reported significantly inverse associations.
|
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Du, Meixia, Zhao, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: PubMed, Scopus, Embase, CNKI, China biomedical literature database (CBM), and WanFang data knowledge were searched
for articles published from January 1, 2020, to July 16, 2020. The increase in MAP, heart rate and respiratory rate, as well as the decrease in SBP, DBP and SpO2 are all independent risk factors for death in patients with COVID-19. These factors are simple
and easy to monitor, and individualized treatment can be given to patients in time, reducing the mortality rate and improving treatment efficiency |
|
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Variation of SARS-CoV-2 viral loads by sample type,
disease severity and time: a systematic review |
Edwards, Thomas, Santos, et al |
medRxiv |
Review Literature| Revue de littérature |
SR: searches were conducted in MEDLINE, EMBASE, BioRxiv and MedRxiv. . VLs are higher in saliva and sputum and in individuals
who are asymptomatic of with severe COVID-19. Diagnostic testing strategies should consider that VLs vary by sample type, disease severity and time since symptoms onset.
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Garcia-Albeniz, Xabier, Del Amo, et al |
medRxiv |
Review Literature| Revue de littérature |
MA: search of PubMed, Embase, medRxiv, and clinicaltrials.gov. The available evidence indicates that HCQ reduces the
risk of COVID-19 by about 20%. Yet the findings from the randomized trials were widely interpreted as evidence of lack of effectiveness of HCQ, simply because they were not statistically significant when taking them individually. |
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Griswold, Dylan Paul, Gempeler, et al |
medRxiv |
Review Literature| Revue de littérature |
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Hassanipour, Soheil, Bagheri Faradonbeh, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: searched PubMed via LitCovid hub, Embase, Scopus, Web of sciences, and Google scholar on 07 April 2020. Fever
was the most common signs and symptoms in pregnant women with COVID-19. Among the laboratory tests, the highest amount was related to elevated neutrophil ratio.
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He, Zhe, Erdengasileng, et al |
medRxiv |
Review Literature| Revue de littérature |
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Hopfer, H, Herzig, et al |
Histopathology |
Review Literature| Revue de littérature |
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Kanamori, H, Weber, et al |
Clin Infect Dis |
Review Literature| Revue de littérature |
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Kharoud, HarmeetK, Asim, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: PubMed, MEDLINE, and SCOPUS databases were searched to include studies conducted between January 1, 2020, and
July 15, 2020. The most prevalent laboratory findings in COVID-19 children were elevated Creatinine Kinase and neutropenia. These were followed by elevated LDH, thrombocytosis, lymphocytosis, neutrophilia, elevated D Dimer, Elevated CRP, elevated ESR, leukocytosis,
elevated AST and leukopenia. There was a low prevalence of elevated ALT and lymphopenia in children with COVID- 19.
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Lazarus, Gilbert, Audrey, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: Searches were conducted through PubMed, Ovid EMBASE, CENTRAL, EBSCO MEDLINE, CINAHL, Scopus, and WHO COVID-19
database for studies published up to 8 September 2020. High level of FBG at admission was independently associated with poor prognosis in COVID-19 patients.
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COVID-19 Infection: Concise Review Based on the Immunological Perspective |
Lotfinejad, P, Asadzadeh, et al |
Immunol Invest |
Review Literature| Revue de littérature |
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Lugli, Gianmarco, Ottaviani, et al |
medRxiv |
Review Literature| Revue de littérature |
SR: literature search was performed using PubMed, Embase, and Scopus, restricting the search to the main outbreak period
in Italy (from 20 February to 22 June, 2020). Our work highlights the changes taking place in the Italian public healthcare system in order to tackle the developing health crisis due to the COVID-19 pandemic. The findings of our review may be useful to analyze
future directions for the healthcare system in the case of new pandemic scenarios. |
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Inhalation of Heliox as a potential treatment for the ARDS caused by COVID-19 |
Ma, Juan, Shi, et al |
Research Square prepub |
Review Literature| Revue de littérature |
|
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Risk of adverse COVID-19 outcomes for people living
with HIV: a rapid review and meta-analysis |
Mellor, Maya, Bast, et al |
medRxiv |
Review Literature| Revue de littérature |
Rapid Review-MA: searched databases including Embase, Medline, medRxiv, and Google Scholar up to 26th August 2020.
Evidence is emerging that suggests a moderately increased risk of COVID-19 mortality amongst PLWH. |
|
Systematic review and meta-analysis identifies potential
host therapeutic targets in COVID-19 |
Parkinson, Nicholas, Rodgers, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: search of PubMed was conducted on 28/04/2020 and updated weekly until 06/07/2020. From 32 datasets, the top
ranked gene was PPIA, encoding cyclophilin A, a drug- gable target using cyclosporine.Other highly-ranked genes included proposed prognostic factors (CXCL10, CD4, CD3E) and investigational therapeutic tar- gets (IL1A) for COVID-19. Gene rankings also inform
the interpretation of COVID-19 GWAS results, implicating FYCO1 over other nearby genes in a disease-associated locus on chromosome 3. |
|
Patanavanich, Roengrudee, Glantz, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: searched PubMed and Embase for studies published from January 1-May 25, 2020. Smoking is an independent risk
for having severe progression of COVID-19, including mortality. The effects seem to be higher among young people. |
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Diagnosis of SARS-CoV-2: A Review on the Current Scenario and Future Outlook |
Priyanka, Choudhary, OP, et al |
Acta Virol |
Review Literature| Revue de littérature |
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Rahimi, Iman, Chen, et al |
Research Square prepub |
Review Literature| Revue de littérature |
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Ramonfaur, Diego, Gonzalez, et al |
medRxiv |
Review Literature| Revue de littérature |
SR: queried Pubmed and Google scholar search engines fo publications from 2020. Our interpretation of the literature
is that the benefits PTX may bring to a patient with COVID-19 outweigh the risks this drug might pose on them. |
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Sadjadi, Mahan, Moerschel, et al |
medRxiv |
Review Literature| Revue de littérature |
Rapid SR: search was carried out in MEDLINE, EMBASE, PsychINFO, Global Health, CINAHL and Web of Science on 13 March
2020. There are many barriers, on different levels, to the implementation of social distancing measures. Among other findings, the review identifies the need for good communication as well as the need for authorities to provide comprehensive support as two
key opportunities to increase acceptability and adherence. |
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Ocular Complications in the Prone Position in the Critical Care Setting: The COVID-19
Pandemic |
Sanghi, P, Malik, et al |
J Intensive Care Med |
Review Literature| Revue de littérature |
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Chloroquine and hydroxychloroquine for COVID-19: Perspectives on their failure in repurposing |
Shah, RR |
J Clin Pharm Ther |
Review Literature| Revue de littérature |
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Stall, NM, Johnstone, et al |
J Am Med Dir Assoc |
Review Literature| Revue de littérature |
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Van Walle, Ivo, Leitmeyer, et al |
medRxiv |
Review Literature| Revue de littérature |
MA: Evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially.
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Remdesivir for the treatment of COVID-19: A living
systematic review |
Verdugo-Paiva, Francisca, Acuna, et al |
medRxiv |
Review Literature| Revue de littérature |
SR-MA: conducted searches in the LOVE (Living OVerview of Evidence) platform for COVID-19 until 25 August 2020. The
evidence is insufficient for the outcomes critical for making decisions about the role of remdesivir in the treatment of patients with COVID-19, so it is not possible to balance the potential benefits, if any, with the adverse effects and costs. |
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Wang, M, Liao, et al |
Acta Virol |
Review Literature| Revue de littérature |
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Wildwing, Tamar, Holt, et al |
medRxiv |
Review Literature| Revue de littérature |
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PMC7158813; [Whether to make decisions «on the fly» regarding treatment for SARS-CoV-2
infection] |
Abril López de Medrano, V, Merino de Lucas, et al |
Rev Clin Esp |
Commentary/Editorial| Commentaire/Éditorial |
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COVID-19 outbreak and suicides in Nepal: Urgency of immediate action |
Acharya, SR, Shin, et al |
Int J Soc Psychiatry |
Commentary/Editorial| Commentaire/Éditorial |
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Agarwal, M, Ranjan, et al |
Expert Rev Anti Infect Ther |
Commentary/Editorial| Commentaire/Éditorial |
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Bandaru, SV, Augustine, et al |
J Laryngol Otol |
Commentary/Editorial| Commentaire/Éditorial |
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Bansal, P |
J Assoc Physicians India |
Commentary/Editorial| Commentaire/Éditorial |
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Bellinghausen, AL, LaBuzetta, et al |
Crit Care |
Commentary/Editorial| Commentaire/Éditorial |
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Blakely, T, Thompson, et al |
Med J Aust |
Commentary/Editorial| Commentaire/Éditorial |
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Bradley, Heather, Fahimi, et al |
medRxiv |
Commentary/Editorial| Commentaire/Éditorial |
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Lack of consideration of sex and gender in clinical
trials for COVID-19 |
Brady, Emer, Nielsen, et al |
medRxiv |
Commentary/Editorial| Commentaire/Éditorial |
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Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models |
Brzezinski, D, Kowiel, et al |
Protein Sci |
Commentary/Editorial| Commentaire/Éditorial |
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Byrne, P, James, et al |
BJPsych Bull |
Commentary/Editorial| Commentaire/Éditorial |
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Allied health service-learning student placements in remote northern Australia during COVID-19 |
Campbell, N, Stothers, et al |
Aust J Rural Health |
Commentary/Editorial| Commentaire/Éditorial |
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Lockdown impact on COVID-19 epidemics in regions across metropolitan France |
Cauchemez, Simon, Kiem, et al |
The Lancet |
Commentary/Editorial| Commentaire/Éditorial |
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Chiu, CY, Sarwal, et al |
J Gastroenterol Hepatol |
Commentary/Editorial| Commentaire/Éditorial |
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Creswell, KG, Bachrach, et al |
Alcohol Clin Exp Res |
Commentary/Editorial| Commentaire/Éditorial |
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Cron, RandyQ, Schulert, et al |
The Lancet Rheumatology |
Commentary/Editorial| Commentaire/Éditorial |
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Dentener, F, Emberson, et al |
Philos Trans A Math Phys Eng Sci |
Commentary/Editorial| Commentaire/Éditorial |
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The role of neurotropism in psychiatric patients with COVID-19 |
Diaz, AD, Baweja, et al |
Eur Arch Psychiatry Clin Neurosci |
Commentary/Editorial| Commentaire/Éditorial |
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Dilworth, TJ, Brummitt, et al |
Infect Control Hosp Epidemiol |
Commentary/Editorial| Commentaire/Éditorial |
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Dîrzu, DS |
Int J Clin Pract |
Commentary/Editorial| Commentaire/Éditorial |
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Letter To The Editor - Covid-19 Pandemic And The Mental Health Of The Elderly |
Erden Aki, ŞÖ |
Turk Psikiyatri Derg |
Commentary/Editorial| Commentaire/Éditorial |
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Pre-exposure prophylaxis during the SARS-CoV-2 pandemic: can PrEP prevent COVID-19-related
symptoms? |
Fernandes, DE, Ferreira, et al |
Epidemiol Infect |
Commentary/Editorial| Commentaire/Éditorial |
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Finch, T |
Health Commun |
Commentary/Editorial| Commentaire/Éditorial |
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Franco-Paredes, Carlos, Ghandnoosh, et al |
The Lancet Infectious Diseases |
Commentary/Editorial| Commentaire/Éditorial |
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Continuous Glucose Monitors and Automated Insulin Dosing Systems in the Hospital
Consensus Guideline |
Galindo, RJ, Umpierrez, et al |
J Diabetes Sci Technol |
Commentary/Editorial| Commentaire/Éditorial |
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Graham, PA |
J Air Transp Manag |
Commentary/Editorial| Commentaire/Éditorial |
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Grant, Alastair |
medRxiv |
Commentary/Editorial| Commentaire/Éditorial |
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PMC7328560; Open synthesis and the coronavirus pandemic in 2020 |
Haddaway, NR, Akl, et al |
J Clin Epidemiol |
Commentary/Editorial| Commentaire/Éditorial |
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Student-led interprofessional influenza vaccination clinic in a time of coronavirus |
Hanrahan, JR, Carroll, et al |
Med Educ |
Commentary/Editorial| Commentaire/Éditorial |
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Lifting lockdown policies: A critical moment for COVID-19 stigma |
Hargreaves, JR, Logie, et al |
Glob Public Health |
Commentary/Editorial| Commentaire/Éditorial |
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COVID-19 and cardiac surgery: The perspective from United Kingdom |
Harky, A, Harrington, et al |
J Card Surg |
Commentary/Editorial| Commentaire/Éditorial |
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Emotional exhaustion among the South Korean workforce before and after COVID-19 |
Hwang, H, Hur, et al |
Psychol Psychother |
Commentary/Editorial| Commentaire/Éditorial |
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Iliopoulos, DC |
J Card Surg |
Commentary/Editorial| Commentaire/Éditorial |
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Pneumomediastinum as a
Presenting Feature of COVID-19-an Observation |
Joshi, S, Bhatia, et al |
J Assoc Physicians India |
Commentary/Editorial| Commentaire/Éditorial |
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COVID-19 Care
in India: Evolving Paradigms from Public Health to Critical Care |
Joshi, SR |
J Assoc Physicians India |
Commentary/Editorial| Commentaire/Éditorial |
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Karnik, ND, Trivedi, et al |
J Assoc Physicians India |
Commentary/Editorial| Commentaire/Éditorial |
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Khan, RIN, Malla, et al |
Hum Reprod |
Commentary/Editorial| Commentaire/Éditorial |
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Considerations about Cognitive-Communication deficits following COVID-19 |
Khatoonabadi, AR, Joanette, et al |
Psychiatry Clin Neurosci |
Commentary/Editorial| Commentaire/Éditorial |
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Klemmedson, D |
J Am Dent Assoc |
Commentary/Editorial| Commentaire/Éditorial |
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Characteristics of US Adults Delaying Dental Care Due to the COVID-19 Pandemic |
Kranz, AM, Gahlon, et al |
JDR Clin Trans Res |
Commentary/Editorial| Commentaire/Éditorial |
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Leite-Moreira, A, Adão, et al |
Cardiovasc Res |
Commentary/Editorial| Commentaire/Éditorial |
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Ethical implications of coronavirus disease 2019 for ENT surgeons - a discussion |
Leonard, CG |
J Laryngol Otol |
Commentary/Editorial| Commentaire/Éditorial |
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Emergency Biosafety Management Practice in Laboratory of Shelter Hospital |
Liu, YS, Peng, et al |
Curr Med Sci |
Commentary/Editorial| Commentaire/Éditorial |
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Limits and opportunities of SARS-CoV-2 antigen rapid
Tests: an experience based perspective |
Lusebrink, Jessica, Schildgen, et al |
medRxiv |
Commentary/Editorial| Commentaire/Éditorial |
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Understanding the effects of COVID-19 on health care and systems |
Mercier, Grégoire, Arquizan, et al |
The Lancet Public Health |
Commentary/Editorial| Commentaire/Éditorial |
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Low risk of SARS-CoV-2 transmission by fomites in real-life conditions |
Mondelli, MarioU, Colaneri, et al |
The Lancet Infectious Diseases |
Commentary/Editorial| Commentaire/Éditorial |
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Can CPAP machines be repurposed to solve the ventilator shortage? |
Nguyen, Johnny, Kesper, et al |
Research Square prepub |
Commentary/Editorial| Commentaire/Éditorial |
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Palafox, B, Renedo, et al |
Trop Med Int Health |
Commentary/Editorial| Commentaire/Éditorial |
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Feline infectious peritonitis (FIP) and coronavirus disease 19 (COVID-19): are they similar? |
Paltrinieri, S, Giordano, et al |
Transbound Emerg Dis |
Commentary/Editorial| Commentaire/Éditorial |
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Parolin, Zachary |
The Lancet Public Health |
Commentary/Editorial| Commentaire/Éditorial |
|
|
|
Pozza, Andrea, Ferretti, et al |
Research Square prepub |
Commentary/Editorial| Commentaire/Éditorial |
|
|
|
AASM takes the pulse of the sleep field and responds to COVID-19 |
Ramar, K |
J Clin Sleep Med |
Commentary/Editorial| Commentaire/Éditorial |
|
|
Potential therapeutic effects of Resveratrol against SARS-CoV-2 |
Ramdani, LH, Bachari, et al |
Acta Virol |
Commentary/Editorial| Commentaire/Éditorial |
|
|
Lessons on the COVID-19 pandemic, for and by primary care professionals worldwide |
Rawaf, S, Allen, et al |
Eur J Gen Pract |
Commentary/Editorial| Commentaire/Éditorial |
|
|
Seitlinger, J, Banga Nkomo, et al |
J Thorac Oncol |
Commentary/Editorial| Commentaire/Éditorial |
|
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|
Shabani, E, Dowlatshahi, et al |
Eur J Clin Microbiol Infect Dis |
Commentary/Editorial| Commentaire/Éditorial |
|
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|
Skinner, HD |
Cancer |
Commentary/Editorial| Commentaire/Éditorial |
|
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Non-Pharmaceutical Intervention Discovery with Topic Modeling |
Smith, Jonathan, Ghotbi, et al |
arXiv |
Commentary/Editorial| Commentaire/Éditorial |
|
|
Sparks, MA, South, et al |
Hypertension |
Commentary/Editorial| Commentaire/Éditorial |
|
|
|
Stirrups, Robert |
The Lancet Infectious Diseases |
Commentary/Editorial| Commentaire/Éditorial |
|
|
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Confronting antimicrobial resistance beyond the COVID-19 pandemic and the 2020
US election |
Strathdee, SteffanieA, Davies, et al |
The Lancet |
Commentary/Editorial| Commentaire/Éditorial |
|
|
A cross-section of UK prostate cancer diagnostics during the COVID-19 era - a shifting paradigm? |
Stroman, L, Cathcart, et al |
BJU Int |
Commentary/Editorial| Commentaire/Éditorial |
|
|
Surkova, Elena, Nikolayevskyy, et al |
The Lancet Respiratory Medicine |
Commentary/Editorial| Commentaire/Éditorial |
|
|
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IAP ALS Update on Resuscitation Guidelines During COVID-19 Pandemic |
Tiwari, L, Taneja, et al |
Indian J Pediatr |
Commentary/Editorial| Commentaire/Éditorial |
|
|
Toor, J, Adams, et al |
Clin Infect Dis |
Commentary/Editorial| Commentaire/Éditorial |
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|
|
Vilcek, S |
Acta Virol |
Commentary/Editorial| Commentaire/Éditorial |
|
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Changes in Older People's Activities During the Coronavirus Disease 2019 Pandemic
in Japan |
Yamada, Y, Uchida, et al |
J Am Med Dir Assoc |
Commentary/Editorial| Commentaire/Éditorial |
|
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Safeguarding the physical health of people with severe mental disorders during the COVID-19
pandemic |
Zhang, S, Das-Munshi, et al |
BJPsych Bull |
Commentary/Editorial| Commentaire/Éditorial |
|
Appendix: Process and definitions.
A daily search for new publications is conducted in PubMed, Scopus,
BioRxiv and MedRxiv, SSRN,
Research Square,
arXiv for all publications related to COVID-19 disease or SARS-CoV-2 using the search terms (COVID-19 OR SARS-CoV-2
OR "novel CoV" OR "novel coronavirus" OR nCoV) adapted to each database. The capture is cross-referenced with publication announcements on the COVID-19 dashboards set up by a number of publishers and google. Publishers include
Lancet,
Elsevier,
The New England Journal of Medicine,
BMJ, Wiley,
Springer Nature, ChinaCDCweekly.
Additionally the database is cross-referenced with other literature scans e.g.
WHO publication list and activities by collaborators. Members of the Emerging Sciences group develop 1 -2 point summaries of each publication. Please email Lisa Waddell for additional information:
Lisa.Waddell@canada.ca.
References are compiled in a reworks database that has citations since the beginning of the outbreak. All references can be accessed at this
link and by the categories listed below. The daily scan has also been compiled in an excel sheet and copies can be provided upon request or
accessed
here.
Category Definitions:
Modelling/ prediction: Predictive modeling is a process that uses data mining and probability
to forecast outcomes. Each model is made up of a number of predictors, which are variables that are likely to influence future results.
Epidemiology:
the branch of medicine which deals with the incidence, distribution, and possible control of diseases and other factors relating to health. Includes Ro, attack rates, case number doubling time, case fatality
rate, serial interval, clinical attack rate, asymptomatic fraction, proportion of asymptomatic and infective*
Transmission: The passage of a pathogen causing communicable disease from an infected host
to an uninfected host via direct or indirect routes.
Clinical data
of cases: Includes clinical parameters such as incubation period, latent period, period of communicability, duration of illness, duration of hospitalization, host risk factors, as well as clinical profiles of patients; presenting symptoms, symptoms over
course of illness, sequelae, comorbidities.*
Surveillance: Public health surveillance is the continuous, systematic collection, analysis and
interpretation of health-related data. Surveillance data will likely be number of cases suspected/confirmed, number of deaths, number recovered. *
Coronavirology: All research relating to the virus; its characteristics, genetic make-up, phylogenetic
analyses
Diagnostics / Pathogen detection:
All studies on identification of the virus; culture, PCR, antibody/antigen tests etc.
Therapeutics:
Studies of substances that may be used to treat infected hosts including passive immunization products.
Vaccine Research:
Studies of vaccine candidates to prevent infection with 2019-nCoV including clinical trials.
Public Health Priorities:
These citations will focus on what the current research priorities are and/or where knowledge gaps exist.
Public Health interventions*:
Any study evaluating how effective a public health intervention is or maybe (in the case of a predictive model).
Public Health response:
These papers are typically overviews of past and current activities, they often also identify knowledge gaps and suggest future activities or objectives.
Infection Prevention and Control/
Prévention et contrôle des infections (IPAC/PCI): Any research on the effectiveness of IPC interventions should also be tagged as IPC
Health care Response:
This foci would include a description of activities to deal with 2019-nCoV cases including, but not limited to: set up of a special emergency multi-disciplinary intensive care team; Bed and medical equipment preparation/ stock piling supplies; Education
and training of staff; Early case recognition and classification of disease severity.
Economics: papers discussing/ forecasting the economics of COVID-19 pandemic.
Zoonotic:
all literature discussing the transmission to and from or occurrence of naturally acquired SARS-COV-2 infection in animals.
Review Literature:
All articles that summarize the published literature can be tagged as a review. This includes systematic review, meta-analysis, scoping review, overviews, umbrella reviews*
Commentary/Editorial:
For commentaries, editorials, letters to the editor, other types of opinion pieces where there is no new data collected by the author or analysis conducted by the author, please tag these within the commentary category.
News articles that have not scientific information.
*Lists are not exhaustive
Annexe: Processus et définitions.
Une recherche quotidienne des nouvelles publications est effectuée dans PubMed, Scopus,
BioRxiv and MedRxiv,
SSRN,
Research Square,
arXiv
pour toutes les publications relatives à la maladie COVID-19 ou au SRAS-CoV-2 en utilisant les termes de recherche (COVID-19 OU SARS-CoV-2 OU « novel CoV » OU « novel coronavirus » OU nCoV). La saisie renvoie à des annonces de publication
sur les tableaux de bord du nCoV mis en place par un certain nombre d'éditeurs et par Google. Parmi les éditeurs figurent
Lancet,
Elsevier,
The New England Journal of Medicine,
BMJ,
Wiley,
Springer Nature,
ChinaCDCweekly. En outre, la base de données renvoie à d'autres survols de publications, e.g.
la liste des publications de l'OMS,
et à des activités des collaborateurs. Les membres du groupe scientifique émergent préparent des résumés en 1 ou 2 points de chaque publication. Pour en savoir plus, veuillez envoyer un courriel à Lisa Waddell au :
Lisa.Waddell@canada.ca.
Les références sont compilées dans une base de données Refworks qui contient des citations depuis le début de l'épidémie. Toutes les références sont accessibles à partir de ce
lien et par les catégories énumérées ci-dessous. L'analyse quotidienne a également été compilée
dans une feuille Excel et des copies peuvent être fournies sur demande ou consultées
ici.
Définitions des catégories :
Modélisation / prédiction :
La modélisation prédictive est un processus qui utilise l'exploration de données et la probabilité pour prévoir les résultats. Chaque modèle est composé de plusieurs prédicteurs, qui sont des variables susceptibles d'influencer les résultats futurs.
Épidémiologie :
Branche de la médecine qui traite de l'incidence, de la répartition et du contrôle éventuel des maladies et d'autres facteurs liés à la santé. Comprend le taux de reproduction de base (Ro),
les taux d'attaque, le temps de doublement du nombre de cas, le taux de létalité, l'intervalle sériel, le taux d'attaque clinique, la fraction asymptomatique, la proportion de cas asymptomatiques et infectieux*.
Transmission :
Passage d'un agent pathogène causant une maladie transmissible d'un hôte infecté à un hôte non infecté par des voies directes ou indirectes.
Données cliniques
des cas : Comprend les paramètres cliniques tels que la période d'incubation, la période de latence, la période de contagiosité, la durée de la maladie, la durée de l'hospitalisation, les facteurs de risque de l'hôte, ainsi que les profils
cliniques des patients; les symptômes présentés, les symptômes au cours de la maladie, les séquelles, les comorbidités.*
Surveillance :
La surveillance de la santé publique est la collecte, l'analyse et l'interprétation continues et systématiques de données relatives à la santé. Les données de surveillance concerneront probablement le nombre de cas suspects / confirmés,
le nombre de décès, le nombre de personnes guéries. *
Coronavirologie : Toutes les recherches relatives
au virus, ses caractéristiques, sa constitution génétique et les analyses phylogénétiques.
Diagnostics / Détection d'agents pathogènes :
Toutes les études sur l'identification du virus : culture, PCR, tests de dépistage d'anticorps ou d’antigènes, etc.
Thérapeutique :
Étude des substances pouvant être utilisées pour traiter les hôtes infectés, y compris les produits d'immunisation passive.
Recherche sur les vaccins :
Études des candidats à la vaccination pour prévenir l'infection par le 2019-nCoV, y compris des essais cliniques.
Priorités de santé publique :
Ces citations porteront sur les priorités actuelles de recherche et/ou sur les lacunes dans les connaissances.
Interventions de santé publique* :
Toute étude évaluant l'efficacité (réelle ou possible) d'une intervention de santé publique (dans le cas d'un modèle prédictif).
Réponse de la santé publique :
Ces articles sont généralement des aperçus des activités passées et actuelles, qui identifient souvent les lacunes dans les connaissances et suggèrent des activités ou des objectifs futurs.
Prévention et contrôle des infections/Infection Prevention and Control (PCI/IPAC) :
Les recherches sur l'efficacité des interventions en PCI doivent également être marquées comme PCI.
Réponse des soins de santé :
Ce point comprendrait une description des activités pour traiter les cas de 2019-nCoV, notamment : mise en place d'une équipe multidisciplinaire spéciale de soins intensifs d'urgence; préparation des lits et des équipements médicaux
/ stockage des fournitures; sensibilisation et formation du personnel; reconnaissance précoce des cas et classification de la gravité de la maladie.
Modèle animal:
Zoonotic:
all literature discussing the transmission to and from or occurrence of naturally acquired SARS-COV-2 infection in animals.
Économie: documents discutant / prévoyant l'économie de la pandémie de COVID-19
Revue de la documentation :
Tous les articles qui résument les documents publiés peuvent être marqués comme une revue. Cela comprend les revues systématiques, les méta-analyses, les études de la portée, les aperçus, les examens généraux*.
Commentaires/Éditorial :
Pour les commentaires, éditoriaux, lettres à la rédaction, autres types d'articles d'opinion pour lesquels aucune nouvelle donnée n'est collectée ou aucune analyse n'est effectuée par l'auteur, veuillez les marquer dans la catégorie des
commentaires.
journaux
Articles de presse qui n'ont pas d'informations scientifiques.
* Les listes ne sont pas exhaustives