Good afternoon,

There are 160 citations in today’s scan. 142 were considered primary research or review literature.

Highlights today include:

PUBLIC HEALTH INTERVENTION

· Rowland et al. developed a mathematical model that captures correlations between state-level social distancing policies and infection kinetics for all U.S. states, and use it to illustrate the link between social policy decisions, disease dynamics, and an effective reproduction number that changes over time. The authors found that the potential for second waves of infection, which result after reopening states without an increase to immunity, can be mitigated by returning social distancing policies as soon as possible after the waves are detected.

· Yilmazkuday, H., investigates the effects of wearing a face mask, by using a difference-in-difference design, where U.S. county-level data on changes in COVID-19 cases or deaths are regressed on lagged changes in social interaction of people measured by Google mobility. Wearing a face mask starts working to fight against COVID-19 only if more than 75% of people in a county "always" wear a face mask, while the effects of social interaction on COVID-19 are statistically eliminated when more than 85% of people in a county "always" wear a face mask.

· Brooks-Pollock et al developed a stochastic transmission model based to evaluate alternative mitigation interventions for a representative university. If asymptomatic cases are half as infectious as symptomatic cases then 5,760 (3,940 - 7,430) out of 28,000 students. If asymptomatic cases are as infectious as symptomatic cases then three times as many cases could occur, with 94% (93% - 94%) of the student population getting infected during the first term. Reducing face-to-face teaching is likely to be the single most effective intervention, and this conclusion is robust to varying assumptions about asymptomatic transmission.

· O’Donoghue et al present a study using anonymized cell phone GPS data to analyze trends in traffic patterns to businesses that may be potentially high-risk from January 2020 to June 2020 in order to define a “business risk index”.  The index provides a way for policymakers and hospital decision makers to monitor the potential risk of COVID-19 transmission from businesses based on the frequency and density of visits to businesses serving as a metric to monitor and evaluate reopening strategies.

EPIDEMIOLOGY

· Wilkins et al found that the crude prevalence rate of seropositivity among a cohort of healthcare workers in Chicago was 4.8%. Exposure to COVID-19 patients and longer duration patient therapies were each associated with higher risk for seropositive status; however, the community burden of COVID-19 remains a significant source of exposure to SARS CoV-2 infection among healthcare workers in Chicago.

· Smith et al. assessed the association of temperature, humidity, UV radiation, and population density with estimates of the transmission rate (R). Using data from the U.S., the authors explored transmission correlations across US states using comparative regression and integrative epidemiological modelling. The authors found that policy intervention and reductions in individuals’ mobility are the major predictors of SARS-CoV-2 transmission rates. Still, in their absence, lower temperatures and higher population densities are correlated with increased SARS-CoV-2 transmission.

· Raham. Possible role of latent TB and BCG and malaria have been already suggested to create innate cross heterogeneous immunity. We look for influence of these factors on Covid-19 mortality in 80 malarious countries. Findings show TB prevalence is associated with reduced COVID-19 mortality and malaria have an additional effect in reducing COVID-19 mortality. The results show with robust statistical support that TB prevalence was also associated with reduced COVID-19 mortality with additional effect that is also observed in TB and BCG coverage rate. 

· Wilson, et al estimate the risk of COVID-19 outbreaks in a case study COVID-free destination country (New Zealand), associated with shore leave for merchant ship crews. Introduction of SARS-CoV-2 through shore leave from international shipping crews is likely, even after long voyages. The risk can be substantially mitigated by control measures such as PCR testing and mask use.

TREATMENT

· Rosas et al. conducted a randomized clinical trial to test the efficacy of tocilizumab in treating COVID-19. Four hundred fifty-two patients were randomized; the modified-intention-to-treat population included 294 tocilizumab-treated and 144 placebo-treated patients. Clinical status at day 28 was not statistically significantly improved for tocilizumab versus placebo. There was no difference in mortality at day 28 between tocilizumab and placebo. The median time to hospital discharge was eight days shorter with tocilizumab than placebo. The median duration of ICU stay was 5.8 days shorter with tocilizumab than the placebo. In the safety population, serious adverse events occurred in 34.9% of 295 patients in the tocilizumab arm and 38.5% of 143 in the placebo arm.

DIAGNOSTICS

· Thanh et al present a sample pooling approach and the results of its application for mass screening of SARS-CoV-2 in >96,000 asymptomatic individuals. Their approach did not compromise the sensitivity of PCR, while increasing the throughput and reducing 77% of the costs. Futhermore, 22/32 asymptomatic cases would have been missed without mass screening.

CORONAVIROLOGY

· Huang et al. systematically examined 285 ACE2 variants from mammals, birds, fish, reptiles, and amphibians, and found that the binding energies calculated on the modeled Spike-RBD/ACE2 complex structures correlate closely with the effectiveness of animal infections as determined by multiple experimental datasets. Built on the optimized binding affinity cutoff, authors suggested a set of 96 mammals, including 48 experimentally investigated ones, which are permissive to SARS-CoV-2, with candidates from primates, rodents, and carnivores at the highest risk of infection.

PUBLIC HEALTH RESPONSE

· Dabo et al. assess the early impact of COVID-19 on vaccine activities by comparing current trends to trends over the past year when vaccine coverage of major antigens. Overall, the Expanded Vaccination Program recorded a median vaccination coverage of less than 80% for all the vaccines introduced and the analysis of the interrupted time series shows that the interruption of the vaccination program was significant for all the vaccines.

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

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

PUBLICATIONS	AUTHORS / AUTEURS	SOURCE	FOCI / DOMAINE	SUMMARY / SOMMAIRE
Use of Unofficial Newspaper Data for COVID-19 Death Surveillance	Ahamad,  MazbahulG,  Ahmed, et al	medRxiv	Epidemiology| Épidémiologie Surveillance	This paper highlights the critical importance of unofficially reported newspaper-based deaths from coronavirus disease 2019 (COVID 19) like illness (CLI) together with officially confirmed death counts to support improvements in COVID 19 death surveillance.  Between March 8 and August 22, 2020, 2,156 CLI deaths were recorded based on newspaper reporting for a count that was 55% of the officially confirmed death count (n = 3,907). This shows that newspaper reports tend to cover a significant number of COVID-19 related deaths. Our forecast also indicates an approximate total of 406 CLI expected for the six weeks ahead, which could contribute to a total of 2,413 deaths including 2,007 confirmed deaths expected from August 23 to October 3, 2020.
Probabilistic and mean-field model of COVID-19 epidemics with user mobility and contact tracing	Akian,  M,  G	ArXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	We propose a detailed discrete-time model of COVID-19 epidemics coming in two flavours, mean-field and probabilistic. The main contribution lies in several extensions of the basic model that capture i) user mobility - distinguishing routing, i.e. change of residence, from commuting, i.e. daily mobility - and ii) contact tracing procedures. We confront this model to public data on daily hospitalizations, and discuss its application as well as underlying estimation procedures.
Who Is Still Travelling by Public Transport during COVID-19? Socioeconomic Factors Explaining Travel Behaviour in Stockholm Based on Smart Card Data	Almlöf,  Erik,  Rubensson, et al	SSRN- Lancet prepublication	Public Health response| Interventions de santé publique Economics | Économie	This study analysed the propensity to stop travelling by public transport during COVID-19 for the holders of 1.8 million smart cards in Stockholm, Sweden.  Suggested two models for explaining the change in travel pattern, linking socioeconomic data with the probability to stop travelling. Ans found that education level, income and age are strong predictors, but that workplace type also substantially affect the propensity of public transport travel.
Analysis of twenty-week time-series of confirmed cases of New Coronavirus COVID-19 and their simple short-term prediction for Georgia and Neighboring Countries (Armenia, Azerbaijan, Turkey, Russia) in amid of a global pandemic	Amiranashvili,  AvtandilG,  Khazaradze, et al	medRxiv	Epidemiology| Épidémiologie	This study presents the results of a comparative statistical analysis of the daily data associated with New coronavirus COVID-19 infection of confirmed cases (Č) of the population in Georgia (GEO), Armenia (ARM), Azerbaijan (AZE), Turkey (TUR) and Russia (RUS) amid a global pandemic (WLD) in the period from March 14 to July 31, 2020. . It was found that daily, monthly and mean weekly real values of Č for all the studied locations practically fall into the 99% confidence interval of the predicted values of Č for the specified time period. A dangerous situation with the spread of coronavirus infection may arise when the mean weekly values of Č of the 99% upper level of the forecast confidence interval are exceeded within 1-2 weeks. Favorable - when the mean weekly values of Č decrease below 99% of the lower level of the forecast confidence interval.
Mask-Wearing During the COVID-19 Pandemic	Aravindakshan,  Ashwin,  Boehnke, et al	medRxiv	Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	This study investigates reported mask use and its association with the spread of COVID-19. The results indicate that reported mask-wearing could play an important role in mitigating the growth of COVID-19. Widespread mask-wearing within a country associates with an expected 7% (95% CI: 3.94%-9.99%) decline in the growth rate of daily active cases of COVID-19 in the country. This daily decline equates to an expected 88.5% drop in the growth of daily active cases over a 30-day period when compared to zero percent mask-wearing, all else held equal. The decline in daily growth rate due to the combined effect of reported mask-wearing, reduced social mobility, and non-pharmaceutical interventions averages 28.1% (95% CI: 24.2%-32%). These estimates remain robust across multiple sensitivity analyses.
SARS-CoV-2 detection by extraction-free qRT-PCR for massive and rapid COVID-19 diagnosis during a pandemic	Avetyan,  Diana,  Chavushyan, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	This study compared the performance of qRT-PCR in direct heat-inactivated, heat-inactivated/pelleted samples against RNA in a group of 74 subjects (44 positive and 30 negative). In addition, compared the sensitivity of heat-inactivated/pelleted in another group of 196 COVID-19 positive samples. The study suggests that swab sample heat-inactivation and pelleting show higher accuracy for SARS-CoV-2 detection PCR assay compared to heat-inactivation only (89% vs 83% of the detection in RNA). The accuracy of detection using direct samples varied depending on the sample transport and storage media as well as the viral titer. This study suggests that purified RNA provides more accurate results, however, direct qRT-PCR may help to significantly increase testing capacity.
How to Make COVID-19 Contact Tracing Apps work: Insights From Behavioral Economics	Ayres,  Ian,  Romano, et al	medRxiv	Public health interventions*| Interventions de santé publique Surveillance	This study carried out an online experiment to show that Contact Tracing Apps (CTAs) can still play a key role in containing the spread of COVID-19, provided that they are re-conceptualized to account for insights from behavioral science. The authors devised that in-app notifications are effective in inducing prudent behavior like wearing a mask or staying home. In particular, people that are notified that they are taking too much risk and could become a superspreader engage in more prudent behavior. Building on this result, suggestted that CTAs should be re-framed as Behavioral Feedback Apps (BFAs). The main function of BFAs would be providing users with information on how to minimize the risk of contracting COVID-19, like how crowded a store is likely to be. Moreover, the BFA could have a rating system that allows users to flag stores that do not respect safety norms like wearing masks. These functions can inform the behavior of app users, thus playing a key role in containing the spread of the virus even if a small percentage of people download the BFA. While effective contact tracing is impossible when only 3% of the population downloads the app, less risk taking by small portions of the population can produce large benefits. BFAs can be programmed so that users can also activate a tracing function akin to the one currently carried out by CTAs. Making contact tracing an ancillary, opt-in function might facilitate a wider acceptance of BFAs.
The major predictors of testing positive for COVID-19 among symptomatic hospitalized patients	barasa,  samson	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	The aim of this study was to identify patients who were likely to test positive for COVID-19 among symptomatic patients suspected of having COVID-19 during hospitalization by comparing COVID-19 positive and negative patients.  Charts of 277 and 18 COVID-19 negative and positive patients respectively were analyzed. Dyspnea (61%) was the most common symptom among COVID-19 negative patients, while 72% and 61% COVID-19 positive patients had cough and fever respectively. COVID-19 positive patients were more likely to present initially with cough 1.082 (1.022 - 1.145)], fever 1.066 (1.014 - 1.121)] and be 50 to 69 years old 1.094 (1.021 - 1.172)]. Dyspnea, weakness, lymphopenia and bilateral chest image abnormality were not associated with COVID-19 positivity. COVID-19 positive patients were less likely to have non-COVID-19 respiratory viral illness 1.068 (1.019 - 1.119)], human immunodeficiency virus 0.849 (0.765 - 0.943)] and heart failure history 0.093 (0.891 - 0.978)]. Other chronic medical problems (hypertension, diabetes mellitus, chronic obstructive pulmonary disease and coronary artery disease) were not associated with testing positive for COVID-19.
Bayesian Beta-Binomial Prevalence Estimation Using an Imperfect Test	Baxter,  J	ArXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	Following Diggle 2011, Greenland 1995], we give a simple formula for the Bayesian posterior density of a prevalence parameter based on unreliable testing of a population. This problem is of particular importance when the false positive test rate is close to the prevalence in the population being tested. An efficient Monte Carlo algorithm for approximating the posterior density is presented, and applied to estimating the Covid-19 infection rate in Santa Clara county, CA using the data reported in Bendavid 2020]. We show that the true Bayesian posterior places considerably more mass near zero, resulting in a prevalence estimate of 5,000--70,000 infections (median: 42,000) (2.17% (95CI 0.27%--3.63%)), compared to the estimate of 48,000--81,000 infections derived in Bendavid 2020] using the delta method. A demonstration, with code and additional examples, is available at this http URL.
Demographics Matter! The Potentially Disproportionate Effect of COVID-19 on Hospital Ratings	Belasen,  ArielR,  Tracey, et al	SSRN- Lancet prepublication	Healthcare Response | Réponse des soins de santé	Since 2016, the Centers for Medicare and Medicaid Services (CMS) has been displaying HCAHPS Star Ratings on Hospital Compare, which has driven hospitals to improve quality and reduce costs. These ratings measure Medicare beneficiaries’ experience with their health plans and the health care system. We provide evidence that low-rated hospitals have much more variability in patient experience ratings than high-rated ones. Moreover, the experiences at low-rated hospitals are more sensitive to county demographic factors, which means exogenous shocks, like COVID-19, will likely affect these hospitals differently, as such shocks are known to disproportionately affect their communities. Specifically, our results imply that low-rated hospitals with more variability in their HCAHPS responses are more likely to face adverse patient experiences due to COVID-19 than high-rated hospitals.
Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020	Belloir,  Antoine,  Blanquart, et al	medRxiv	Epidemiology| Épidémiologie	This study quantified the impact of control measures and the fraction of infected individuals that are detected. Developed a deterministic transmission model based on the renewal equation and fitted the model to daily case and death data in the first few months of 2020 in 79 countries and states, representing more than 4 billions individuals. Based on a region-specific infected fatality ratio,  inferred the time-varying probability of case detection and the time-varying decline in transmissiblity. The model was validated by the good correlation between the predicted total number of infected and that found in serosurveys; and most importantly by the strong correlation between the inferred probability of detection and the number of daily tests per inhabitant, with 50% detection achieved with 0.003 daily tests per inhabitants. Most of the decline in transmission was explained by the reductions in transmissibility (social distancing), which avoided 107 deaths in the regions studied over the first four months of 2020. In contrast, symptom-based testing and isolation was not an efficient way to control the spread of the disease, as a large part of transmission happens before symptoms and only a small fraction of infected individuals was typically detected. Also developed a phenomenological model to link the number of daily tests with the probability of detection and verified the prediction that increasing test capacity increases the probability of detection less than proportionally. Together these results suggest that little control can be achieved by symptom-based testing and isolation alone.
Modelling COVID-19 -- I A dynamic SIR(D) with application to Indian data	Bhattacharjee,  M,  B	ArXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	We propose an epidemiological model using an adaptive dynamic three compartment (with four states) SIR(D) model. We illustrate our method on the Indian COVID-19 data for the period March 14 - August 31, 2020. The time series data plots of the 36 states and union territories shows a clear presence of inter-regional variation in the prognosis of the epidemic. The time series of estimates of the model enables us to carry out daily, weekly and also long term predictions, including construction of predictive bands. We obtain an excellent agreement between the actual data and the model predicted data at the regional level. Our estimates of the current reproduction number turn out to be more than 2 in three regions (Andhra Pradesh, Maharashtra and Uttar Pradesh) and between 1.5 and 2 in 13 regions. Each of these regions have experienced an individual trajectory, which typically involves initial phase of shock(s) followed by a relatively steady lower level of the reproduction number.
Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2	Bhattacharya,  Dr Debdutta,  Parai, et al	medRxiv	Coronavirology| Coronavirologie Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to nasopharyngeal swab (NPS) for diagnosis of SARS-CoV-2. A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples.
SARS-CoV-2 Antibody Formation Among Healthcare Workers	Birch,  Thomas,  Barkama, et al	medRxiv	Epidemiology| Épidémiologie Immunology | Immunologie	Many frontline healthcare workers throughout the world have been exposed to COVID-19 infection in the workplace and the community. We describe the nature of infection and the durability of antibodies among various types of healthcare workers at an acute care community hospital in northern New Jersey adjacent to New York City, part of the epicenter of the first wave of the US epidemic. Exposure was concentrated among frontline workers and in clusters among support staff. The antibody response correlated with symptoms and job type.
Ventilation and the SARS-CoV-2 Coronavirus Analysis of outbreaks in a restaurant and on a bus in China,and at a Call Center in South Korea	Birnir,  Bjorn	medRxiv	Epidemiology| Épidémiologie Transmission	In this paper, we describe an outbreak among lay-Buddhists, on a bus, traveling to a ceremony in Zhejiang province, China, and an outbreak in a Call Center in Seoul, Korea. The analysis and comparison of these cases, leads to the conclusion that the SARS-CoV-2 Coronavirus attacks in two steps: The first step is a linear spread between individuals with a couple of days delay. The second step is an exponential spread effected by the air-conditioning system affecting a much larger number of people. Thus in the second step, the ventilation becomes the super-spreader.
Ignoring the elephant in the room: factors contributing to inadequate access to contraception and sources of contraception during novel coronavirus diseases 2019 in South Africa	Bolarinwa,  Obasanjo Afolabi	medRxiv	Public Health response| Interventions de santé publique	This study examines the factors contributing to inadequate access to contraception and sources of contraception during the COVID-19 pandemic in South Africa (SA).  Over one-quarter of South Africans could not access contraception and more than every 7 in 10 South Africans preferred public or government hospital as source of contraception. Female South Africans (OR=0.89 CI:0.7487-1.0719) and those aged 65 years above (OR=0.67 CI:0.4485-0.9988) were 33% and 11% respectively less likely to have access to contraception. The preferred sources of contraception were associated with the selected demographic and economic variables at P<0.05.
Discovery of a Novel Inhibitor of Coronavirus 3CL Protease as a Clinical Candidate for the Potential Treatment of COVID-19	Boras,  Britton,  Jones, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	The designed phosphate prodrug PF-07304814 is metabolized to PF-00835231 which is a potent inhibitor in vitro of the coronavirus family 3CL pro, with selectivity over human host protease targets. Furthermore, PF-00835231 exhibits potent in vitro antiviral activity against SARS-CoV-2 as a single agent and it is additive/synergistic in combination with remdesivir. We present the ADME, safety, and in vitro antiviral activity data to warrant clinical evaluation.
Development, clinical translation, and utility of a COVID-19 antibody test with qualitative and quantitative readouts	Bortz,  RobertH,  Florez, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	Here, we describe a laboratory-developed antibody test that uses readily available research-grade reagents to detect SARS-CoV-2 exposure in patient blood samples with high sensitivity and specificity. We further show that this test affords the estimation of viral spike-specific IgG titers from a single sample measurement, thereby providing a simple and scalable method to measure the strength of an individual's immune response. The accuracy, adaptability, and cost-effectiveness of this test makes it an excellent option for clinical deployment in the ongoing COVID-19 pandemic.
Title: COVID-19Predict - Predicting Pandemic Trends	Bosch,  Jurgen,  Wilson, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	We have designed a COVID-19 dashboard with the goal of providing concise sets of summarized data presentations to simplify interpretation of basic statistics and location-specific current and short-term future risks of infection. COVID-19 Predict produces 2,100 daily predictions or calculations on the state level (50 States x3 models x7 days x2 cases and deaths) and 131,964 (3,142 Counties x3 models x7 days x2 cases and deaths) on the county level. To assess how robust our models have performed in making short-term predictions over the course of the pandemic, we used available case data for all 50 U.S. states spanning the period January 20 - August 16 2020 in a retrospective analysis. Results showed a 3.7% to -0.2% mean error of deviation from the actual case predictions to date.
High COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions	Brooks-Pollock,  Ellen,  Christensen, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	We developed a stochastic transmission model based on realistic mixing patterns between students. We evaluated alternative mitigation interventions for a representative university. Our model predicts, for a set of plausible parameter values, that if asymptomatic cases are half as infectious as symptomatic cases then 5,760 (3,940 - 7,430) out of 28,000 students, 20% (14% - 26%), could be infected during the first term, with 950 (656 - 1,209) cases infectious on the last day of term. If asymptomatic cases are as infectious as symptomatic cases then three times as many cases could occur, with 94% (93% - 94%) of the student population getting infected during the first term. We predict that one third of infected students are likely to be in their first year, and first year students are the main drivers of transmission due to high numbers of contacts in communal residences. We find that reducing face-to-face teaching is likely to be the single most effective intervention, and this conclusion is robust to varying assumptions about asymptomatic transmission. Supplementing reduced face-to-face testing with COVID-secure interactions and reduced living circles could reduce the percentage of infected students by 75%. Mass testing of students would need to occur at least fortnightly, is not the most effective option considered, and comes at a cost of high numbers of students requiring self-isolation. When transmission is controlled in the student population, limiting imported infection from the community is important.
Bacterial pulmonary superinfections are associated with unfavourable outcomes in critically ill COVID-19 patients	Buehler,  PhilippK,  Zinkernagel, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	We aimed to investigate the burden of superinfections in COVID-19 patients. In this prospective single centre cohort study in an intensive care setting patients aged ≥ 18 years with COVID-19 acute respiratory distress syndrome were assessed for concomitant microbial infections by longitudinal analysis of tracheobronchial secretions, bronchoalveolar lavages and blood. In 45 critically ill COVID-19 patients, we identified 19 patients with superinfections (42.2%) by longitudinal analysis of 433 TBS, 35 BAL and 455 blood samples, respectively. On average, superinfections were detected on day 10 after ICU admission. The most frequently isolated clinically relevant bacteria were Enterobacteriaceae, Streptococcus pneumoniae, and Pseudomonas aeruginosa. Ventilator-free survival was substantially lower in patients with superinfection (subhazard ratio 0.37, 95%-CI 0.15-0.90, p=0.028). Patients with pulmonary superinfections more often had bacteraemia, virus reactivations, yeast colonization, and needed ICU treatment for a significantly longer time.
CoV2-ID, a MIQE-compliant sub-20-minute 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19	Bustin,  S,  C	Research Square prepub	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	We have used the MIQE guidelines to develop two versions of a unique fiveplex RT-qPCR test, termed CoV2-ID, that allows the detection of three viral target genes, a human internal control for confirming the presence of human cells in a sample and a control artificial RNA for quality assessment and potential quantification. Viral targets can be detected either separately with separate fluorophores or jointly using the same fluorophore, thus increasing the test’s reliability and sensitivity. It is robust, can consistently detect two copies of viral RNA, with a limit of detection of a single copy and can be completed in around 15 minutes. It was 100% sensitive and 100% specific when tested on 23 RNA samples extracted from COVID-19 positive patients and five COVID-19 negative patients. We also propose using multiple cycle fluorescence detection, rather than real-time PCR to reduce significantly the time taken to complete the assay as well as assuage the misunderstandings underlying the use of quantification cycles (Cq).
Elovanoids downregulate canonical SARS-CoV-2 cell-entry mediators and enhance protective signaling in human alveolar cells	Calandria,  J,  B	Research Square prepub	Coronavirology| Coronavirologie	We uncovered that very-long-chain polyunsaturated fatty acid precursors (VLC-PUFA,n-3) activate ELV biosynthesis in lung cells. Both ELVs and their precursors reduce the binding to RBD. ELVs downregulate angiotensin-converting enzyme 2 (ACE2) and enhance the expression of a set of protective proteins hindering cell surface virus binding and upregulating defensive proteins against lung damage. These findings open avenues for potential preventive and disease-modifiable therapeutic approaches for COVID-19.
Infection Kinetics of Covid-19: Is Lockdown a Potent Containment Tool?	Chattopadhyay,  AK,  C	ArXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	Harnessing the predictive powers of Machine Learning within a 6 dimensional infection kinetic model, depicting interactive evolution of 6 infection stages - healthy susceptible (H), predisposed comorbid susceptible (P), infected (I), recovered (R), herd immunized (V) and mortality (D) - the model, PHIRVD, provides the first accurate mortality prediction of 18 countries at varying stages of strategic lockdown, up to 30 days beyond last data training. PHIRVD establishes mortality-to-infection ratio as the correct pandemic descriptor, substituting reproduction number, and highlights the importance of early and prolonged but strategic lockdown to contain secondary relapse.  Ideal lockdown imposition and withdrawal times have been predicted and validated, including for ongoing regimen.
Distinct regimes of particle and virus abundance explain face mask efficacy for COVID-19	Cheng,  Yafang,  Ma, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions de santé publique Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI)	Regions with a higher proportion of people wearing masks show better control of COVID-19, but the effectiveness of masks is still under debate due to their limited and variable efficiencies in removing respiratory particles. Here, we analyze experimental data and perform model calculations to show that this contrast can be explained by the different abundance regimes between particles and viruses. Upon short-term exposure, respiratory particles are usually in a particle-rich regime, but respiratory viruses are often in a virus-limited regime where the numbers of viruses inhaled by susceptible people are below or close to the infectious dose. This virus-limited regime ensures mask efficacy and synergy of multiple preventive measures in reducing the infection risk.
Remote learning of biochemistry during the COVID-19 pandemic: case of undergraduate students in Bogota, Colombia	Contreras-Rodríguez,  LE,  Sandoval-Hernández, et al	Research Square prepub	Public Health response| Interventions de santé publique	This study describes student perception of remote biochemistry classes at Universidad Nacional de Colombia (Bogota). Methods: A virtual survey was applied to undergraduate students of dentistry and biology programs to assess their perception of the quality and academic impact of remote classes during the mandatory lockdown decreed by the Colombian government for semester I of 2020. Results: The students demonstrated an overall acceptance of the remote biochemistry classes, highlighting that the quality of the classes facilitated the understanding of the topics, increased assessment performance, and significantly promoted self-learning (according to 84.6% of the respondents). Although some students reported having experienced reduced attention to the classes throughout the semester, most of them (80.8%) would remotely attend the biochemistry course again.
Early effect of the Covid-19 epidemic on vaccine coverage of major antigens in Guinea: an analysis of the interrupted time series of national immunization coverage	Dabo,  Moustapha,  Yombouno, et al	medRxiv	Public Health response| Interventions de santé publique	This present study aimed to assess the early impact of COVID-19 on vaccine activities by comparing current trends to trends over the past year when vaccine coverage of major antigens (BCG, OPV, DTP-HepB-Hib, MMR, IPV, and Td) had improved considerably. Methods: The study was carried out at the Expanded Vaccination Program (EPI) of the Republic of Guinea from February 2019 to June 2019. It was a comparative retrospective cohort study on the trends in administrative coverage of the different antigens used in the framework of vaccination. We performed interrupted time series (STI) analysis using the delayed dependent variable model ANCOVA type II Sum Squares with significance for a p-value less than 0.05 to confirm the link between the occurrence of Covid-19 and the collapse of vaccine coverage. Results: Overall, the EPI recorded a median vaccination coverage of less than 80% for all the vaccines introduced and the analysis of the interrupted time series shows that the interruption of the vaccination program was significant for all the vaccines.
SARS2 simplified scores to estimate risk of hospitalization and death among patients with COVID-19	Dashti,  Hesam,  Roche, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	In this study, we examined utility of simpler models for estimating risk of hospitalization of patients with COVID-19 and mortality of these patients based on demographic characteristics (sex, age, race, median household income based on zip code) and smoking status of 12,347 patients who tested positive at Mass General Brigham centers. The corresponding electronic health records were queried from 02/26/2020 to 07/14/2020 to construct derivation and validation cohorts. The derivation cohort was used to fit a generalized linear model for estimating risk of hospitalization within 30 days of COVID-19 diagnosis and mortality within approximately 3 months for the hospitalized patients. On the validation cohort, the model resulted in c-statistics of 0.77 for hospitalization outcome, and 0.72 for mortality among hospitalized patients. Higher risk was associated with older age, male sex, black ethnicity, lower socioeconomic status, and current/past smoking status.
Daytime variation in SARS-CoV-2 infection and cytokine production	Diallo,  Aissatou Bailo,  Gay, et al	bioRxiv	Coronavirology| Coronavirologie	We analyzed circadian rhythm implication in SARS-CoV-2 virus infection of isolated human monocytes, key actor cells in Covid-19 disease, from healthy subjects. The circadian gene expression of Bmal1 and Clock genes was investigated with q-RTPCR. Monocytes were infected with SARS-CoV-2 virus strain and viral infection was investigated by One-Step qRT-PCR and immunofluorescence. Using Cosinor analysis, we showed that Bmal1 and Clock transcripts exhibited circadian rhythm in monocytes with an acrophase and a bathyphase at Zeitgeber Time (ZT)6 and ZT17. After forty-eight hours, the amount of SARS-CoV-2 virus increased in the monocyte infected at ZT6 compared to ZT17. The high virus amount at ZT6 was associated with significant increased release in IL-6, IL-1β and IL-10 compared to ZT17. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response.
Impacts of the COVID-19 epidemic on the department of stomatology in a tertiary hospital: a case study in the General Hospital of the Central Theater Command, Wuhan, China	Dong,  Qingshan,  Kuria, et al	medRxiv	Healthcare Response | Réponse des soins de santé	The aim of this study is to depict the impacts of COVID-19 pandemic on the clinical services and academic activities in the department of stomatology of a tertiary hospitals in Wuhan, China. Methods: We obtained historical data of the Department of Stomatology from the Health Information System of the General Hospital of Central Theater Command, Wuhan, China between January 2018 and June 2020. Results: A significant decrease was noted in the monthly average number of patients seeking the outpatient services for the year 2020. The monthly numbers of patients seeking outpatient services were decreased by two thirds from 2018 to 2020. The number of emergency cases also decreased significantly by 64% in 2020.
Reopening Businesses and Risk of COVID-19 Transmission	Donoghue,  AshleyL,  Dechen, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Transmission Public health interventions*| Interventions de santé publique	Importance: The United States has the highest number of confirmed COVID-19 cases in the world, with over 150,000 COVID-19-related deaths as of July 31, 20201. The true risk of a COVID-19 resurgence as states prepare to reopen businesses is unknown. Objective: To quantify the potential risk of COVID-19 transmission in business establishments by building a risk index for each business that measures transmission risk over time. Design: This retrospective case series study uses anonymized cell phone GPS data to analyze trends in traffic patterns to businesses that may be potentially high-risk from January 2020 to June 2020. Setting: Massachusetts, Rhode Island, Connecticut, New Hampshire, Vermont, Maine, New York, and California. Participants: 1,272,260 businesses within 8 states from January 2020 - June 2020. Exposure(s): We monitored business traffic before the pandemic, during the pandemic and after early phases of reopening in 8 states. Main Outcome: Our primary outcome is our business risk index. The index was built using two metrics: visitors per square foot and the average duration of visits. Visitors per square foot account for how densely visitors are packed into businesses. The average duration of visits accounts for the length of time visitors are spending in a business. Results: Potentially risky traffic behaviors at businesses decreased by 30% by April. Since the end of April, the risk index has been increasing as states reopen. On average, it has increased between 10 to 20 percentage points since April and is moving towards pre-pandemic levels of traffic. There are some notable differences in trends across states and industries. Conclusion: Our risk index provides a way for policymakers and hospital decision makers to monitor the potential risk of COVID-19 transmission from businesses based on the frequency and density of visits to businesses. Traffic is slowly moving towards pre-pandemic levels. This can serve as an important metric as states monitor and evaluate their reopening strategies.
Evaluating ten commercially-available SARS-CoV-2 rapid serological tests using the STARD (Standards for Reporting of Diagnostic Accuracy Studies) method	Dortet,  Laurent,  Ronat, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes Immunology | Immunologie	Numerous SARS-CoV-2 rapid serological tests have been developed, but their accuracy has usually been assessed using very few samples, and rigorous comparisons between these tests are scarce. In this study, we evaluated and compared 10 commercially-available SARS-CoV-2 rapid serological tests using the STARD methodology (Standards for Reporting of Diagnostic Accuracy Studies). 250 sera from 159 PCR-confirmed SARS-CoV-2 patients (collected from 0 to 32 days after onset of symptoms) were tested with rapid serological tests. Control sera (N=254) were retrieved from pre-COVID periods from patients with other coronavirus infections (N=11), positive rheumatoid factors (N=3), IgG/IgM hyperglobulinemia (N=9), malaria (n=5), or no documented viral infection (N=226). All samples were tested using rapid lateral flow immunoassays (LFIA) from ten manufacturers. Only four tests achieved ≥98% specificity, with other tests ranging from 75.7%-99.2%. Sensitivities varied by the day of sample collection, from 31.7%-55.4% (Days 0-9), 65.9%-92.9% (Days 10-14), and 81.0%-95.2% (>14 days) after the onset of symptoms, respectively. Only three tests evaluated met French Health Authorities' thresholds for SARS-CoV-2 serological tests (≥90% sensitivity + ≥98% specificity). Overall, the performances between tests varied greatly, with only a third meeting acceptable specificity and sensitivity thresholds. Knowing the analytical performance of these tests will allow clinicians to use them with more confidence, could help determine the general population's immunological status, and may diagnose some patients with false-negative RT-PCR results.
Covid-19 Across European Regions: The Role of Border Controls	Eckardt,  Matthias,  Kappner, et al	SSRN- Lancet prepublication	Modelling/ prediction| Modélisation/prédiction Public health interventions*| Interventions de santé publique	Attempts to constrain the spread of Covid-19 included the temporal reintroduction of travel restrictions and border controls within the Schengen area. While such restrictions clearly involve costs, their benefits have been disputed. We use a new set of daily regional data of confirmed Covid-19 cases from the respective statistical agencies of 18 Western European countries. Our data starts with calendar week 10 (starting 2nd March 2020) and extends to calendar week 17 (ending 26th April 2020), which allows us to test for treatment effects of border controls. We use Poisson models with fixed effects and controls for the stringency of national measures, as well as a Bayesian spatio-temporal specification using an integrated nested Laplace approximation (INLA) to take unobserved spatio-temporal heterogeneity into account. Both approaches suggest that border controls had a significant effect to limit the pandemic.
No association between circulating levels of testosterone and sex hormone-binding globulin and risk of COVID-19 mortality in UK biobank	Fan,  Xikang,  Yang, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	Background: Sex-disaggregated data suggest that men with coronavirus disease 2019 (COVID-19) are more likely to die than women. Whether circulating testosterone or sex hormone-binding globulin (SHBG) contributes to such sex differences remains unknown. Objective: To evaluate the associations of circulating total testosterone (TT), free testosterone (FT), and SHBG with COVID-19 mortality. Design: Prospective analysis. Setting: UK Biobank. Participants: We included 1306 COVID-19 patients (678 men and 628 women) who had serum TT and SHBG measurements and were free of cardiovascular disease or cancer at baseline (2006-2010). Main outcome measures: The death cases of COVID-19 were identified from National Health Service death records updated at 31 July 2020. Unconditional logistic regression was performed to estimate the odds ratio (OR) and 95% confidence intervals (CI) for mortality. Results: We documented 315 deaths of COVID-19 (194 men and 121 women). After adjusting for potential confounders, we did not find any statistically significant associations for TT (OR per 1-SD increase = 1.03, 95% CI: 0.85-1.25), FT (OR per 1-SD increase = 0.95, 95% CI: 0.77-1.17), or SHBG (OR per 1-SD increase = 1.09, 95% CI: 0.87-1.37) with COVID-19 mortality in men. Similar null results were observed in women ( TT: OR per 1-SD increase = 1.10, 95% CI: 0.85-1.42; FT: OR per 1-SD increase = 1.10, 95% CI: 0.82-1.46; SHBG: OR per 1-SD increase = 1.16, 95% CI: 0.89-1.53). Conclusions: Our findings do not support a significant role of circulating testosterone or SHBG in COVID-19 prognosis
Deep learning for predicting COVID-19 malignant progression	Fang,  Cong,  Bai, et al	medRxiv	Clinical data| Données cliniques	As COVID-19 is highly infectious, many patients can simultaneously flood into hospitals for diagnosis and treatment, which has greatly challenged public medical systems. Treatment priority is often determined by the symptom severity based on first assessment. However, clinical observation suggests that some patients with mild symptoms may quickly deteriorate. Hence, it is crucial to identify patient early deterioration to optimize treatment strategy. To this end, we develop an early-warning system with deep learning techniques to predict COVID-19 malignant progression. Our method leverages clinical data and CT scans of outpatients and achieves an AUC of 0.920 in the single-center study and an average AUC of 0.874 in the multicenter study. Moreover, our model automatically identifies crucial indicators that contribute to the malignant progression, including Troponin, Brain natriuretic peptide, White cell count, Aspartate aminotransferase, Creatinine, and Hypersensitive C-reactive protein.
The Long-Term Distributional and Welfare Effects of Covid-19 School Closures	Fuchs-Schündeln,  Nicola,  Krueger, et al	SSRN- Lancet prepublication	Public health interventions*| Interventions de santé publique Public Health response| Interventions de santé publique Economics | Économie	Using a structural life-cycle model, we quantify the long-term impact of school closures during the Corona crisis on children affected at different ages and coming from households with different parental characteristics. In the model, public investment through schooling is combined with parental time and resource investments in the production of child human capital at different stages in the children's development process. We quantitatively characterize both the long-term earnings consequences on children from a Covid-19 induced loss of schooling, as well as the associated welfare losses. Due to self-productivity in the human capital production function, skill attainment at a younger stage of the life cycle raises skill attainment at later stages, and thus younger children are hurt more by the school closures than older children. We find that parental reactions reduce the negative impact of the school closures, but do not fully offset it. The negative impact of the crisis on children's welfare is especially severe for those with parents with low educational attainment and low assets. The school closures themselves are primarily responsible for the negative impact of the Covid-19 shock on the long-run welfare of the children, with the pandemic-induced income shock to parents playing a secondary role.
Adapting Lot Quality Assurance Sampling to accommodate imperfect tests: application to COVID-19 serosurveillance in Haiti	Fulcher,  IsabelR,  Clisbee, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	Background: Lot Quality Assurance Sampling (LQAS), a tool used for monitoring health indicators in low resource settings resulting in "high" or "low" classifications, assumes that determination of the trait of interest is perfect. This is often not true for diagnostic tests, with imperfect sensitivity and specificity. Here, we develop Lot Quality Assurance Sampling for Imperfect Tests (LQAS-IMP) to address this issue and apply it to a COVID-19 serosurveillance study in Haiti. Development: As part of the standard LQAS procedure, the user specifies allowable classification errors for the system, which is defined by a sample size and decision rule. We show that when an imperfect diagnostic test is used, the classification errors are larger than specified. We derive a modified procedure, LQAS-IMP, that accounts for the sensitivity and specificity of a diagnostic test to yield correct classification errors. Application: At Zanmi Lasante health facilities in Haiti, the goal was to assess the prior circulation of COVID-19 among healthcare workers (HCWs) using a limited number of antibody tests. As the COVID-19 antibody tests were known to have imperfect diagnostic accuracy, we used the LQAS-IMP procedure to define valid systems for sampling at eleven hospitals in Haiti. Conclusions: The LQAS-IMP procedure accounts for imperfect sensitivity and specificity in system design; if the accuracy of a test is known, the use of LQAS-IMP extends LQAS to applications for indicators that are based on laboratory tests, such as COVID-19 antibodies
Mathematical Modeling and a Month Ahead Forecast of the Coronavirus Disease 2019 (COVID-19) Pandemic: An Indian Scenario	Ganiny,  Suhail,  Nisar, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	India, the second-most populous country in the world, has been lately witnessing a daily surge in the COVID-19 infected cases. India is currently among the worst-hit nations worldwide, due to the COVID-19 pandemic, and ranks just behind Brazil and USA. In order to prevent the further worsening of the situation, predicting the future course of the pandemic is of utmost importance. In this paper, we model the past trajectory (March 01, 2020 - July 25, 2020) and make a month-long (July 26, 2020 - August 24, 2020) forecast of the future evolution of the COVID-19 pandemic in India using an autoregressive integrated moving average (ARIMA) model. According to our forecasting results, India is likely to have 3,800,989 cumulative infected cases, 1,634,142 cumulative active cases, 2,110,697 cumulative recoveries and 56,150 cumulative deaths by August 24, 2020, if the current trend of the pandemic continues to prevail. The implications of these forecasts are that in the upcoming month the infection rate of COVID-19 in India is going to escalate, while as the rate of recovery and the case-fatality rate is likely to reduce. In order to avert these possible scenarios, the administration and health-care personnel need to formulate and implement robust control measures, while the general public needs to be more responsible and strictly adhere to the established and newly formulated guidelines to slow down the spread of the pandemic and prevent it from transforming into a catastrophe
Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide	Gao,  Dong,  Li, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly become a global public health threat due to the lack of effective drugs or vaccines against SARS-CoV-2. The efficacy of several repurposed drugs has been evaluated in clinical trials. Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. However, definitive evidence for the therapeutic efficacy of enzalutamide in COVID-19 is lacking. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. TMPRSS2 knockout significantly inhibited SARS-CoV-2 infection in vivo. Enzalutamide effectively inhibited SARS-CoV-2 infection in human prostate cancer cells (LNCaP) but not in human lung cancer cells or patient-derived lung organoids. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Moreover, we observed distinct AR binding patterns between prostate cells and lung cells and a lack of direct binding of AR to TMPRSS2 in human lung cells. Thus, our findings do not support the postulated protective role of enzalutamide in treating COVID-19.Competing Interest StatementThe authors have declared no competing interest.
Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France	Germain,  Nicolas,  Herwegh, et al	medRxiv	Epidemiology| Épidémiologie Transmission Immunology | Immunologie	Background: The COVID-19 pandemic has altered organ and tissue donations as well as transplantation practices. SARS-CoV-2 serological tests could help in the selection of donors. We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA. Methods: 235 tissue donors at the Lille Tissue bank between November 1, 2019 and March 16, 2020 were included. Archived serum samples were tested for SARS-CoV-2 antibodies using two FDA-approved kits. Results: Most donors were at higher risks for severe COVID-19 illness including age over 65 years (142/235) and/or presence of co-morbidities (141/235). According to the COVID-19 risk assessment of transmission, 183 out of 235 tissue donors presented with a low risk level and 52 donors with an intermediate risk level of donor derived infection. Four out of the 235 (1.7%) tested specimens were positive for anti-SARS-CoV-2 antibodies: 2 donors with anti-N protein IgG and 2 other donors with anti-S protein total Ig. None of them had both type of antibodies. Conclusion: Regarding the seroprevalence among tissue donors, we concluded that the transmission probability to recipient via tissue products was very low at the beginning of the outbreak.
Impact of the COVID-19 pandemic on emergency department CT for suspected diverticulitis: A natural experiment to explain patients’ and clinicians’ assessment of risk and willingness to undergo CT scanning?	Gibson,  ALG,  C	Research Square prepub	Healthcare Response | Réponse des soins de santé	Purpose: This study examined the impact of the COVID-19 pandemic on emergency department CT use for acute non-traumatic abdominal pain, to better understand why imaging volume so drastically decreased during the COVID-19 pandemic. Methods: This was a retrospective review of emergency imaging volumes from January 5 to May 30, 2020. Weekly volume data were collected for total imaging studies, abdominopelvic CT, and abdominopelvic CTs positive for common causes of acute non-traumatic abdominal pain. Two emergency radiology attendings scored all diverticulitis cases independently and weekly volume data for uncomplicated and complicated diverticulitis cases was also collected. Volume data prior to and during the COVID-19 pandemic was compared, using 2019 volumes as a control. Results: During the COVID-19 pandemic, overall emergency imaging volume decreased 30% compared to 2019 (p = 0.002). While the number of emergency abdominopelvic CTs positive for appendicitis and small bowel obstruction did not significantly change during the COVID-19 pandemic, the number of cases of diverticulitis decreased significantly compared to 2019 (p = 0.001). This reduction can be specifically attributed to decreased uncomplicated diverticulitis cases, as the number of uncomplicated diverticulitis cases dropped significantly (p = 0.002) while there was no significant difference in the number of complicated diverticulitis cases (p = 0.09). Conclusions: Reduced emergency abdominopelvic CT volume during the COVID-19 pandemic can partially be explained by decreased imaging of lower acuity patients. This data may help formulate future strategies for imaging resource utilization with an improved understanding of the relationship between perceived imaging risk and symptom acuity.
A Poisson Regression Analysis of COVID-19 Pandemic: Implication on Food Security in North Eastern Nigeria	Giroh,  Yuniyus Dengle,  Nachandiya, et al	SSRN- Lancet prepublication	Public Health response| Interventions de santé publique	The North East region of Nigeria is the worst hit by activities of Boko Haram terrorist group displacing homes, livelihoods, destruction to lives and properties with Internally Displaced Persons (IDPs) with about 3.6 million people projected to be in severe acute food in security. The COVID-19 Pandemic has further aggravated the precarious food security in the region. The study was therefore conducted to examine COVID-19 cases in the region and its likely effects on food security. The data for the study was extracted from the daily COVID-19 cases update released by the Nigeria Centre for Disease Control (NCDC) online database from February 28th, 2020 – 31st August 2020. The extracted data were analyzed using descriptive statistics and Poisson Regression. Results of the analysis revealed that admitted and discharged cases had negative and inverse relationship with COVID-19 related deaths in the North East region of the country. Furthermore, increased cases have a positive and significant effect on the number of deaths. The effect of the pandemic has also worsen food security with decrease in minimum food items needed for survival of a household in a month as a result of the increase in the Survival Minimum Expenditure Basket (SMEB) from N19,072($47.68) to N19,345 ($48.36) in selected markets in the region.
Shedding of infectious SARS-CoV-2 from airways in hospitalized COVID-19 patients in relation to serum antibody responses	Glans,  Hedvig,  Gredmark-Russ, et al	medRxiv	Transmission Clinical data| Données cliniques Immunology | Immunologie	To understand the risk of transmission of SARS-CoV-2 in hospitalized COVID-19 patients we simultaneously assessed the presence of SARS-CoV-2 RNA, live infectious virus in the airways, and virus-specific IgG and neutralizing antibodies in sera in 36 hospitalized COVID-19 patients. SARS-CoV-2 could be cultured from four patients, all with low or undetectable antibody response. Our data suggests that the level of SARS-CoV-2 antibodies may correlate to risk for shedding live SARS-CoV-2 virus in hospitalized COVID-19 patients.
COVID-19 in Kerala: analysis of measures and impacts	Goult,  E,  S	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	In the absence of an effective vaccine or drug therapy, non-Pharmaceutical Interventions are the only option for control of the outbreak of the coronavirus disease 2019, a pandemic with global implications. Each of the over 200 countries affected1 has followed its own path in dealing with the crisis, making it difficult to evaluate the effectiveness of measures implemented, either individually, or collectively. In this paper we analyse the case of the south Indian state of Kerala, which received much praise in the international media for its success in containing the spread of the disease in the early months of the pandemic, but is now in the grips of a second wave. We use a model to study the trajectory of the disease in the state during the first four months of the outbreak. We then use the model for a retrospective analysis of measures taken to combat the spread of the disease, to evaluate their impact. Because of the unusual aspects of the Kerala case, we argue that it is a model worthy of a place in the discussion on how the world might best handle this and other, future, pandemics.
Whether Early Pulse Steroid dose is associated with lower mortality in COVID-19 critically ill Patients- An exploratory retrospective Chart Review	Goyal,  Abhishek,  Saigal, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques Therapeutics| Thérapeutique	Optimal dose steroid as per defined optimum(<24 hours and doses tailored to P/F at presentation) criteria can offer protective effect from mortality which persists after adjusting for age. This protective effect was not found to be negatively influenced by the risk of infection.
COVIDNet-CT: A Tailored Deep Convolutional Neural Network Design for Detection of COVID-19 Cases from Chest CT Images	Gunraj,  H,  W	ArXiv	Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes Healthcare Response | Réponse des soins de santé	Authors introduce COVIDNet-CT, a deep convolutional neural network architecture that is tailored for detection of COVID-19 cases from chest CT images via a machine-driven design exploration approach. Additionally, we introduce COVIDx-CT, a benchmark CT image dataset derived from CT imaging data collected by the China National Center for Bioinformation comprising 104,009 images across 1,489 patient cases.
SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike	Guthmiller,  JennaJ,  Stovicek, et al	bioRxiv	Clinical data| Données cliniques Coronavirology| Coronavirologie Immunology | Immunologie	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a global pandemic. The antigen specificity and kinetics of the antibody response mounted against this novel virus are not understood in detail. Here, we report that subjects with a more severe SARS-CoV-2 infection exhibit a larger antibody response against the spike and nucleocapsid protein and epitope spreading to subdominant viral antigens, such as open reading frame 8 and non-structural proteins. Subjects with a greater antibody response mounted a larger memory B cell response against the spike, but not the nucleocapsid protein. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. Together, this study reveals that subjects with a more severe SARS-CoV-2 infection exhibit a greater overall antibody response to the spike and nucleocapsid protein and a larger memory B cell response against the spike.Competing Interest StatementThe authors have declared no competing interest.
Outdoor PM2.5 Concentration and Rate of Change in COVID-19 Infection in 31 Provincial Capital Cities in China	Han,  Yang,  Lam, et al	medRxiv	Epidemiology| Épidémiologie	Motivated by the findings that exposure to daily outdoor PM2.5 (P) may increase the risk of influenza infection, our study examines if immediate exposure to outdoor P will modify the rate of change in the daily number of COVID-19 infections (R), for (1) 31 Chinese provincial capital cities and (2) Wuhan, China, using regression modelling. A causal relationship between P and R across 31 provincial capital cities in China was established via matching. A higher P resulted in a higher R in China. A 10 μg/m3 increase in P gave a 0.9% increase in R (p < 0.05). An interaction analysis between P and absolute humidity (AH) showed a statistically significant positive relationship between P × AH and R (p < 0.01). When AH was ≤ 8.6 g/m3, higher P and AH gave a higher R (p < 0.01). Interpretation: Given that P can exacerbate R, we recommend the installation of air purifiers and improving air ventilation to reduce the effect of P on R. Given that an increasing AH that falls below 8.6 g/m3 exacerbated R, dehumidifiers can be used to reduce AH and R. Further, given the increasing discussions/observations that COVID-19 can be airborne, surgical masks should be used to protect one from contracting the virus via the viral-particulate transmission pathway
The impact of asthma on mental health & wellbeing during COVID-19 lockdown	Higbee,  DanielH,  Nava, et al	medRxiv	Public Health response| Interventions de santé publique	People with asthma have worse mental health & wellbeing during lockdown compared to people without asthma. Although the effect of asthma on mental health is of similar magnitude between the generations, younger participants with asthma declined to lower levels of mental health despite reporting less symptoms, COVID-19 infection and self-isolation.
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors	Hoffmann,  HH,  Schneider, et al	bioRxiv	Coronavirology| Coronavirologie	Focused CRISPR screens targeting host factors in the SARS-CoV-2 interactome were performed for SARS-CoV-2, HCoV-229E, HCoV-NL63, and HCoV-OC43 coronaviruses. Focused interactome CRISPR screens achieve higher resolution compared to genome-wide screens, leading to the identification of critical factors missed by the latter. Parallel CRISPR screens against multiple coronaviruses uncover host factors and pathways with pan-coronavirus and virus-specific functional roles.
Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2	Huang,  Xiaoqiang,  Zhang, et al	bioRxiv	Coronavirology| Coronavirologie zoonoses	Using this pipeline, we systematically examined 285 ACE2 variants from mammals, birds, fish, reptiles, and amphibians, and found that the binding energies calculated on the modeled Spike-RBD/ACE2 complex structures correlate closely with the effectiveness of animal infections as determined by multiple experimental datasets. Built on the optimized binding affinity cutoff, we suggested a set of 96 mammals, including 48 experimentally investigated ones, which are permissive to SARS-CoV-2, with candidates from primates, rodents, and carnivores at the highest risk of infection.
Development of a serological assay to identify SARS-CoV-2 antibodies in COVID-19 patients	Huynh,  Angela,  Arnold, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	Authors describe an enzyme-linked immunosorbent assay (ELISA) that detects antibodies against the following SARS-CoV-2 recombinant proteins: the full-length spike (S) protein and the receptor-binding domain (RBD). Our assay is sensitive and specific for immunoglobulin (Ig) G, IgA and IgM anti-S protein and anti-RBD antibodies.
Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity	Inde,  Zintis,  Yapp, et al	bioRxiv	Clinical data| Données cliniques Coronavirology| Coronavirologie	Angiotensin-converting enzyme 2 (ACE2) maintains cardiovascular and renal homeostasis but also serves as the entry receptor for the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), the causal agent of novel coronavirus disease 2019 (COVID-19). Authors show that ACE2 transcripts are expressed in the lung and trachea shortly after birth, downregulated during childhood, and again expressed at high levels in late adulthood. The work provides the framework for translation of apoptosis modulating drugs as novel treatments for COVID-19.
Lessons from the COVID-19 pandemic: People's experiences and satisfaction with telehealth during the COVID-19 pandemic in Australia	Isautier,  JenniferMJ,  Copp, et al	medRxiv	Public Health response| Interventions de santé publique	The objective of this study was to determine how participants perceived telehealth consults in comparison to traditional in-person visits, and to investigate whether people believe that telehealth services would be useful beyond the pandemic. Telehealth appointments were reported to be comparable to traditional in-person medical appointments by most of our sample.
The influence of pH on SARS-CoV-2 infection and COVID-19 severity	Jimenez,  Leandro,  Codo, et al	medRxiv	Clinical data| Données cliniques	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect a broad range of human tissues by using the host receptor angiotensin-converting enzyme 2 (ACE2). Authors showed that patients with Barrett's esophagus (BE) have a higher expression of ACE2 in BE tissues compared to normal squamous esophagus, and that the lower pH associated with BE may drive this increase in expression. They showed in two independent cohorts of COVID-19 patients that previous use of proton pump inhibitors is associated with 2- to 3-fold higher risk of death compared to those not using the drugs.
Mortality and risk factors among US Black, Hispanic, and White patients with COVID-19	Jun,  Tomi,  Nirenberg, et al	medRxiv	Epidemiology| Épidémiologie	Authors followed 3,086 COVID-19 patients hospitalized on or before April 13, 2020 within an academic health system in New York (The Mount Sinai Health System) until June 2, 2020. Multivariable logistic regression was used to evaluate demographic, clinical, and laboratory factors as independent predictors of in-hospital mortality. In this large, racially and ethnically diverse cohort of COVID-19 patients in New York City, we identified similarities and important differences across racial and ethnic groups in risk factors for in-hospital mortality.
Hyaluronan is abundant in COVID-19 respiratory secretions	Kaber,  Gernot,  Kratochvil, et al	medRxiv	Therapeutics| Thérapeutique	Authors hypothesized that hyaluronan, an extracellular matrix glycosaminoglycan produced at sites of active inflammation that promotes edema in other settings, might be a component of COVID-19 secretions. Therapeutic strategies targeting hyaluronan should be investigated further for potential use in patients with COVID-19.
A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation	Kang,  Sisi,  Yang, et al	bioRxiv	Coronavirology| Coronavirologie	Authors isolated and profiled a panel of 32 N protein-specific monoclonal antibodies (mAb) from a quick recovery coronavirus disease-19 (COVID-19) convalescent, who had dominant antibody responses to SARS-CoV-2 N protein rather than to Spike protein. B cell profiling, structural determination, and protease activity assays identify a functional antibody to N protein.
Molecular Characterization, Phylogenetic and Variation Analyzes of SARS-CoV-2 strains in Turkey	Karamese,  Murat,  Ozgur, et al	bioRxiv	Coronavirology| Coronavirologie	Authors present the sequence analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients.  The results indicated that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences.
On Machine Learning-Based Short-Term Adjustment of Epidemiological Projections of COVID-19 in US	Kefayati,  Sarah,  Huang, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	Authors present early results from a systemic analysis of short-term adjustment of epidemiological modeling of COVID 19 pandemic in US during March-April 2020. They found that counties clustered with New York County resulted in best preforming model with maximum of R2= 0.90 and minimum of R2= 0.85 for state-based and COVID-based clustering strategy, respectively.
A Geotemporal Clustering Model for COVID-19 Projection	Keskin,  NB	SSRN- Lancet prepublication	Epidemiology| Épidémiologie	Authors propose a geotemporal clustering based algorithm to predict the state-level COVID-19 cases in the United States, using the state-level population and historical COVID-19 case data as input. Results indicate that in the next 20 days, states may be in starkly different situations if there are no interventions.
The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein	Knierman,  MichaelD,  Lannan, et al	SSRN- Lancet prepublication	Vaccine Research| Recherche sur les vaccins	In this study mass spectrometry was used to identify 529 unique sequences from SARS-CoV-2 spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. This work represents the most precise and comprehensive immunopeptidomic investigation with SARS-CoV-2 spike glycoprotein and allows detailed analysis of features which may aid vaccine development to end the current COVID-19 pandemic.
Modeling the dynamics of SARS-CoV-2 immunity waning, antigenic drifting, and population serology patterns	Koopman,  JamesS,  Simon, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	Reinfection with SARS-CoV-2 can result from either waning immunity, a drift in the virus that escapes previously stimulated immunity, or both. Authors constructed an SIR transmission model of waning and drifting that can be fitted to cross-neutralization serological data. Given the parameters, the model predicts infection patterns.
SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically disordered region	Kumar,  Amit,  Kumar, et al	bioRxiv	Coronavirology| Coronavirologie	Nonstructural protein 1 (NSP1) of SARS-CoV-2 plays a key role in downregulation of RIG-I pathways and interacts with 40 S ribosome. Recently, the cryo-EM structure in complex with 40S ribosome is deciphered. However, the structure of full length NSP1 without any partner has not been studies. Also, the conformation of NSP1-C terminal region in isolation is not been studied. In this study, we have investigated the conformational dynamics of NSP1C-terminal region (NSP1-CTR; amino acids 130-180) in isolation and under different solvent environments. The NSP1-CTR is found to be intrinsically disordered in aqueous solution. Further, we used alpha helix inducer, trifluoroethanol, and found induction of alpha helical conformation using CD spectroscopy. Additionally, in the presence of SDS, NSP1-CTR is showing a conformational change from disordered to ordered, possibly gaining alpha helix in part. But in presence of neutral lipid DOPC, a slight change in conformation is observed. This implies the possible role of hydrophobic interaction and electrostatic interaction on the conformational changes of NSP1. The changes in structural conformation were further studied by fluorescence-based studies, which showed significant blue shift and fluorescence quenching in the presence of SDS and TFE. Lipid vesicles also showed fluorescence-based quenching. In agreement to these result, fluorescence lifetime and fluorescence anisotropy decay suggests a change in conformational dynamics. The zeta potential studies further validated that the conformational dynamics is mostly because of hydrophobic interaction. In last, these experimental studies were complemented through Molecular Dynamics (MD) simulation which have also shown a good correlation and testify our experiments. We believe that the intrinsically disordered nature of the NSP1-CTR will have implications in disorder based binding promiscuity with its interacting proteins.Competing Interest StatementThe authors have declared no competing interest.
How has the COVID-19 Pandemic Affected Outdoor Recreation in the U.S.? A Revealed Preference Approach	Landry,  Craig,  Bergstrom, et al	SSRN- Lancet prepublication	Public Health response| Interventions de santé publique	This study examines the effects of the COVID-19 pandemic on outdoor recreation visits and values using a unique revealed preference travel cost method approach. Demand models are estimated using data on pre- and post-pandemic visits reported in a nationwide survey of outdoor recreation participants. The demand models incorporate visitors’ COVID-19 related subjective risk perceptions as a pre- and post-pandemic measure of site quality. Our results suggest that the COVID-19 pandemic has had negative effects on both recreation visits and values. We recommend that recreation site managers focus on innovative ways to reduce the COVID-19 related welfare losses measured in this study.
The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample	Leightley,  Daniel,  Vitiello, et al	medRxiv	Epidemiology| Épidémiologie Immunology | Immunologie	We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at King's College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.
Does the COVID-19 Pandemic Affect People’s Social and Economic Preferences? Evidence from China	Li,  King King,  Huang, et al	SSRN- Lancet prepublication	Public Health response| Interventions de santé publique	This study investigates the effect of the COVID-19 pandemic on people’s preferences including social preference in terms of trust and trustworthiness, risk attitude, ambiguity attitude, and time preference. We compare the preferences of 5382 subjects in three sets of large-scale online experiments with samples drawn from provinces across mainland China before (Studies 1 and 2) and after (Study 3) the COVID-19 pandemic. We find that after the outbreak, the subjects overall are more trusting (7% higher) and more trustworthy (12% higher), which suggests the first effect dominates. We also find that the subjects are more risk averse and less patient after the outbreak, which is consistent with the idea that the fear generated by the pandemic induces risk aversion and impatience. Finally, using two large mobility datasets derived from anonymized mobile phone records, we show that people’s preferences are not affected by social distancing.
A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD	Li,  Tingting,  Han, et al	bioRxiv	Coronavirology| Coronavirologie Vaccine Research| Recherche sur les vaccins	The spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614G pseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.Competing Interest StatementThe authors have declared no competing interest.
Semi-Supervised Active Learning for COVID-19 Lung Ultrasound Multi-symptom Classification	Liu,  L,  L	ArXiv	Clinical data| Données cliniques	Ultrasound (US) is a non-invasive yet effective medical diagnostic imaging technique for the COVID-19 global pandemic. However, due to complex feature behaviors and expensive annotations of US images, it is difficult to apply Artificial Intelligence (AI) assisting approaches for lung's multi-symptom (multi-label) classification. To overcome these difficulties, we propose a novel semi-supervised Two-Stream Active Learning (TSAL) method to model complicated features and reduce labeling costs in an iterative procedure. The core component of TSAL is the multi-label learning mechanism, in which label correlations information is used to design multi-label margin (MLM) strategy and confidence validation for automatically selecting informative samples and confident labels. On this basis, a multi-symptom multi-label (MSML) classification network is proposed to learn discriminative features of lung symptoms, and a human-machine interaction is exploited to confirm the final annotations that are used to fine-tune MSML with progressively labeled data. Moreover, a novel lung US dataset named COVID19-LUSMS is built, currently containing 71 clinical patients with 6,836 images sampled from 678 videos. Experimental evaluations show that TSAL using only 20% data can achieve superior performance to the baseline and the state-of-the-art. Qualitatively, visualization of both attention map and sample distribution confirms the good consistency with the clinic knowledge.
The impact of the Covid-19 pandemic on emergency and elective hip surgeries in Norway	Magnusson,  Karin,  Helgeland, et al	medRxiv	Healthcare Response | Réponse des soins de santé	This study aimed to assess the effects of Covid-19 pandemic lockdown restrictions on the number of emergency and elective hip joint surgeries, and explore whether these procedures are more/less affected by lockdown restrictions than other hospital care. After-lockdown elective hip surgeries were one third the number of before-lockdown (IRR ~0.3), which is a greater drop than the drop seen in all-cause elective hospital care (IRR ~0.6) (no age/sex differences). Men aged 35-69 had half the number of emergency hip fracture surgeries (IRR ~0.6), whereas women aged ≥70 had the same number of emergency hip fracture surgeries after lockdown (IRR ~1). Only women aged 35-69 and men aged ≥70 had emergency hip fracture surgery rates after lockdown comparable to what may be expected based on analyses of all-cause acute care (IRR ~0.80)
Modelling the first wave of the COVID-19 epidemic in the Czech Republic and the role of government interventions	Majek,  Ondrej,  Ngo, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique Public Health response| Interventions de santé publique	In the Czech Republic, the first COVID-19 cases were confirmed on 1 March 2020; early population interventions were adopted in the following weeks. A simple epidemiological model was developed to help decision-makers understand the course of the epidemic and perform short-term predictions. In this paper, we present the use of the model and estimated changes in the reproduction number (decrease from > 2.00 to < 1.00 over March and April) following adopted interventions.
The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning	Marvel,  SkylarW,  House, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	We created a Pandemic Vulnerability Index (PVI) to support counties and municipalities by integrating baseline data on relevant community vulnerabilities with dynamic data on local infection rates and interventions. The PVI visually synthesizes county-level vulnerability indicators, enabling their comparison in regional, state, and nationwide contexts. Considering an outlook horizon from 1 to 28 days, the overall PVI scores are significantly associated with key vulnerability-related outcome metrics of cumulative deaths, population adjusted cumulative deaths, and the proportion of deaths from cases. The modeling results indicate the most significant predictors of case counts are population size, proportion of black residents, and mean PM2.5. The machine learning forecast results were strongly predictive of observed cases and deaths up to 14 days ahead. The modeling reinforces an integrated concept of vulnerability that accounts for both dynamic and static data streams and highlights the drivers of inequities in COVID-19 cases and deaths. These results also indicate that local areas with a highly ranked PVI should take near-term action to mitigate vulnerability.
Effect of Lockdown Implementation, Environmental & Behavioural factors, Diet and Virus Mutations on COVID-19 Outcomes: A Study on Critical Containment Zones of Indian state of Maharashtra	Mohite,  Onkar Tanaji,  Avhad, et al	medRxiv	Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	This work details the study of critical containment zones in Maharashtra within a time (April 9 2020 - July 31 2020) in the context of COVID-19. The effects of lockdown implementation, community isolation, environmental factors, demographic aspects, behavioural factors, diet etc. have been investigated. The effect of the aforementioned factors on the infected cases, cumulative infected cases, recoveries, cumulative recoveries, active cases, deaths and cumulative deaths are analyzed. The integrated effects of the aforementioned factors on COVID- 19 outcomes are further amplified due to adequate and inadequate health facilities. The study will be helpful to scientists, researchers, pharmacists and biotechnologists in new vaccine design & to accommodate above factors for the betterment of susceptible & infected people of Maharashtra and similar demographies across the globe. Further, it pinpoints the need for more awareness and control strategies among the people to reduce the havoc, stress, fear, anxiety, pathogenicity and thereby reducing mortality.
Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines	Mohseni,  Amir Hossein,  Taghinezhad-S, et al	bioRxiv	Coronavirology| Coronavirologie Vaccine Research| Recherche sur les vaccins	The coronavirus disease 2019 (COVID-19) is triggered by severe acute respiratory syndrome mediated by coronavirus 2 (SARS-CoV-2) infection and was declared by WHO as a major international public health concern. While worldwide efforts are being advanced towards vaccine development, the structural modeling of TCR-pMHC (T Cell Receptor-peptide-bound Major Histocompatibility Complex) regarding SARS-CoV-2 epitopes and the design of effective T cell vaccine based on these antigens are still unresolved. Here, we present both pMHC and TCR-pMHC interfaces to infer peptide epitopes of the SARS-CoV-2 proteins. Accordingly, significant TCR-pMHC templates (Z-value cutoff > 4) along with interatomic interactions within the SARS-CoV-2-derived hit peptides were clarified. Also, we applied the structural analysis of the hit peptides from different coronaviruses to highlight a feature of evolution in SARS-CoV-2, SARS-CoV, bat-CoV, and MERS-CoV. Peptide-protein flexible docking between each of the hit peptides and their corresponding MHC molecules were performed, and a multi-hit peptides vaccine against the S and N glycoprotein of SARS-CoV-2 was designed. Filtering pipelines including antigenicity, and also physiochemical properties of designed vaccine were then evaluated by different immunoinformatics tools. Finally, vaccine-structure modeling and immune simulation of the desired vaccine were performed aiming to create robust T cell immune responses. We anticipate that our design based on the T cell antigen epitopes and the frame of the immunoinformatics analysis could serve as valuable supports for the development of COVID-19 vaccine.Competing Interest StatementThe authors have declared no competing interest.
Cerebral Venous Sinus Thrombosis Associated with SARS-CoV-2; a Multinational Case Series	Mowla,  Ashkan,  Shakibajahromi, et al	medRxiv	Clinical data| Données cliniques	We present a series of cerebral venous sinus thrombosis (CVST) cases with SARS-CoV-2 infection by collecting cases of CVST in SARS-CoV-2 infected patients admitted to nine tertiary stroke centers from the beginning of the pandemic to June 30th, 2020.  A total of 13 patients fulfilled the inclusion criteria with six patients were discharged with good outcomes (mRS≤2) and three patients died in hospital.
Spatial and temporal trends in social vulnerability and COVID-19 incidence and death rates in the United States	Neelon,  Brian,  Mutiso, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	The purpose of this retrospective longitudinal study was to examine temporal trends among counties with high and low social vulnerability and to quantify disparities in these trends over time. Results indicate that the impact of COVID-19 is not static but can migrate from less vulnerable counties to more vulnerable counties over time.
Drivers Affecting the Acceptance and Use of Electronic Learning Among Ugandan University Students in the COVID-19 Era. A Cross-Sectional Survey Among Three Universities	Nelson,  Twinamasiko,  Julius, et al	SSRN- Lancet prepublication	Public Health response| Interventions de santé publique	The present study sought to determine the factors affecting the acceptance and use of electronic learning among Ugandan University students in three universities through questionnaires and semi-structured interviews. Overall, 69.2% (n = 400) had good knowledge, 22.5% (n = 130) had good/positive attitudes toward e-learning. Factors associated with knowledge were place of residence (p = 0.023) and gender (p = 0.025). Factors associated with attitudes were age (p = 0.021) and place of residence (p = 0.000). The semi-structured interviews revealed connectivity and skills challenges as the main barriers for implementation of e-learning.
In silico prediction of COVID-19 test efficiency with DinoKnot	Newman,  Tara,  Chang, et al	bioRxiv	Coronavirology| Coronavirologie Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	Using in silico analysis we aimed to determine how the secondary structure of the SARS-CoV-2 RNA genome affects the interaction between the reverse primer during qRT-PCR and how it relates to the experimental primer-probe test efficiencies. We introduce the program DinoKnot (Duplex Interaction of Nucleic acids with pseudoKnots) that follows the hierarchical folding hypothesis to predict the secondary structure of two interacting nucleic acid strands (DNA/RNA) of similar or different type. We additionally predicted three mutations that may prevent primer binding, reducing the ability for SARS-CoV-2 detection.
A snap shot of space and time dynamics of COVID-19 risk in Malawi. An application of spatial temporal model	Ngwira,  Alfred,  Kumwenda, et al	medRxiv	Epidemiology| Épidémiologie	The aim of this study was to investigate the distribution of COVID-19 in both space and time in Malawi. Semiparametric spatial temporal models were fitted to the number of weekly confirmed cases as an outcome data, with time and location as independent variables. The study found significant main effect of location and time with the two interacting. The spatial distribution of COVID-19 showed major cities being at greater risk than rural areas.
Seroprevalence of SARS-CoV-2 Antibodies Among 925 Staff Members in an Urban Hospital Accepting COVID-19 Patients in Osaka Prefecture, Japan	Nishida,  Tsutomu,  Iwahashi, et al	medRxiv	Clinical data| Données cliniques Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI) Immunology | Immunologie	To evaluate the effectiveness of our hospital's current nosocomial infection control, we conducted a cross-sectional serological survey of the anti-SARS-CoV-2 antibody (immunoglobulin G) among the staff of our hospital, who are treating coronavirus disease 2019 (COVID-19) patients. The overall prevalence of seropositivity for anti-SARS-CoV-2 IgG was 0.43% (4/925), which was similar to the control seroprevalence of 0.54% (16/2970)) in the general population in Osaka during the same period according to a government survey conducted with the same assay. Seropositive rates did not significantly differ according to job title, exposure to suspected or confirmed COVID-19 patients, or any other investigated factors. The subclinical SARS-CoV-2 infection rate in our hospital was not higher than that in the general population under our nosocomial infection control measures
Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity	Ou,  Junxian,  Zhou, et al	bioRxiv	Epidemiology| Épidémiologie Coronavirology| Coronavirologie	To investigate whether naturally occurring mutations in the RBD have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between mutated SARS-CoV-2 RBDs and the human ACE2 receptor. Then by applying molecular dynamics simulations for three mutant types (V367F, W436R, N354D/D364Y) we found a higher binding affinity to human ACE2,  Genome phylogenetic analysis of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F + D614G), which emerged later and formed a distinct sub-cluster.
Gender disparities in access to care for time-sensitive conditions during COVID-19 pandemic in Chile	Pacheco,  Jorge,  Crispi, et al	medRxiv	Public Health response| Interventions de santé publique	The aim of this study was to evaluate disparities in access to care in Chile during the COVID-19 pandemic from a gender-based perspective by conducting a quasi-experimental design using a difference-in-difference approach. Our results find a large drop in new diagnosis for time-sensitive conditions ( cardiovascular diseases and oncologic conditions) during the COVID-19 pandemic in Chile and that this reduction was greater for women.
Use of Artificial Intelligence Techniques in the Prediction of the Pre and Asymptomatic Patient to COVID-19	Pantaleón-Matamoros,  Efain,  Barbosa Mirabal, et al	SSRN- Lancet prepublication	Surveillance	The present work presents a new methodology based on the multivariate analysis of the health process and the detection and monitoring of collective health for different regions. The system under development uses algorithms based on artificial neural networks (ANN), creating an intelligent tool capable of detecting disease patterns from health conditions, variation of vital signs (temperature, pulse and respiratory rate) and present pathologies to target COVID-19.  The system created in massive epidemiological monitoring, geo locates areas with asymptomatic patients, with potential for transmission.
Impact and Correlation of Air Quality and Climate Variables with COVID-19 Morbidity and Mortality in Dhaka, Bangladesh	Pavel,  Md Riad Sarkar,  Salam, et al	medRxiv	Epidemiology| Épidémiologie	We have studied air quality indicators (PM2.5, PM10, AQI, and NO2), CO2 emission, and climate variables (temperature, relative humidity, rainfall, and wind velocity) in the extremely polluted and densely populated Southeast Asian megacity Dhaka, Bangladesh from March to June 2020 tin order to investigate the correlation between air quality data and COVID-19 mortality and  morbidity. A significant correlation was observed between COVID-19 cases and air quality indicators. A strong correlation was obtained between climate variables and the total number of COVID-19 morbidity and mortality representing a favorable condition for spreading the virus.
Estimating COVID-19 contribution to total excess mortality	Pimenoff,  VilleN,  Elfstrom, et al	medRxiv	Epidemiology| Épidémiologie	We compared the total excess mortality per week in relation to the reported Covid-19 related deaths in the Stockholm region (Sweden). Total excess mortality peaked under the weeks of high COVID-19-related mortality, but 25% of these deaths were not recognized as Covid-related. Most of these deaths occurred outside hospitals. Total all-cause mortality in excess to average all-cause mortality during the epidemic peak period may provide a comprehensive picture of the total burden of COVID19-related deaths.
Increased prolonged sitting in rheumatoid arthritis patients during the COVID-19 pandemic: a within-subjects, accelerometer-based study	Pinto,  Ana Jessica,  Rezende, et al	medRxiv	Public Health response| Interventions de santé publique	Using a within-subjects design with objective measurement (via validated accelerometers), we assessed rheumatoid arthritis patients' physical activity and sedentary behavior levels prior to and during the social distancing measures implemented in Sao Paulo, Brazil. The findings indicate that imposed social distancing measures to contain the COVID-19 outbreak were associated with decreased physical activity and increased prolonged sitting among rheumatoid arthritis patients.
Diagnosing Community-Acquired Pneumonia: diagnostic accuracy study of a cough-centred algorithm for use in primary and acute-care consultations	Porter,  Paul,  Brisbane, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	The aim of this study is to develop and test a smartphone-based algorithm for diagnosing Community-acquired pneumonia (CAP) without need for clinical examination or radiology inputs.  The algorithm had high percent agreement (PA) with the clinical diagnosis of CAP in the total cohort (n=322, Positive PA=86%, Negative PA=86%, AUC=0.95).  It offers improved accuracy over current protocols when clinical evaluation is difficult. It provides increased capabilities for primary and acute care, including telehealth services, required during the COVID-19 pandemic.
Type I Interferon Limits Viral Dissemination-Driven Clinical Heterogeneity in a Native Murine Betacoronavirus Model of COVID-19	Qing,  Hua,  Sharma, et al	bioRxiv	Animal model | Modèle animal	Here we describe a murine model of COVID-19 using respiratory infection with the native mouse betacoronavirus MHV-A59. We find that whereas high viral inoculums uniformly led to hypoxemic respiratory failure and death, lethal dose 50% (LD50) inoculums led to a recapitulation of most hallmark clinical features of COVID-19, including lymphocytopenias, heart and liver damage, and autonomic dysfunction. We find that extrapulmonary manifestations are due to viral metastasis and identify a critical role for type-I but not type-III interferons in preventing systemic viral dissemination. Early, but not late treatment with intrapulmonary type-I interferon, as well as convalescent serum, provided significant protection from lethality by limiting viral dissemination. We thus establish a Biosafety Level II model that may be a useful addition to the current pre-clinical animal models of COVID-19 for understanding disease pathogenesis and facilitating therapeutic development for human translation.
Socio-demographic correlate of knowledge and practice toward novel coronavirus among people living in Mosul-Iraq: A cross-sectional study	Qubais,  Balsam,  Al-Shahrabi, et al	medRxiv	Public Health response| Interventions de santé publique	This study aimed to assess the socio-demographic correlate of knowledge and practices of Iraqi living in Mosul-Iraq towards novel coronavirus during its rapid rise. Results showed knowledge and practice mean score of (12.91\1.67) and (21.56\2.92) with cumulative knowledge and practice of 86% and 76% respectively towards 2019-nCoV. Socio-demographic characteristics such as age, marital status, gender, level of education and employment were statistically related with a higher mean score of knowledge and practice towards the virus as P<0.05.
Novel Coronavirus (COVID-19) health awareness among the United Arab Emirates Population	Qubais,  Balsam,  Elbarazi, et al	medRxiv	Public Health response| Interventions de santé publique	The aim of this study was to evaluate the knowledge and practices toward COVID-19 among the general public in the UAE during the current outbreak COVID-19. The total correct score of knowledge and practices questions was high 85% and 90%, respectively. Males gender, other marital status, and illiterate/primary educational levels had a lower level of knowledge and practices than others. participants aged 18-29 had little higher knowledge than other ages but had a lower level in practices, people who live in Abu Dhabi had better knowledge and practice than other emirates, employed people had a lower level of knowledge but higher in practice. Binary logistic regression analysis presented that females, 18-29 years, and married participants significantly associated with a higher score of knowledge, while female gender, over 30 years old, the martial status of singles, college-level and higher, unemployed, were significantly associated with high mean practice score.
Analysis of the interventions adopted due to the COVID-19 on ARI morbility for Colombia	Quijano-Angarita,  Alvaro,  Espinosa, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	The official declaration of a pandemic in March 2020 due to the Sars-CoV-2 virus coincided with the influenza season in Colombia and with environmental alerts about low air quality that increase its incidence. The objective of this document is the application of a flexible model for the identification of the pattern and monitoring of ARI morbility for Colombia by age group that shows atypical patterns in the reported series for 5 departments and that coincide with the decisions implemented to contain the COVID-19
Influence of Malaria Edemicity and Standardized TB Prevalence to BCG Coverage on Covid-19 Mortality	Raham,  Tareef Fadhil	medRxiv	Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	Possible role of latent TB and BCG and malaria have been already suggested to create innate cross heterogeneous immunity. We look for influence of these factors on Covid-19 mortality in 80 malarious countries. Findings show TB prevalence is associated with reduced COVID-19 mortality and malaria have an additional effect in reducing COVID-19 mortality. The results show with robust statistical support that TB prevalence was also associated with reduced COVID-19 mortality with additional effect that is also observed in TB and BCG coverage rate.
S494 O-glycosylation site on the SARS-COV-2 RBD Affects the Virus Affinity to ACE2 and its Infectivity; A Molecular Dynamics Study	Rahnama,  Shadi,  Azimzadeh Irani, et al	bioRxiv	Coronavirology| Coronavirologie	Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. We showed that the decoration of S494 with core and elongated O-glycans results in stabilized interactions on the direct RBD-ACE2 interface with more favorable binding free energies for longer oligosaccharides. Hence, the further drug design attempts should take this crucial factor into account, while suggesting any novel therapeutic candidate.
Two Extremes of the Mortality Rate in the Indian States Due to COVID-19	Ramasamy,  Kannamani	SSRN- Lancet prepublication	Epidemiology| Épidémiologie	Other than Lakshadweep, all other states and union territories are affected in India. Though most of the states have confirmed cases, the rate of death is not the same in all states or regions. Some of the states are highly affected with massive death rate, and few are affected less with a lower death rate. In this paper, we discuss various facts and COVID-19 situation of the highly affected states and the states that are affected less. Critically, we analyse the states based on the rate of death to the confirmed cases and rate of death to the total population of the states. Also, we attempted to analyse and to understand the cause for high and low death rates in various states.
Increased extravascular lung water index (EVLWI) reflects rapid inflammatory oedema and mortality in COVID-19 associated ARDS	Rasch,  Sebastian,  Schmidle, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	In this study we evaluate whether EVLWI is higher in patients with COVID-19 associated ARDS as compared to controls and whether Extravascular lung water index (EVLWI) has the potential to monitor disease progression.  EVLWI in COVID-19-patients was noticeably elevated and significantly higher than in the control group (17 (11-38) vs. 11 (6-26) mL/kg; p<0.001). High pulmonary vascular permeability index values (2.9 (1.0-5.2) versus 1.9 (1.0-5.2); p=0.003) suggest inflammatory oedema. By contrast, the cardiac parameters SVI, GEF and GEDVI were comparable. High EVLWI values were associated with viral persistence, prolonged intensive care treatment and mortality (23.2±6.7% vs. 30.3±6.0%, p=0.025).
Relationship between Weather and Sociodemographic Indicators and COVID-19 Infection in Iraq	Rasul,  Azad,  Ibrahim, et al	SSRN- Lancet prepublication	Epidemiology| Épidémiologie Clinical data| Données cliniques	This study evaluates the influence of weather variables, sociodemographic characteristics and their corresponding records of COVID-19 infections in Iraq cities, using Pearson’s correlation and variance-based sensitivity analysis (Sobol). Results show that atmospheric pressure (r = -0.37, p < 0.001) and air temperature (r = -0.32, p < 0.001) correlate significantly (p < 0.001) with the COVID-19 infection in Iraq. Based on Sobol method, the study also found that relative humidity (Sobol =0.89), air temperature (Sobol =0.52), and atmospheric pressure (Sobol =0.46), are the most important input variables. On the other hand, some of the socioeconomic and demographic characteristics of the referenced population found to correlate significantly with the records of COVID-19 infection are population density (r = 0.93, p ≤ 0.01), passenger per airport (r = 0.81, p ≤ 0.01), population total (r = 0.80, p ≤ 0.01) and urbanization (r = 0.46, p ≤ 0.01). Similarly, by using Sobol model, the number of passenger per airport (Sobol =0.77), population density (Sobol =0.31), old depratio (Sobol =0.22) and population total (Sobol =0.21) were found the most important variables.
Evaluating the effects of cardiometabolic exposures on circulating proteins which may contribute to SARS-CoV-2 severity	Richardson,  TomG,  Fang, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques	In this study, we have applied Mendelian randomization (MR) to systematically evaluate the effect of 10 cardiometabolic risk factors and genetic liability to lifetime smoking on 97 circulating host proteins postulated to either interact or contribute to the maladaptive host response of SARS-CoV-2. In total, we identified evidence supporting 105 effects between risk factors and circulating proteins which were robust to multiple testing corrections and sensitivity analyses.  For example, body mass index provided evidence of an effect on 23 circulating proteins with a variety of functions, such as inflammatory markers c-reactive protein (IVW Beta=0.34 per standard deviation change, 95% CI=0.26 to 0.41, P=2.19x10-16) and interleukin-1 receptor antagonist (IVW Beta=0.23, 95% CI=0.17 to 0.30, P=9.04x10-12). Further analyses using multivariable MR provided evidence that the effect of BMI on lowering immunoglobulin G, an antibody class involved in protecting the body from infection, is substantially mediated by raised triglycerides levels (IVW Beta=-0.18, 95% CI=-0.25 to -0.12, P=2.32x10-08, proportion mediated=44.1%). The strongest evidence that any of the circulating proteins highlighted by our initial analysis influence SARS-CoV-2 severity was identified for soluble glycoprotein 130 (odds ratio=1.81, 95% CI=1.25 to 2.62, P=0.002), a signal transductor for interleukin-6 type cytokines which are involved in the bodys inflammatory response. However, based on current case samples for severe SARS-CoV-2 we were unable to replicate findings in independent samples.
SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population	Rigatti,  StevenJ,  Stout, et al	medRxiv	Epidemiology| Épidémiologie Immunology | Immunologie	We performed SARS-CoV-2 antibody tests on 50,130 consecutive life insurance applicants who were having blood drawn for the purpose of underwriting (life risk assessment). The overall prevalence of SARS-CoV-2 was 3.0%, and was fairly consistent across the age range and similar in males and females. Several of the routine laboratory tests obtained were significantly different in antibody-positive vs. antibody-negative subjects, including albumin, globulins, bilirubin, and the urine albumin:creatinine ratio. The BMI was also significantly higher in the antibody-positive group. Geographical distribution revealed a very high level of positivity in the state of New York compared to all other areas (17.1%). Using state population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020.
Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance	Riley,  Steven,  Ainslie, et al	medRxiv	Epidemiology| Épidémiologie Surveillance	We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020.  The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3.
Covid-19 epidemic curve in Brazil: A sum of multiple epidemics, whose income inequality and population density in the states are correlated with growth rate and daily acceleration	Rodrigues,  CarlosA,  Pinto, et al	medRxiv	Epidemiology| Épidémiologie	The objective of this work is to measure the diversity of epidemic curves and understand the importance of socioeconomic variables in the acceleration, peak cases and deaths by Covid-19 in Brazilian states. Maximum acceleration of peak cases, peak of cases, maximum acceleration of deaths and peak of deaths are associated with the Gini index and population density, but did not correlate with HDI and per capita income.
Tocilizumab in Hospitalized Patients With COVID-19 Pneumonia	Rosas,  Ivan,  Bräu, et al	medRxiv	Clinical data| Données cliniques Therapeutics| Thérapeutique RCT	Patients hospitalized with severe COVID-19 pneumonia receiving standard care were randomized (2:1) to double-blinded intravenous tocilizumab 8 mg/kg or placebo. 452 patients were randomized; the modified-intention-to-treat population included 294 tocilizumab-treated and 144 placebo-treated patients. Clinical status at day 28 was not statistically significantly improved for tocilizumab versus placebo (P=0.36). There was no difference in mortality at day 28 between tocilizumab (19.7%) and placebo (19.4%) (difference, 0.3% [95% CI, -7.6 to 8.2]; nominal P=0.94). Median time to hospital discharge was 8 days shorter with tocilizumab than placebo (20.0 and 28.0, respectively; nominal P=0.037; hazard ratio 1.35 [95% CI 1.02 to 1.79]). Median duration of ICU stay was 5.8 days shorter with tocilizumab than placebo (9.8 and 15.5, respectively; nominal P=0.045). In the safety population, serious adverse events occurred in 34.9% of 295 patients in the tocilizumab arm and 38.5% of 143 in the placebo arm.
COVID-19 infection data encode a dynamic reproduction number in response to policy decisions with secondary wave implications	Rowland,  MA,  S	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	We developed a mathematical model that captures correlations between state-level “social distancing” policies and infection kinetics for all U.S. states, and use it to illustrate the link between social policy decisions, disease dynamics, and an effective reproduction number that changes over time, for case studies of Massachusetts, New Jersey, and Washington states. In general, our findings indicate that the potential for second waves of infection, which result after reopening states without an increase to immunity, can be mitigated by a return of social distancing policies as soon as possible after the waves are detected.
A comparative survey of betacoronavirus strain molecular dynamics identifies key ACE2 binding sites	Rynkiewicz,  PX,  Babbitt, et al	bioRxiv	Coronavirology| Coronavirologie	Here, employing large replicate sets of GPU accelerated molecular dynamics simulations, we statistically compare atom fluctuations of the known human target proteins in both the presence and absence of different strains of the viral receptor binding domain (RBD) of the S spike glycoprotein. We identify a common interaction site between the N-terminal helices of ACE2 and the viral RBD in all strains (hCoV-OC43, hCoV-HKU1, MERS-CoV, SARS-CoV1, and SARS-CoV-2) and a second more dynamically complex RBD interaction site involving the ACE2 amino acid sites K353, Q325, and a novel motif, AAQPFLL (386-392) in the more recent cross-species spillovers (i.e. absent in hCoV-OC43).
Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model	Ryu,  Seungjin,  Shchukina, et al	bioRxiv	Clinical data| Données cliniques Animal model | Modèle animal	To investigate how aging compromises defense against COVID-19, we developed a model of natural murine beta coronavirus (mCoV) infection with mouse hepatitis virus strain MHV-A59 (mCoV-A59) that recapitulated majority of clinical hallmarks of COVID-19. Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of γδ T cells in lungs.
A deep-learning model for evaluating and predicting the impact of lockdown policies on COVID-19 cases	Said,  B> A,  E	ArXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	In this research work, we propose a deep-learning prediction model for evaluating and predicting the impact of various lockdown policies on daily COVID-19 cases. Our evaluation experiments, conducted on Qatar as a use case, shows that the proposed approach achieved competitive prediction accuracy. Additionally, our findings highlighted that lifting restrictions particularly on schools and border opening would result in significant increase in the number of cases during the study period.
Sero-surveillance (IgG) of SARS-CoV-2 among Asymptomatic General population of Paschim Medinipur District, West Bengal, India(Conducted during last week of July and 1st week of August 2020) - A Joint Venture of VRDL Lab (ICMR), Midnapore Medical College &	Satpati,  Parthasarathi,  Sarangi, et al	medRxiv	Epidemiology| Épidémiologie Immunology | Immunologie	Primary Objective: To estimate the seroprevalence for SARS CoV 2 infection in the general asymptomatic population at Paschim Medinipur District. f the 458 asymptomatic general population,19 asymptomatic people found to be seropositive IgG for SARS CoV 2 with Mean or average total seropositivity rate of 4.15%. 19 Out of 30 (63.33%) RTPCR positive patients found Seronegative. Median of Days between RTPCR test and sero negativity found was 60 with minimum 28 days to maximum 101 days and Range of 73 days and a standard deviation of 19.46.
Air quality change due to COVID-19 lockdown in India and its perception by public	Sekar,  A,  J	Research Square prepub	Public health interventions*| Interventions de santé publique Public Health response| Interventions de santé publique	On average, an approximately 40% improvement in the air quality index was observed, contributed by a reduction in 40% of PM10, 44% of PM2.5, 51% of NO2 and 21% of SO2. The survey for public perception showed that 60% of the 1750 respondents perceived improvement in air quality.
Relationship between nursing home COVID-19 outbreaks and staff neighborhood characteristics	Shen,  Karen	medRxiv	Epidemiology| Épidémiologie	this paper finds that staff neighborhood characteristics are a large and significant predictor of COVID-19 outbreaks. One standard deviation increases in average staff tract population density, public transportation use, and non-white share were associated with 1.3 (SE .33), 1.4 (SE .35), and 0.9 (SE .24) additional deaths per 100 beds, respectively.
Environment influences SARS-CoV-2 transmission in the absence of non-pharmaceutical interventions	Smith,  ThomasP,  Flaxman, et al	medRxiv	Epidemiology| Épidémiologie	Objective: Assessing the association of temperature, humidity, UV radiation, and population density with estimates of transmission rate (R). Using data from the United States of America, we explore correlates of transmission across USA states using comparative regression and integrative epidemiological modelling. We find that policy intervention (`lockdown') and reductions in individuals' mobility are the major predictors of SARS-CoV-2 transmission rates, but in their absence lower temperatures and higher population densities are correlated with increased SARS-CoV-2 transmission.
Immunologically distinct responses occur in the CNS of COVID-19 patients	Song,  Eric,  Chow, et al	bioRxiv	Immunology | Immunologie Animal model | Modèle animal	Here, we examined the immune milieu in the CNS through the analysis of cerebrospinal fluid (CSF) and in circulation through analysis of peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with neurological symptoms. Single cell sequencing with paired repertoire sequencing of PBMCs and CSF cells show evidence for unique immune response to SARS-CoV-2 in the CNS. Strikingly, anti-SARS-CoV-2 antibodies are present in the CSF of all patients studied, but the antibody epitope specificity in the CSF and relative prevalence of B cell receptor sequences markedly differed when compared to those found in paired serum. Finally, using a mouse model of SARS-CoV-2 infection, we demonstrate that localized CNS immune responses occur following viral neuroinvasion, and that the CSF is a faithful surrogate for responses occurring uniquely in the CNS.
SARS-COV-2 genomic surveillance in the Brazilian Western Amazon region: evolutionary history of epidemic dissemination and genetic signature in Rondônia, Brazil	Souza,  LFB,  L	Research Square prepub	Epidemiology| Épidémiologie Coronavirology| Coronavirologie	This study aimed to investigate information about the evolutionary history of epidemic spread and genetic aspects of SARS-CoV-2 strains isolated on the Western Amazon, in the State of Rondônia, Brazil. It was possible to detect a total of 22 mutations. At least two events of introduction were detected, corresponding to the B.1 and B.1.1 European lineages.  An introduction was observed possibly through Argentina as well as through the Minas Gerais state.
The Effect of Early Hydroxychloroquine-based Therapy in COVID-19 Patients in Ambulatory Care Settings: A Nationwide Prospective Cohort Study	Sulaiman,  Tarek,  Mohana, et al	medRxiv	Epidemiology| Épidémiologie Clinical data| Données cliniques Therapeutics| Thérapeutique	This observational prospective cohort study took place in 238 ambulatory fever clinics in Saudi Arabia. Our study looked at those who received Hydroxychloroquine (HCQ)-based therapy along with supportive care (SC) and compared them to patients who received SC alone. Early intervention with HCQ-based therapy in patients with mild to moderate symptoms at presentation was associated with lower adverse clinical outcomes among COVID-19 patients, including hospital admissions, ICU admission, and/or death.
Temporal Analysis of COVID-19 Peak Outbreak	Tewari,  A	ArXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	The intent of this research is to explore how mathematical models, specifically Susceptible-Infected-Removed (SIR) model, can be utilized to forecast peak outbreak timeline of COVID-19 epidemic amongst a population of interest starting from the date of first reported case. The predicted peak COVID-19 outbreak timelines for ten Indian states is presented.
A novel sample pooling strategy and its application for mass screening of SARS-CoV-2 in an outbreak of COVID-19 in Vietnam	Thanh,  Ton That,  Nhan, et al	medRxiv	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	We present a sample pooling approach and the results of its application for mass screening of SARS-CoV-2 in >96,000 asymptomatic individuals. Our approach did not compromise the sensitivity of PCR, while increasing the throughput and reducing 77% of the costs. 22/32 asymptomatic cases would have been missed without mass screening.
Mitochondrial induced T cell apoptosis and aberrant myeloid metabolic programs define distinct immune cell subsets during acute and recovered SARS-CoV-2 infection	Thompson,  Elizabeth,  Cascino, et al	medRxiv	Clinical data| Données cliniques Immunology | Immunologie	By interrogating metabolic programs in the peripheral blood mononuclear cells (PBMC) of acutely infected COVID-19 patients, we identified novel and distinct immune cell subsets. Our studies identified a non-clonal population of T cells expressing high H3K27me3 and voltage-dependent anion channel (VDAC). Further, we observed a marked increase in Hexokinase II+ polymorphonuclear-myeloid derived suppressor cells (PMN-MDSC) in acute COVID-19 patients with moderate or severe disease.  Finally, we identified a population of monocytic MDSC (M-MDSC) expressing high carnitine palmitoyltransferase I (CPT1a) and VDAC in acute COVID-19 patients, whose presence correlated with severity of disease.
Clinical Characteristics and Risk Factors of Disseminated Intravascular Coagulation in Patients with COVID-19 in Wuhan, China	Tian,  Jianbo,  Yue, et al	SSRN- Lancet prepublication	Epidemiology| Épidémiologie Clinical data| Données cliniques	In this retrospective observational study we aimed to systematically characterize the clinical features and examine risk factors for disseminated intravascular coagulation (DIC) development in COVID-19 patients Higher proportion of patients with DIC and COVID-19 developed into death than non DIC patients. In addition to previously reported coagulation-related markers, such as FDP, D-dimer, and platelet, we also identified several novel risk factors associated with DIC development, including decreased fibrinogen and ALB, and elevated  IL-6 and TNF-a.
Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies	Topriceanu,  Constantin-Cristian,  Wong, et al	medRxiv	Public Health response| Interventions de santé publique	A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Females  and those with a chronic illness experienced significantly more cancellations during lockdown. Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown. Age and socioeconomic position were not associated with cancellation or care hours.
nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification	Ueda,  Hiroki	bioRxiv	Coronavirology| Coronavirologie	Here, we presented a new software, called nanoDoc, for detecting post-transcriptional modifications from direct RNA sequencing data using a deep neural network. We applied this software to SARS-CoV-2 data and identified commonly modified sites among three groups.
Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data	Vaughan,  TimothyG,  Sciré, et al	medRxiv	Epidemiology| Épidémiologie Coronavirology| Coronavirologie	We estimate the basic reproductive number and case counts for 15 distinct SARS-CoV-2 outbreaks, distributed across 10 countries and one cruise ship, based solely on phylodynamic analyses of genomic data. Results indicate that prior to significant public health interventions, the reproductive numbers for a majority of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.8. Finally, we provide genome-based estimates of the cumulative case counts for each outbreak, which allow us to speculate on the amount of unreported infections within the populations housing each outbreak.
Evaluation of stability and inactivation methods of SARS-CoV-2 in context of laboratory settings	Westhaus,  Sandra,  Widera, et al	bioRxiv	Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI)	In this study, we evaluated common lysis buffers that are used in molecular biological laboratories for their ability to inactivate SARS-CoV-2, in order to restrict laboratory born spread among scientists and lab personnel. Guanidine thiocyanate, SDS, and Triton-X containing lysis buffers were effective in inactivation of SARS-CoV-2. Furthermore, we compared chemical and non-chemical inactivation methods (e.g. ethanol, UV-C light) and analyzed the stability of the virus on surfaces used in laboratory environment. We found that even after months of storage under laboratory conditions at 4°C, the virus had hardly lost any of its infectivity.
Seroprevalence and Correlates of SARS-CoV-2 Antibodies in Healthcare Workers in Chicago	Wilkins,  John,  Gray, et al	medRxiv	Epidemiology| Épidémiologie Immunology | Immunologie	We conducted a cross-sectional analysis of baseline data from the Northwestern Healthcare Worker SARS-CoV-2 Serology Cohort Study to identify factors associated with SARS-CoV-2 infection. The crude prevalence rate of seropositivity was 4.8%. Exposure to COVID-19 patients, and longer duration patient therapies were each associated with higher risk for seropositive status; however, the community burden of COVID-19 remains a significant source of exposure to SARS CoV-2 infection among healthcare workers in Chicago.
COVID-19: Mechanistic model calibration subject to active and varying non-pharmaceutical interventions	Willis,  MarkJ,  Wright, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	Our aim is to demonstrate the effectiveness of parameter regression methods to calibrate an established epidemiological model describing COVID-19 infection rates subject to active and varying non-pharmaceutical interventions (NPIs). We observe that the effective reproduction number response to NPIs is non-linear with variable response rate, magnitude and direction.
Estimating the Risk of Outbreaks of COVID-19 Associated with Shore Leave by Merchant Ship Crews: Simulation Studies for a Case Country	Wilson,  Nick,  Blakely, et al	medRxiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	We aimed to estimate the risk of COVID-19 outbreaks in a case study COVID-free destination country, associated with shore leave for merchant ship crews. Introduction of SARS-CoV-2 through shore leave from international shipping crews is likely, even after long voyages. The risk can be substantially mitigated by control measures such as PCR testing and mask use.
Lung Damage Mechanisms For COVID-19 and Other Lung Infections, and Driving Force in Leukecyte Recruitment and Migration	Wu,  Jianqing,  Zha, et al	SSRN- Lancet prepublication	Clinical data| Données cliniques	To understand lung damage caused by COVID-19, we deduced two-phase lung damage mechanisms. After the lungs are infected with SARS-CoV-2 virus, the affected lung tissue swells and surface properties of pulmonary capillaries change, resulting in an increased flow resistance of affected capillaries.
Analysis of Impact on Environment: Pre and Post Lockdown	Yadav,  Akshita	SSRN- Lancet prepublication	Public health interventions*| Interventions de santé publique Public Health response| Interventions de santé publique	This analytical research is done using secondary data of environmentalist’s report and several legal websites such as IQAir, LexisNexis etc. to understand the effect of lockdown on environment. Economic cessation such as this lockdown, did reduce emission of pollutants but after lockdown is lifted the activities are likely to be resumed.
COVID CT-Net: Predicting Covid-19 From Chest CT Images Using Attentional Convolutional Network	Yazdani,  S,  M	ArXiv	Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	In this work we developed a deep learning framework to predict COVID-19 from CT images.
Fighting Against COVID-19 Requires Wearing a Face Mask by Not Some but All	Yilmazkuday,  Hakan	SSRN- Lancet prepublication	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	This paper investigates the effects of wearing a face mask, by using a difference-in-difference design, where U.S. county-level data on changes in COVID-19 cases or deaths are regressed on lagged changes in social interaction of people measured by Google mobility. Wearing a face mask starts working to fight against COVID-19 only if more than 75% of people in a county "always" wear a face mask, while the effects of social interaction on COVID-19 are statistically eliminated when more than 85% of people in a county "always" wear a face mask.
Anakinra and Intravenous IgG versus Tocilizumab in the Treatment of COVID-19 Pneumonia	Zantah,  Massa,  Dominguez Castillo, et al	medRxiv	Clinical data| Données cliniques Therapeutics| Thérapeutique	We report our experience in treating COVID-19 pneumonia associated with cytokine storm with either subcutaneous Anakinra given concomitantly with intravenous immunoglobulin (IVIG), or intravenous Tocilizumab. 84 consecutive patients who received either treatment; and treating COVID-19 pneumonia associated with cytokine storm features with either subcutaneous Anakinra/IVIG or intravenous Tocilizumab is associated with improved clinical outcomes in most subjects. The choice of treatment does not appear to affect morbidity or mortality.
Single-cell RNA sequencing of Tocilizumab-treated peripheral blood mononuclear cells as an in vitro model of inflammation	Zarinsefat,  Arya,  Hartoularos, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	We performed single-cell RNA sequencing of comparing stimulated PBMCs before and after Tocilizumab treatment. We leveraged this data to create an in vitro cytokine storm model, to better understand the effects of Tocilizumab in the presence of inflammation. Tocilizumab-treated cells had reduced expression of inflammatory-mediated genes and biologic pathways, particularly amongst monocytes. These results support the hypothesis that Tocilizumab may hinder the cytokine storm of COVID-19.
Racial disparities in COVID-19 mortality are driven by unequal infection risks	Zelner,  Jon,  Trangucci, et al	medRxiv	Epidemiology| Épidémiologie Public Health Priorities| Priorités de santé publique	We used individual-level COVID-19 incidence and mortality data from the U.S. state of Michigan and found rates of incidence and mortality more than twice as high than Whites for all groups other than Native Americans. Of these, Blacks experienced the greatest burden of confirmed and probable COVID-19 infection and mortality. This work suggests that well-documented racial disparities in COVID-19 mortality in hard-hit settings are driven primarily by variation in household, community and workplace exposure rather than case-fatality rates.
A bacterial artificial chromosome (BAC)-vectored noninfectious replicon of SARS-CoV-2	Zhang,  Yang,  Song, et al	bioRxiv	Coronavirology| Coronavirologie	To facilitate antiviral screening against SARS-CoV-2 without requirement for high biosafety level facility, we developed a bacterial artificial chromosome (BAC)-vectored replicon of SARS-CoV-2, nCoV-SH01 strain. We also constructed a four-plasmid in-vitro ligation system that is compatible with the BAC system, which makes it easy to introduce desired mutations into the assembly plasmids for in-vitro ligation. This replicon system would be helpful for performing antiviral screening and dissecting virus-host interactions.
Country distancing increase reveals the effectiveness of travel restrictions in stopping COVID-19 transmission	Zhong,  L,  D	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	Despite remarkably successful approaches in predicting the ongoing pandemic's spatiotemporal patterns, we lack an intrinsic understanding of the travel restrictions' efficiency and effectiveness. We the countries' closeness based on disease spread using country distancing; and our method estimates that 53.6% of travel restrictions as of June 1, 2020, are ineffective. Our approach offers a practical guide that indicates when and where to implement travel restrictions, tailed to the real-time national context.
Clinical effectiveness of drugs in hospitalized patients with COVID-19 infection: a systematic review and meta-analysis	Abeldano Zuniga,  Roberto Ariel,  Coca, et al	medRxiv	Review Literature| Revue de littérature	SR-MA: search was carried out in PubMed, Scopus, and Web of Science databases, between August 20th and September 9th, 2020. Dexamethasone would have a better result in hospitalized patients, especially in low-resources settings.
Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis	Chen,  Xinhua,  Chen, et al	medRxiv	Review Literature| Revue de littérature	SR-MA:  PubMed, Embase, Web of Science, medRxiv, bioRxiv, SSRN and Wellcome were searched for English-language papers published from December 1, 2019 to August 28, 2020.  The overall quality of seroprevalence studies examined was low. The relatively low seroprevalence among general populations suggest that in most settings, antibody-mediated herd immunity is far from being reached.
Taste alteration in COVID-19: a rapid review with data synthesis reveals significant geographical differences	Cirillo,  Icola N	medRxiv	Review Literature| Revue de littérature	Rapid Review: National Library of Medicine (MEDLINE/PubMed) and medRxiv were searched from their inception until September 3, 2020.  These data show that there is a distinct geographical distribution of GD in COVID-19 patients and this may explain the differences of diagnostic criteria for COVID-19 case definition.
On the reliability of predictions on Covid-19 dynamics: a systematic and critical review of modelling techniques	Gnanvi,  JanyceE,  Salako, et al	medRxiv	Review Literature| Revue de littérature	SR: conducted a global systematic literature review to summarize trends in the modelling techniques used for Covid-19 from January 1st 2020 to June 30th 2020.  Our findings suggest that while predictions made by the different models are useful to understand the pandemic course and guide policy-making, there should be cautious in their usage.
RAAS blockers and region-specific variations in COVID-19 outcomes: findings from a systematic review and meta-analysis	Kaur,  Upinder,  Chakrabarti, et al	medRxiv	Review Literature| Revue de littérature	SR-MA: search was performed for published (using MEDLINE/PubMed and Google Scholar) and preprint (using bioRxiv and medRxiv) studies of interest. The last search was conducted on 9th July 2020. Use of RAAS blockers is not associated with increased risk of mortality in COVID-19 patients. Reduced mortality is seen in hypertensive patients with COVID-19 and therefore the drugs should be continued in this subset. US and European patients are at higher risk of severe outcomes.
Efficacy of face mask in preventing respiratory virus transmission: A systematic review and meta-analysis	Liang,  Mingming,  Gao, et al	Travel Medicine and Infectious Disease	Review Literature| Revue de littérature	SR-MA: Relevant articles were retrieved from PubMed, Web of Science, ScienceDirect, Cochrane Library, and Chinese National Knowledge Infrastructure (CNKI), VIP (Chinese) database. This study adds additional evidence of the enhanced protective value of masks, we stress that the use masks serve as an adjunctive method regarding the COVID-19 outbreak.
Impacts of COVID-19 on the Transport Sector and Measures as Well as Recommendations of Policies and Future Research: A Report on SIG-C1 Transport Theory and Modelling	Qu,  Xiaobo,  Gao, et al	SSRN- Lancet prepublication	Review Literature| Revue de littérature
Practical Analysis of Mental Health Assistance in Elementary and Middle Schools under COVID-19 Pandemic: A Case Study of City A in Jiangsu, China	Quan,  Lixin	SSRN- Lancet prepublication	Review Literature| Revue de littérature
Therapeutic management of patients with COVID-19: a systematic review	Tobaiqy,  M,  Qashqary, et al	Infection Prevention in Practice	Review Literature| Revue de littérature	SR:  Articles for review were selected from Embase, Medline and Google Scholar. Readily accessible peer-reviewed, full articles in English published from 1st December 2019 to 26th March 2020 were included. This is the first systematic review to date related to medication used to treat patients with COVID-19. Only 41 studies were eligible for inclusion, most of which were conducted in China. Corticosteroid treatment was reported most frequently in the literature.
SARS-CoV-2 transmission via speech-generated respiratory droplets	Bax,  Adriaan,  Bax, et al	The Lancet Infectious Diseases	Commentary/Editorial| Commentaire/Éditorial
Data Analytics and Assessment of the Drugs for COVID-19	Bose,  Tanima,  Alsmadi, et al	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Racial Inequality in Health Care During a Pandemic	Bruce,  al t,  Raphael, et al	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Of Cross-Immunity, Herd Immunity and Country-Specific Plans: Experiences from COVID-19 in India	Chakrabarti,  Sankha Shubhra,  Kaur, et al	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Correction to: Use of medical face masks versus particulate respirators as a component of personal protective equipment for health care workers in the context of the COVID-19 pandemic	Conly,  J,  Seto, et al	Antimicrob Resist Infect Control	Commentary/Editorial| Commentaire/Éditorial
Cannabis and Coronavirus: Impact on Medical Cannabis Industries in Three States	DeWitt,  Samuel	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Silicon thin film transistor-based aptamer sensor for COVID-19 detection	Farrow,  T,  L	Research Square prepub	Commentary/Editorial| Commentaire/Éditorial
The Impact of Covid-19 on the Mental Health of Health Care Providers	Feist,  C	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
PMC7397184; Rapid Decay of Anti-SARS-CoV-2 Antibodies in Persons with Mild Covid-19	Ibarrondo,  FJ,  Fulcher, et al	N Engl J Med	Commentary/Editorial| Commentaire/Éditorial
Sharing When Stranger Equals Danger: Ridesharing During Covid-19 Pandemic	Ivaldi,  Marc,  Palikot, et al	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Privacy in Pandemic: Law, Technology, and Public Health in the COVID-19 Crisis	Li,  TiffanyC	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Overview of Vietnam's Scientific Publications in the Period COVID-19	Luong,  Dinh-Hai,  Nguyen, et al	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
The Impact of COVID-19 on Event Management Industry	Madray,  JS	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
History of the Discovery and Development of Biomodulina T (InmunyVital®), a Useful Immunomodulator with a Broad Range of Clinical Applications	Martin,  RRR	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Hack the Pandemic: Lessons from How the Taiwan Government Embraced the Hacker Mindset to Embrace Digital Infrastructure and Subvert COVID-19	Nabben,  Kelsie	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Management of COVID-19 in a nursing home: the role of a mobile multidisciplinary medicine team	Poupin,  P,  N'D	Research Square prepub	Commentary/Editorial| Commentaire/Éditorial
Online Eucharistic Celebration and the Spiritual Well-Being of the Catholic Faithful of San Isidro Labrador Parish, Cuenca, Batangas during COVID-19 Pandemic	Rosales,  Renniel Jayson	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
The Intellectual Property of COVID-19	Rutschman,  Ana Santos	SSRN- Lancet prepublication	Commentary/Editorial| Commentaire/Éditorial
Comments on the Preliminary Framework for Equitable Allocation of COVID-19 Vaccine	Santos Rutschman,  Ana,  Barnes-Weise, et al	SSRN- Lancet prepublication	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.

Immunology:

Animal Model:

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.

Immunologie :

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