Subject: Daily Scan of COVID-19 Scientific Publications / survol journalier des publications scientifiques du COVID-19, 2020-09-18

Good afternoon,

There are 214 citations in today’s scan. 133 were considered primary research or review literature.

Highlights today include:

PUBLIC HEALTH INTERVENTIONS

· Chiu, Fischer, & Ndeffo-Mbah developed a transmission dynamic model to evaluate the impact of relaxation of restrictions on COVID-19 dynamics in the United States. As of July 22, 2020, only three states were on track to curtail their epidemic curve. Thirty-nine states and the District of Columbia may have to double their testing and/or tracing rates and/or rolling back reopening by 25%, while eight states require an even greater measure of combined testing, tracing, and social distancing.

TRANSMISSION

· Barrs et al tested 50 cats from coronavirus disease households or close contacts in Hong Kong, China, for SARS-CoV-2 RNA in respiratory and fecal samples. They found 6 cases of apparent human-to-feline transmission involving healthy cats. Virus genomes sequenced from 1 cat and its owner were identical.

EPIDEMIOLOGY

· Ravindran et al investigated a cluster of COVID-19 cases in returning Australian residents who attended wedding events in Bali, Indonesia between March 15-21, 2020. Attendees participated in various social events and were in close proximity, providing multiple opportunities for transmission. COVID-19 was identified in 56% of attendees (23/41). Attack rates ranged from 64% to 87% for different exposures. Authors could not identify a single risk exposure that accounted for all cases; it is therefore likely there were multiple episodes of transmission.

· Zeng et al., studied the association between the daily wearing of eyeglasses and the susceptibility to COVID-19. In this cohort study of patients hospitalized with COVID-19 in Suizhou, China, the proportion of inpatients with COVID-19 who wore glasses for extended daily periods (>8 h/d) was smaller than that in the general population, suggesting that daily wearers of eyeglasses may be less susceptible to COVID-19.

· Zaid et al., evaluated the contribution of platelets to inflammation and thrombosis in COVID-19 patients. Blood was collected from 115 COVID-19 patients presenting non-severe (n=71) and severe (n=44) respiratory symptoms. Assessment of cytokines in plasma and platelets revealed the modulation of platelet-associated cytokine levels in both non-severe and severe COVID-19 patients, pointing to a direct contribution of platelets to the plasmatic cytokine load. Levels of D-dimers failed to correlate with any measured indicators of platelet activation. Functionally, platelets were hyperactivated in COVID-19 subjects presenting non-severe and severe symptoms, with aggregation occurring at suboptimal thrombin concentrations. 

· McAndrews, et al., generated a quantitative serological ELISA using recombinant S-RBD and N-protein for the detection of circulating antibodies in 138 serial serum samples from 30 reverse transcription PCR–confirmed, SARS-CoV-2–hospitalized patients, as well as 464 healthy and non–COVID-19 serum samples. Our studies show that detection of N-protein–binding antibodies does not always correlate with presence of S-RBD–neutralizing antibodies and caution against the extensive use of N-protein–based serology testing for determination of potential COVID-19 immunity.

CLINICAL DATA

· Masset et al., report two cases of BK virus replication in two kidney transplant recipients (3 months and 15 years prior in the two patients, respectively) after mild SARS-CoV-2 infection. These cases highlight that SARS-CoV-2 infection, even non-severe, can disrupt the immune system and particularly lymphocytes, thus leading to viral replication, and should be monitored in kidney transplant recipients.

· Kim, et al., retrospectively reviewed real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test results of mild or asymptomatic COVID-19 patients in Korea between 9 March 2020 and 10 April 2020. Patients underwent an upper respiratory RT-PCR test every week until discharge. The detection of SARS-CoV-2 lasting more than 3 weeks was common in mild or asymptomatic patients. Upper respiratory RT-PCR results were frequently reversed from negative to positive.

IMMUNOLOGY

· Chang et al., studied COVID-19-specific immunity in 19 healthy volunteers and found that a combination of five antigenic pools induced the strongest cellular immune response. A secondary in vitro booster stimulation of the T cells with the DC-peptides induced increased anti-viral immune responses in all individuals (including the no responders), suggesting that booster immunization in a vaccine scheme may elicit a broad protection in immune naïve population.

THERAPEUTICS

· Guvenmez et al., analyzed a new inhaler treatment (NIT) in a clinical study. The molecules tested have antiviral, antioxidant and anti-inflammatory effects without any toxicity and were brought together in a nebulizer based treatment. Mean duration of hospital stay for patients receiving NIT in addition to the normal treatment was significantly lower compared to patients receiving normal treatment only (6.5 ± 1.8 and 17.1 ± 2.4, respectively).

PUBLIC HEALTH REPONSE

· Hammes et al., conducted a cross-sectional study to assess how newspapers from 25 countries are comparing and presenting COVID-19 epidemiological data to their readers. Quality assessment of the comparisons showed that only a minority of newspapers adjusted the data for population size in case comparisons between regions (37,2%) and between countries (25,6%), and the same was true for death comparisons between regions (27,3%) and between countries (27%).

Regards,

Lisa Waddell, Tricia Corrin, Rukshanda Ahmad, Robyn Odell, Maribeth Mitri, Julie Theriault, Dobrila Todoric, Alejandra Dubois, Christina Bancej, Austyn Baumeister, Anam Khan, Musaab Younis, Lien Mi Tien, Dima Ayache, Angela Sloan, Kaitlin Young, Chatura Prematunge, Ainsley Otten, Irene Yong, Drew Greydanus, Shalane Ha, Alex Gilbert, Jessie Varga, Vanessa Zubach

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
Education Research: Impact of SARS-CoV-2 pandemic on neurology trainees in Italy: A resident-driven survey	Abati,  E,  Costamagna, et al	Neurology	Healthcare Response | Réponse des soins de santé	79 residents working in Italy completed a survey. 87.3% of trainees reported a substantial reduction in their neurological duties since SARS-CoV-2 appeared in Italy, and 17.8% were also recruited or volunteered for COVID-19-dedicated wards. Almost 70% of surveyed trainees believe that SARS-CoV-2 pandemic had or will have a negative impact on their formation as neurologists. Trainees reported a consistent exposure (69.6%) to confirmed positive SARS-CoV-2 cases at work, with divergent surveillance and preventive measures taken by local institutions.
Acute kidney injury caused by darunavir in a patient with COVID-19: A Case Report	Abdalla,  Shiema,  Elgassim, et al	Research Square prepub	Clinical data| Données cliniques	Background A highly contagious virus known as SARS-CoV-2 has been a pandemic globally. HIV medications were one of the suggested treatments for COVID-19. Here, we report an unusual adverse drug reaction with darunavir in a SARS-CoV-2-infected patient. Case presentation This is a case presentation of a 53-year-old male with no past medical history who was diagnosed with COVID-19. One week after initiating treatment, the patient developed acute kidney injury, and his serum creatinine increased significantly. Conclusion As there was no clear justification for renal impairment such as a prerenal or postrenal cause, acute kidney injury, possibly crystal-induced nephropathy, was considered an adverse drug reaction from darunavir.
Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness in Egypt at El-Demerdash tertiary hospitals	Agwa,  SaraHA,  Elghazaly, et al	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques Coronavirology| Coronavirologie	The objective of this retrospective cohort study was to explore the start of SARS-CoV-2 in preserved severe acute respiratory infection samples to know the exact time of its emergence in our hospital and to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain. Further, we assessed the clinical characteristics of the severe respiratory infection in patients admitted to El-Demerdash hospitals. The first case of SARS-CoV-2 was detected in a 6 months aged female patient on mid-April 2020; the phylogenetic analysis placed our assembled genome within GISAID Clade GH. Co-infection  was most prevalent in pediatrics than adults, but mortality and ICU admission was higher in adults. Co-morbidities were associated with higher mortality and more severe infection.
COVID-19 and the "Film Your Hospital" Conspiracy Theory: Social Network Analysis of Twitter Data	Ahmed,  W,  López Seguí, et al	J Med Internet Res	Public Health response| Interventions de santé publique	OBJECTIVE: This study set out to evaluate the #FilmYourHospital conspiracy theory on Twitter, attempting to understand the drivers of the conspiracy theory on Twitter.  METHODS: Twitter data related to the #FilmYourHospital hashtag was retrieved and analysed using social network analysis from a 7 day period from Monday 13 April and Monday 20 April. The dataset consisted of 22,785 tweets and 11,333 Twitter users. RESULTS: The most important drivers of the conspiracy theory are ordinary citizens, one of the most influential being a pro-Brexit supporter. It was found that YouTube was the information source most linked to by users.
Kawasaki-like disease in children with COVID-19	Akca,  UK,  Kesici, et al	Rheumatol Int	Epidemiology| Épidémiologie Clinical data| Données cliniques	In this study, we investigated children with typical and atypical Kawasaki disease (KD) likely to be associated with COVID-19. We have reported four children with Kawasaki-like disease probably associated with COVID-19. Pediatric COVID-19 cases may present with atypical/incomplete Kawasaki-like disease. Thus, pediatricians need to be aware of such atypical presentations resembling KD for early diagnosis of COVID-19.
Severity of COVID-19 Infection in ACEI/ARB Users in Two Saudi Public Specialty Hospitals; Retrospective Cohort Study	Alrashed,  AhmedA,  Khan, et al	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques	The aim of this study was to determine the effect of ACEI/ARB use in patients with severe COVID-19. This retrospective cohort study done in two Saudi public specialty hospitals designated as COVID-19 referral facilities. We included 354 patients with confirmed diagnosis of COVID-19 between April and June 2020, of which 146 were ACEI/ARB users and 208 were non-ACEI/ARB users. We conducted a multivariate logistic regression and a sensitivity analysis using propensity score matched (PSM) patients. Compared to non-ACEI/ARB users, ACEI/ARB users had an eight-fold higher risk of developing critical or severe COVID-19 (OR=8.25, 95%CI=3.32-20.53). In general, but especially among patients with hypertension, diabetes, and/or renal disease, ACEI/ARB use is associated with a significantly higher risk of severe or critical COVID-19 disease, and ICU care.
[Social determinants of the incidence of Covid-19 in barcelona: a preliminary ecological study using public data.]	Amengual-Moreno,  M,  Calafat-Caules, et al	Rev Esp Salud Publica	Epidemiology| Épidémiologie	The aim of this work was to determine the relation of social determinants in the incidence of Covid-19 in the city of Barcelona. An observational retrospective ecological study was performed, with the neighbourhood as the population unit, based on data of cumulative incidence published at May 14th, 2020 by the Public Health Agency of Barcelona. It was found that neighbourhoods belonging to the lowest quintile of income had a 42% more incidence than those belonging to the highest quintile. The Pearson correlation was statistically significative between the incidence of Covid-19 and the percentage of population over 75, the percentage of immigration of the neighborhood and the origin of the immigrants, the Available Income per Family Index, the percentage of smokers, and the percentage of people with BMI over 25.
Support for mobilising medical students to join the COVID-19 pandemic emergency healthcare workforce: a cross-sectional questionnaire survey	Astorp,  MS,  Sørensen, et al	BMJ Open	Public Health response| Interventions de santé publique	OBJECTIVE: To identify what motivates medical students to join a pandemic emergency healthcare workforce. DESIGN: Cross-sectional study. SETTING: Aalborg University, Denmark. PARTICIPANTS: All medical students.  Results A total of 486 students of 688 (70.6%) completed the survey within 7 days in March 2020. 80% had decided to join the pandemic emergency healthcare workforce. Ranked median scores for motivational statements in each domain were: care, 100; learn, 90; pride, 83; team, 77; needed, 75; safety, 75; supervision, 75; job, 73; duty, 66; salary, 62; historic, 50. Supervision, salary and duty were given increasing priority with advancing study years. Interestingly, students added that support by the university and clarification of study plans were priorities.
Possible autoimmune encephalitis with claustrum sign in case of acute SARS-CoV-2 infection	Ayatollahi,  P,  Tarazi, et al	Can J Neurol Sci	Clinical data| Données cliniques	Case report of an 18 year old female with COVID-19
The flexibility of ACE2 in the context of SARS-CoV-2 infection	Barros,  EmiliaP,  Casalino, et al	bioRxiv	Coronavirology| Coronavirologie	Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion.
SARS-CoV-2 in Quarantined Domestic Cats from COVID-19 Households or Close Contacts, Hong Kong, China	Barrs,  VR,  Peiris, et al	Emerg Infect Dis	Epidemiology| Épidémiologie Transmission Coronavirology| Coronavirologie zoonoses	We tested 50 cats from coronavirus disease households or close contacts in Hong Kong, China, for severe acute respiratory syndrome coronavirus 2 RNA in respiratory and fecal samples. We found 6 cases of apparent human-to-feline transmission involving healthy cats. Virus genomes sequenced from 1 cat and its owner were identical.
Assessing the Dilution Effect of Specimen Pooling on the Sensitivity of SARS-CoV-2 PCR Tests	Bateman,  AC,  Mueller, et al	J Med Virol	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	Many studies have modeled the efficiency gains of specimen pooling, but few have systematically evaluated the dilution effect of pooling on the sensitivity of tests. Using the frequency distribution of Ct values of our first 838 SARS-CoV-2 positive specimens, we modeled 100 specimens on the same frequency distribution. Given this distribution, we then tested dilutions of 1:5, 1:10, and 1:50 to find the percentage of specimens positive at each Ct value with each pool size.  Using the frequency distribution and the percentage of specimens positive at each Ct value, we estimate that pools of 5 lead to 93% sensitivity, pools of 10 lead to 91% sensitivity, and pools of 50 lead to 81% sensitivity. Pools of 5 and 10 lead to some specimens with Ct values of ≥32 becoming negative, while pools of 50 lead to some specimens with Ct values of ≥28 becoming negative.
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function	Berrio,  Alejandro,  Gartner, et al	bioRxiv	Coronavirology| Coronavirologie	Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. Thermodynamic modeling of RNA stability and structure, however, indicates that RNA secondary structure within both genes in the SARS-CoV-2 genome differs from those of RaTG13, the reconstructed common ancestor, and Pan-CoV-GD (Guangdong). These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system.
Differential serological and neutralizing antibody dynamics after an infection by a single SARS-CoV-2 strain	Billon-Denis,  Emmanuelle	Research Square prepub	Clinical data| Données cliniques Immunology | Immunologie	We report a case series of two coworkers infected by the same SARS-CoV-2 strain, presenting two different immunological outcomes. One patient presented a strong IgG anti-receptor-binding domain immune response correlated with a low and rapidly decreasing titer of neutralizing antibodies. The other patient had a similar response but high neutralizing antibody titers. Thus, host individual factors may be the main drivers of the immune response.
The use of imaging in COVID-19-results of a global survey by the International Society of Radiology	Blažić,  I,  Brkljačić, et al	Eur Radiol	Healthcare Response | Réponse des soins de santé	OBJECTIVES: This survey conducted by the International Society of Radiology and supported by the European Society of Radiology aimed to collect information regarding radiology departments' current practices in the management of patients with COVID-19.  METHODS: Responses from 50 radiology departments involved in the management of COVID-19 patients representing 33 countries across all continents were analyzed.  RESULTS: Imaging is usually not performed in asymptomatic patients (69% of institutions do not image) but is used at the end of confinement (in 60% of institutions). In the majority of institutions, chest imaging is used in suspected or confirmed patients with COVID-19 (89% and 94%). All imaging departments involved in this survey reported the use of imaging in COVID-19 patients showing severe symptoms or who were critically ill.
Adult post COVID-19 multisystem inflammatory syndrome and thrombotic microangiopathy	Boudhabhay,  Idris,  Rabant, et al	Research Square prepub	Clinical data| Données cliniques	We describe a case of post COVID-19 multisystem inflammatory syndrome (MIS) in a 46-year-old man, with biopsy-proven renal thrombotic microangiopathy (TMA). Specific complement inhibition with Eculizumab was initiated promptly and lead to a dramatic improvement of renal function. Our case suggests that post COVID-19 MIS is not restricted to children and that TMA could play a central role in the pathophysiology of this syndrome
Geriatric rehabilitation and Covid-19 : a Case Report	Brika,  Marine,  Bossu, et al	Research Square prepub	Clinical data| Données cliniques	This is a case study of Mr P,  a 93 year old frail patient, hospitalized after a COVID-19 infection. The assessment process of this patient has been supported by an innovative multi-systemic tool developed in view of the COVID-19 clinical consequences and a systemic evaluation of motor functions by the Frail BESTest. This process allowed presenting a mixed clinical picture associating an important respiratory distress (linked with the acute respiratory distress syndrome) and an evident motor frailty. The care plan was developed accordingly, and four assessment were done in the same manner until the return home of Mr P.  This case report illustrates the importance of rehabilitation in the Covid-19 context.
Feasibility and safety of ultrasound-guided minimally invasive autopsy in COVID-19 patients	Brook,  OR,  Piper, et al	Abdom Radiol (NY)	Clinical data| Données cliniques	OBJECTIVES: To determine the feasibility and safety of ultrasound-guided minimally invasive autopsy in COVID-19 patients. METHODS: 60 patients who expired between 04/22/2020-05/06/2020 due to COVID-19 were considered for inclusion in the study, based on availability of study staff. Minimally invasive ultrasound-guided autopsy was performed with 14G core biopsies through a 13G coaxial needle. RESULTS: Pathology findings were concordant with previously reported autopsy findings for COVID-19. Highest SARS-CoV-2 viral load was detected in the lung, liver, and spleen that had small to moderate amount, and low viral load in was detected in the heart in 2/5 (40%). No virus was detected in the kidney (0/3, 0%).
Change in Mental Health Symptoms During the COVID-19 Pandemic: The Role of Appraisals and Daily Life Experiences	Brose,  A,  Blanke, et al	J Pers	Public Health response| Interventions de santé publique	The central purpose of this study was to identify mechanisms underlying change of well-being in times of threat, using the example of the COVID-19 pandemic, with a focus on appraisals of the pandemic and affective states, stress, as well as mindfulness in daily life. We worked with a sample of 460 adults, pre- and post-test information, as well as 7189 observations from the diary phase. Results showed that deterioration in mental health symptoms across the duration of the study was associated with (a) change towards less fortunate appraisals of the pandemic and (b), more negative affect and less mindfulness in daily life. Furthermore, appraisals of the pandemic at pretest predicted experiences in daily life, with more negative appraisals of the pandemic predicting more negative affect and stressor occurrence as well as less mindfulness.
Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding	Byrnes,  JR,  Zhou, et al	mSphere	Clinical data| Données cliniques Vaccine Research| Recherche sur les vaccins	In this approach based on the use of enzyme-linked immunosorbent assays (ELISA), we present natively folded viral Spike protein receptor-binding domain (RBD)-containing antigens via avidin-biotin interactions. Assessment of sera from 144 SARS-CoV-2 patients ultimately revealed that a remarkably consistent and high proportion of antibodies in the anti-RBD pool targeted the epitope responsible for ACE2 engagement (83% ± 11%; 50% to 107% signal inhibition in our largest cohort), further underscoring the importance of tailoring vaccines to promote the development of such antibodies.
Sarilumab versus standard of care for the early treatment of COVID-19 pneumonia in hospitalized patients: SARTRE: a structured summary of a study protocol for a randomised controlled trial	Caballero Bermejo,  AF,  Ruiz-Antorán, et al	Trials	RCT	The aim of the present study is to evaluate if an earlier therapeutic intervention with sarilumab plus SOC (including corticosteroids) may be more effective than current standard of care alone, in preventing progression to respiratory failure in COVID-19 infected patients with interstitial pneumonia.
[(18)F]-FDG PET/CT in oncologic patients with unsuspected asymptomatic infection with SARS-CoV-2	Cabrera Villegas,  A,  Romero Robles, et al	Eur J Nucl Med Mol Imaging	Epidemiology| Épidémiologie Clinical data| Données cliniques	The objective of this study was to investigate the incidence in oncological patients infected with SARS-CoV-2 that are asymptomatic for COVID-19 and at home and that undergo PET/CT for oncologic indications, nonrelated to COVID-19, finding in the PET/CT lung alterations that are suggestive of SARS-CoV-2 infection. results confirm that the prevalence of SARS-CoV-2 infection is higher than suspected and that there are asymptomatic patients that are attending imaging departments to be explored for their baseline oncologic processes. In these patients, PET/CT allows an early diagnosis of COVID-19.
Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein	Caruso,  Manuel,  Roy, et al	bioRxiv	Vaccine Research| Recherche sur les vaccins	We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. First, we showed that a codon optimized version of the S protein could migrate efficiently to the cell membrane. However, efficient production of infectious nanoparticles was only achieved with stable expression of a shorter version of S in its C-terminal domain (DeltaS) in 293 cells that express MLV Gag-Pol (293GP). The incorporation of DeltaS was 15-times more efficient into VLPs as compared to the full-length version, and that was not due to steric interference between the S cytoplasmic tail and the MLV capsid. Indeed, a similar result was also observed with extracellular vesicles released from parental 293 cells. The amount of DeltaS incorporated into VLPs released from producer cells was robust, with an estimated 1.25 microg/ml S2 equivalent (S is comprised of S1 and S2). Thus, a scalable platform that has the potential for production of pan-coronavirus VLP vaccines is described.
A glimpse into the diverse cellular immunity against SARS-CoV-2	Chang,  Lung-Ji,  Chang, et al	Research Square prepub	Clinical data| Données cliniques Immunology | Immunologie	To assess COVID-19-specific immunity in the population, we synthesized selected peptide pools of SARS-CoV-2 structural and functional proteins, including Spike (S), Membrane (M), envelope (E), Nucleocapsid (N) and Protease (P) as target antigens. Survey of the T cell precursor frequencies in healthy individuals specific to these viral antigens demonstrated a diverse cellular immunity, including high, medium, low and no responders. This was further confirmed by in vitro induction of anti-SARS-CoV-2 T cell immune responses using dendritic cell (DC)/T cell coculture, which was consistent with the corresponding T cell precursor frequencies in each individual tested. In general, the combination of all five antigenic pools induced the strongest cellular immune response, and individual donors responded differently to different viral antigens. A secondary in vitro booster stimulation of the T cells with the DC-peptides induced increased anti-viral immune responses in all individuals even in the no responders, suggesting that booster immunization in a vaccine scheme may elicit a broad protection in immune naïve population.
Transition from a Standard to a Hybrid On-Site and Remote Anatomic Pathology Training Model During the COVID-19 Pandemic	Chin,  KE,  Kwon, et al	Arch Pathol Lab Med	Healthcare Response | Réponse des soins de santé	This study aimed to describe the hybrid on-site and remote anatomic pathology training model in response to the COVID-19 pandemic, which was implemented in our pathology department and report the clinical fellows' responses to the survey about their experiences.  The hybrid model was implemented March 25, 2020. Fellows alternate weekly between working on-site and working remotely. On-site, fellows wear personal protective equipment and maintain social distancing. Remotely, fellows use digital pathology to review cases and supplement with online educational activities. Virtual "coffee breaks," meditation, and exercise are part of the curriculum. Online platforms, including WebEx, Google Classroom, and Canvas, are used to continue educational activities. The survey was open May 19 through June 8. Many of the respondents indicated substantial increase in their skill with using digital pathology and online platforms during the pandemic.
State-level needs for social distancing and contact tracing to contain COVID-19 in the United States	Chiu,  WeihsuehA,  Fischer, et al	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	To evaluate the impact of relaxation of restrictions on COVID-19 dynamics and control, we developed a transmission dynamic model and calibrated it to US state-level COVID-19 cases and deaths. We used this model to evaluate the impact of social distancing, testing and contact tracing on the COVID-19 epidemic in each state. As of July 22, 2020, we found only three states were on track to curtail their epidemic curve. Thirty-nine states and the District of Columbia may have to double their testing and/or tracing rates and/or rolling back reopening by 25%, while eight states require an even greater measure of combined testing, tracing, and distancing.
Diabolical dilemmas of COVID-19: An empirical study into Dutch society's trade-offs between health impacts and other effects of the lockdown	Chorus,  C,  Sandorf, et al	PLoS One	Public Health response| Interventions de santé publique	We report and interpret preferences of a sample of the Dutch adult population for different strategies to end the so-called 'intelligent lockdown' which their government had put in place in response to the COVID-19 pandemic. Using a discrete choice experiment, we invited participants to make a series of choices between policy scenarios aimed at relaxing the lockdown, which were specified not in terms of their nature (e.g. whether or not to allow schools to re-open) but in terms of their effects along seven dimensions. We find that the average citizen, in order to avoid one fatality directly or indirectly related to COVID-19, is willing to accept a lasting lag in the educational performance of 18 children, or a lasting (>3 years) and substantial (>15%) reduction in net income of 77 households. Our results suggest that most citizens are willing to trade-off health-related and other effects of the lockdown, implying a consequentialist ethical perspective. Somewhat surprisingly, we find that the elderly, known to be at relatively high risk of being affected by the virus, are relatively reluctant to sacrifice economic pain and educational disadvantages for the younger generation, to avoid fatalities. We also identify a so-called taboo trade-off aversion amongst a substantial share of our sample, being an aversion to accept morally problematic policies that simultaneously imply higher fatality numbers and lower taxes.
COVID-19 in Italy: An Analysis of Death Registry Data	Ciminelli,  G,  Garcia-Mandicó, et al	J Public Health (Oxf)	Epidemiology| Épidémiologie	We exploit in a differences-in-differences regression model to analyze COVID-19-induced mortality. We find that COVID-19 killed more than 0.15% of the local population during the first wave of the epidemic. We also show that official statistics vastly underreport this death toll, by about 60%. Next, we uncover the dramatic effects of the epidemic on nursing home residents in the outbreak epicenter: in municipalities with a high share of the elderly living in nursing homes, COVID-19 mortality was about twice as high as in those with no nursing home intown.
Randomized elimination and prolongation of ACE inhibitors and ARBs in coronavirus 2019 (REPLACE COVID) Trial Protocol	Cohen,  JB,  Hanff, et al	J Clin Hypertens (Greenwich)	RCT	This study centers around angiotensin-converting enzyme 2 (ACE2), which facilitates SARS-CoV-2 host cell entry, and may be impacted by angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), two commonly used antihypertensive classes. The primary outcome is a hierarchical global rank score incorporating time to death, duration of mechanical ventilation, duration of renal replacement or vasopressor therapy, and multiorgan dysfunction severity.
A case of probable Parkinson's disease after SARS-CoV-2 infection	Cohen,  MikhalE,  Eichel, et al	The Lancet Neurology	Clinical data| Données cliniques	This article reports a patient with probable Parkinson's disease, who was diagnosed after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
Patterns of exposure to SARS-CoV-2 carriers manifest multiscale association between urban landscape morphology and human activity	Cotlier,  GabrielI,  Lehahn, et al	Research Square prepub	Epidemiology| Épidémiologie Public Health response| Interventions de santé publique	The drastic measures taken to mitigate its spread of COVID-19 through imposed social distancing, have brought forward the need to better understand the underlying factors controlling spatial distribution of human activities promoting disease transmission. Focusing on results from 17,250 epidemiological investigations performed during early stages of the pandemic outbreak in Israel, we show that the distribution of carriers of SARS-CoV-2 is spatially correlated with two satellite-derived surface metrics: night light intensity and landscape patchiness, the latter being a measure to the urban landscape’s scale-dependent spatial heterogeneity. We find that exposure to SARS-CoV-2 carriers was significantly more likely to occur in “patchy” parts of the city, where the urban landscape is characterized by high levels of spatial heterogeneity at relatively small scales (~10-100m). We suggest that this spatial association reflects a scale-dependent constraint imposed by the city’s morphology on the cumulative behavior of the people inhabiting it.
Lower Rate of COVID-19 in Lupus Patients Receiving Immunosuppressive Drug Regimens	Damirchi,  Mohammadrafi,  Roshandel, et al	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques	The objectives of the study were to: identify the prevalence of COVID-19 in Systemic Lupus Erythematosus (SLE) patients in the Golestan province of Iran; to characterize the clinical course of COVID-19 in these patients; and to identify possible correlation between the incidence of COVID-19, its clinical manifestations and the medication taken by SLE patients. We investigated patients who had been enrolled in our rheumatologic diseases registry system. Patients responded to a questionnaire on their primary disease, comorbidities, medications, development of new symptoms, and medical services which they received, pertinent to COVID-19, during the period of COVID-19 outbreak. The data were analyzed using SPSS 16 software. There were 25 (7%) COVID-19 positive patients out of the 355 responders. 8 (40%) of them were hospitalized, out of which 2 (8%) required intensive care and later expired. COVID-19 incidence was significantly lower in the immunosuppressed group (2.2% vs 10% P-value 0.005). There was no significant correlation between hydroxychloroquine consumption, and the incidence of COVID-19 in SLE patients. Fever, fatigue, dyspnea, and dry cough were the most common clinical symptoms.
Comorbidities role on death in diabetic patients with COVID-19	Emami,  Amir,  Mohammadzadeh, et al	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques	This cross-sectional study was designed to assess risk factors for mortality in diabetic patients with COVID-19. The presentation of SARS-CoV-2 in older diabetic patients with comorbidities (chronic kidney and liver diseases) was associated with a more severe risk of mortality.
New York's perspective of COVID 19: Effect and impact on cardiac surgery	Farrington,  WJ,  Mack, et al	J Card Surg	Healthcare Response | Réponse des soins de santé	Here, we describe our institutional experience with a rapid influx of patients at the epicenter of the pandemic. METHODS: We retrospectively review our experience with the departments of cardiology, cardiothoracic surgery, anesthesia, and critical care medicine and summarize protocols developed in the midst of the pandemic. RESULTS: The rapid influx of patients requiring an intensive level of care required a complete restructuring of units, including the establishment of a new COVID-19 negative unit for the care of patients requiring urgent or emergent non-COVID-19 related care including open-heart surgery. This unique unit allowed for the delivery of safe and effective care in the epicenter of the pandemic.
Levels of genetic diversity of SARS-CoV-2 virus: reducing speculations about the genetic variability of the virus in South America	Felix,  Pierre Teodósio,  do Nascimento Filho, et al	bioRxiv	Epidemiology| Épidémiologie Coronavirology| Coronavirologie	In this work, we evaluated the levels of genetic diversity in 38 complete Genomes of SARS-CoV-2 from six countries in South America, using specific methodologies for paired FST, AMOVA, mismatch, demographic and spatial expansions, molecular diversity and for the time of evolutionary divergence. The analyses showed non-significant evolutionary divergences within and between the six countries, as well as a significant similarity to the time of genetic evolutionary divergence between all populations. Thus, it seems safe to affirm that we will find similar results for the other Countries of South America, reducing speculation about the existence of rapid and silent mutations that, although there are as we have shown in this work, do not increase, until this moment, the genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and drugs in general.
SARS-CoV-2 infection among patients with haematological disorders: Severity and one-month outcome in 66 Danish patients in a nationwide cohort study	Glenthøj,  A,  Jakobsen, et al	Eur J Haematol	Epidemiology| Épidémiologie Clinical data| Données cliniques	Authors discuss patients with haematological disorders who  may be particularly vulnerable to COVID-19. They conducted a prospective, nationwide study including 66 patients in follow-up at Danish haematology departments with a malignant or non-malignant haematological disorder and with verified SARS-CoV-2 infection. Outcomes were intensive care unit (ICU) admission and one-month survival rate. Authors conclude that  the clinical course following SARS-CoV-2 infection is severe in this vulnerable group of patients.
Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia	Gunadi,  Wibawa,  Hendra, et al		Epidemiology| Épidémiologie Coronavirology| Coronavirologie	We report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java, Indonesia. All patients were hospitalized with various symptoms and severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, it appears that clade GH has become the major circulating virus in Indonesia. .
Mining twitter to explore the emergence of COVID-19 symptoms	Guo,  JW,  Radloff, et al	Public Health Nurs	Public Health response| Interventions de santé publique	Because social media data have a potential application in the early identification novel virus symptoms, this study aimed to explore what symptoms mentioned in COVID-19-related social media posts during the early stages of the pandemic. The findings of this study revealed that many COVID-19-related symptoms mentioned in Twitter tweets earlier than the announcement by the CDC.
An Effective Inhaler Medication In The Treatment Of COVID-19 Associated Pneumonia	Guvenmez,  Oguz,  Keskin, et al	Research Square prepub	Clinical data| Données cliniques Therapeutics| Thérapeutique RCT	In the new inhaler treatment (NIT) given in this clinical study, the molecules that have antiviral, antioxidant and anti-inflammatory effects without any toxicity were brought together in a nebulizer based treatment. Patients were randomly assigned with half receiving the normal treatment protocol and the other half receiving the new inhalation treatment protocol in addition to the normal treatment protocol. Pulse oxygen saturation, respiratory rate, percentage of lung involvement, arterial blood gas, and duration of hospitalization were compared after the treatment. Mean duration of hospital stay for patients receiving NIT in addition to the normal treatment was significantly lower compared to patients receiving normal treatment only (6.5 ± 1.8 and 17.1 ± 2.4, respectively).
Quality and readability of web-based Arabic health information on COVID-19: Infodemiology study	Halboub,  Esam,  Al-Akhali, et al	Research Square prepub	Public Health response| Interventions de santé publique	The study sought to assess the quality and readability of the web-based Arabic health information on COVID-19. Selected search engines were searched on 13 April 2020 for specific Arabic terms on COVID-19. The first 100 consecutive websites from each engine were obtained. The quality of the websites was analyzed. Overall, 36 websites were found eligible for quality and readability analyses. Only one website (2.7%) was HONcode certified. No single website attained a high score based on the DISCERN tool; the mean score of all websites was 31.5±12.55. Most of the available web-based Arabic health information on COVID-19 doesn’t have the required level of quality, irrespective of being easy to read and understand by most of the general people.
A case study of a collaborative allied health and nursing crisis response	Hales,  P,  White, et al	J Interprof Care	Healthcare Response | Réponse des soins de santé	The aim of the case study was to evaluate how an interprofessional workforce from the wider organization could be supported to work in critical care as part of a crisis response such as COVID-19.  Ultimately, the study highlights that by identifying and investing in the key enablers, health-care organizations can be better prepared to respond to a global crisis.
Is the press properly presenting the epidemiological data on COVID-19? An analysis of newspapers from 25 countries	Hammes,  Luciano Serpa,  Rossi, et al	Research Square prepub	Public Health response| Interventions de santé publique	We conducted a cross-sectional study to assess how newspapers from 25 countries are comparing and presenting COVID-19 epidemiological data to their readers. 75 newspapers were evaluated.  Quality assessment of the comparisons showed that only a minority of newspapers adjusted the data for population size in case comparisons between regions (37,2%) and between countries (25,6%), and the same was true for death comparisons between regions (27,3%) and between countries (27%). Of those making comparisons, only 13,7% explained the difference in the interpretation of cases and deaths. Of 17 that presented a logarithmic curve, only 29,4% explained its meaning.
Application of disease model to ascertain risk-mitigation strategies during COVID-19 pandemic in 2020, an example from resource-constrained urban settings in Pakistan	Hassan,  Shoaib,  Salman, et al	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission Public health interventions*| Interventions de santé publique	Using officially reported data, this model forecasted COVID-19 prevalence in cosmopolitan cities. Several risk-mitigation strategies were analyzed for effectiveness in controlling disease incidence. Moreover, the reproduction rates to ascertain transmission, herd-immunity threshold, and performance of required laboratory tests were studied. First of its kind, this study estimates sub-national COVID-19 prevalence in dense-urban living in low-middle income settings.
Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia	Helal,  MA,  Shouman, et al	J Biomol Struct Dyn	Coronavirology| Coronavirologie	To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The results showed that this binding is dominated by electrostatic interactions involving residues Arg403, Asn481, and the backbone of Gly502. These data contribute to a better understanding of the mechanism of infection of SARS-CoV-2 to T lymphocytes and could provide valuable insights for the rational design of adjuvant treatment for COVID-19.
Radiotherapy in the fight against pneumonia associated with SARS-CoV-2	Hertzog,  RG,  Bicheru, et al	Int J Radiat Biol	Clinical data| Données cliniques Therapeutics| Thérapeutique	This study aims to explore the concept of applying radiotherapy as a treatment approach in patients with severe pneumonia infected with COVID-19. Article is not available
High affinity modified ACE2 receptors prevent SARS-CoV-2 infection	Higuchi,  Yusuke,  Suzuki, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	We engineered ACE2 to enhance the affinity with directed evolution in human cells. Three cycles of random mutation and cell sorting achieved more than 100-fold higher affinity to RBD than wild-type ACE2. The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus.
Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques	Hoang,  TimothyN,  Pino, et al	bioRxiv	Therapeutics| Thérapeutique Animal model | Modèle animal	Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. Type I IFN antiviral responses and SARS-CoV-2 specific T cell responses remained similar between the two groups. Importantly, however, animals treated with baricitinib showed reduced immune activation, decreased infiltration of neutrophils into the lung, reduced NETosis activity, and more limited lung pathology. Moreover, baricitinib treated animals had a rapid and remarkably potent suppression of alveolar macrophage derived production of cytokines and chemokines responsible for inflammation and neutrophil recruitment. These data support a beneficial role for, and elucidate the immunological mechanisms underlying, the use of baricitinib as a frontline treatment for severe inflammation induced by SARS-CoV-2 infection.
Detection of SARS-CoV-2 in peritoneal fluid from patients with kidney disease and COVID-19: report of two cases	Ibarra-Hernandez,  Margarita	Research Square prepub	Clinical data| Données cliniques	We describe the detection of SARS-CoV-2 in the PF of two patients with COVID 19 and kidney disease. Real-time SARS-CoV-2 polymerase chain reaction (qRT-PCR) in the PF was positive. Two cases highlights the importance of increasing the level of awareness for the presence and possible SARS-CoV-2 transmission through non-respiratory routes, like peritoneal fluid.
Lopinavir-ritonavir is not an effective inhibitor of the main protease activity of SARS-CoV-2 in vitro	Jang,  Minsu,  Park, et al	bioRxiv	Therapeutics| Thérapeutique	In this report, we examined the effect of lopinavir and ritonavir to the activity of the purified main protease (Mpro) protein of SARS-CoV-2, the causative virus of COVID-19. Unexpectedly, lopinavir and ritonavir did not inhibit Mpro activity. These results will aid the drug candidate selection for ongoing and future COVID-19 clinical trials.
Changes in access to educational and healthcare services for individuals with intellectual and developmental disabilities during COVID-19 restrictions	Jeste,  S,  Hyde, et al	J Intellect Disabil Res	Public Health response| Interventions de santé publique	The objectives of this online survey that included both national and international families were to capture changes in access to healthcare and educational services for individuals with intellectual and developmental disabilities (IDDs) that occurred shortly after restrictions were initiated and to survey families on resources that could improve services for these individuals. COVID-19 restrictions have greatly affected access to services for individuals with syndromic IDDs.
Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing	Joung,  J,  Ladha, et al	N Engl J Med	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	In this letter to the editor, authors describe a simple test for detection of SARS-CoV-2. The sensitivity of this test is similar to that of reverse-transcription–quantitative polymerase-chain-reaction (RT-qPCR) assays. STOP (SHERLOCK testing in one pot) is a streamlined assay that combines simplified extraction of viral RNA with isothermal amplification and CRISPR-mediated detection. This testing showed that STOPCovid.v2 had a sensitivity of 93.1% and a specificity of 98.5%.
Clinical Characteristics and Outcome of Pneumomediastinum in Patients with COVID-19 Pneumonia	Kangas-Dick,  A,  Gazivoda, et al	J Laparoendosc Adv Surg Tech A	Epidemiology| Épidémiologie Clinical data| Données cliniques	We sought to summarize the limited body of literature regarding PM in patients with COVID-19 and characterize the presentation and clinical outcomes of PM in patients with severe acute respiratory syndrome (SARS)-COV-2 pneumonia at our institution to better define the incidence, prognosis, and available treatment for this condition. Out of the 346 intubated COVID-19 patients, 34 (10%) had PM. PM, although a rare phenomenon, was more prevalent in COVID-19 patients compared with historical patients with adult respiratory distress syndrome.
The Relationship between Media Advertising and Attitudinal Changes during COVID-19	Khalid,  Atiqa,  Ali, et al	Research Square prepub	Public Health response| Interventions de santé publique	This study also aims to investigate the role and impacts of mass media advertisements to spread COVID-19 awareness in Sahiwal, Pakistan. The researchers selected a sample of n= 179 respondents and used a three-point Likert scale questionnaires for data gathering purposes. The researchers also proposed a self-structured model supported by Social Learning theory, as the primary conceptual framework. The results revealed that media advertisements are significantly (p ≤ .000) spreading disease awareness and positively (p ≤ .000), infusing the attitudinal changes among the audience. The results indicated the power of the media campaigns and their potential impacts on audience behavior.
Prolonged SARS-CoV-2 detection and reversed RT-PCR results in mild or asymptomatic patients	Kim,  SM,  Hwang, et al	Infect Dis (Lond)	Clinical data| Données cliniques	We retrospectively reviewed real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test results of mild or asymptomatic COVID-19 patients in Korea between 9 March 2020 and 10 April 2020. Patients underwent an upper respiratory RT-PCR test every week until discharge. The detection of SARS-CoV-2 lasting more than 3 weeks was common in mild or asymptomatic patients. Upper respiratory RT-PCR results were frequently reversed from negative to positive.
Evaluation of nafamostat mesylate safety and inhibition of SARS-CoV-2 replication using a 3-dimensional human airway epithelia model	Kirkpatrick,  Lynn,  Millard, et al	bioRxiv	Therapeutics| Thérapeutique	We selected a biologically relevant pre-clinical experimental model of SARS-CoV-2 lung infection using a 3D human reconstituted airway epithelial model of nasal origin to characterize the effects of nafamostat on tissue-level cellular ultrastructure and viral infection kinetics. Our results confirm the not only the relevance of this model for the preclinical evaluation of safety and efficacy of antiviral candidates, but also the highly potent nature of nafamostat SARS-CoV-2 antiviral activity. The studies described herein provided evidence demonstrating the therapeutic potential of nafamostat against COVID-19, as well as its safety upon exposure to lung airway cellular.
Reductions in commuting mobility correlate with geographic differences in SARS-CoV-2 prevalence in New York City	Kissler,  SM,  Kishore, et al	Nat Commun	Epidemiology| Épidémiologie	Authors report the prevalence of SARS-CoV-2 in New York City boroughs inferred using tests administered to 1,746 pregnant women hospitalized for delivery. Prevalence was lowest in boroughs with the greatest reductions in morning movements out of and evening movements into the borough.
Virtual Screening of Phytochemical Compounds as Potential Inhibitors against SARS-CoV-2 Infection	Kothandan,  Ram,  Rajan, et al	Research Square prepub	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	The present study investigates the use of various phytochemicals virtually screened from various plant sources in Western Ghats, India and subsequently molecular docking studies were performed to identify the efficacy of the drug in retroviral infection particularly coronavirus infection. Out of 57 phytochemical screened initially based on the structural and physicochemical properties, 39 were effectively used for the docking analysis. The insilico methods used in this study suggests that the compound Piperolactum A to be the most effective inhibitor of S-protein from binding to the GRP78 receptor. By blocking the binding of the S-protein to the CS-GRP78 cell surface receptor, they can inhibit the binding of the virus to the host.
Recovered COVID-19 patients with recurrent viral RNA exhibit lower levels of anti-RBD antibodies	Liu,  B,  Shi, et al	Cell Mol Immunol	Epidemiology| Épidémiologie Clinical data| Données cliniques	In this study, we collected blood samples from 47 recovered patients.  Eight of the 47 recovered patients displayed RP anal or throat swab samples from 8 to 39 days after viral shedding, and 39 patients remained persistently RNA negative (PRN). None of the conditions of these RP patients were severe before recovery.  The median disease duration was 16.5 days for RP patients (ranging from 10 to 24 days), which was not significantly different from that of PRN patients (15 days, ranging from 1 to 40 days). Moreover, the RP patients were significantly younger than the PRN patients (median 34.5 years vs. 54 years, p = 0.019), which is consistent with previous reports. Based on our findings, the anti-RBD IgG level could serve as an indicator of RP status. To minimize the risk of possible viral rebound and retransmission during the current pandemic, close monitoring of anti-RBD IgG levels at viral shedding and a long-term follow-up of patients with lower levels of RBD antibodies is needed.
The effect of control measures on COVID-19 transmission in Italy: Comparison with Guangdong province in China	Liu,  PY,  He, et al	Infect Dis Poverty	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	This study aims to investigate the dynamics of the disease spread in Italy and provide some suggestions on containing the epidemic. We compared Italy's status at the outbreak stage and control measures with Guangdong Province in China by data observation and analysis. A modified autonomous SEIR model was used to study the COVID-19 epidemic and transmission potential during the early stage of the outbreak in Italy. The comparison of specific measures implemented in the two places and the time when the measures were initiated shows that the initial prevention and control actions in Italy were not sufficiently timely and effective. We estimated parameter values based on available cumulative data and calculated the basic reproduction number to be 4.32 before the national lockdown in Italy. Based on the estimated parameter values, we performed numerical simulations to predict the epidemic trend and evaluate the impact of contact limitation, detection and diagnosis, and individual behavior change due to media coverage on the epidemic.
Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are non-specific promiscuous SARS-CoV-2 main protease inhibitors	Ma,  Chunlong,  Hu, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	This study investigated the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. Collectively, the results showed that the inhibition of Mpro by these six compounds is non-specific and the inhibition is abolished or greatly reduced with the addition of reducing reagent DTT. In the absence of DTT, these six compounds not only inhibit Mpro, but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease, the 2Apro and 3Cpro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymatic inhibition potency IC50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity.
Positive Pleural Fluid RT-PCR for Virus Detection in SARS-CoV-2 Pneumonia	Malik,  MI,  Fox, et al	Qjm	Clinical data| Données cliniques	This case report highlights that SARS-CoV-2 can be detected in pleural effusions by RT-PCR. Pleural fluid analysis in this case showed an exudative effusion with high lymphocyte count.
SARS-CoV-2 protein Nsp1 alters actomyosin cytoskeleton and phenocopies arrhythmogenic cardiomyopathy-related PKP2 mutant	Marquez-Lopez,  Cristina,  Roche-Molina, et al	bioRxiv	Coronavirology| Coronavirologie	This study identified the actin-based motor proteins Myh9 and Myh10 as key PKP2 interactors and demonstrated that expression of the ACM-related PKP2 mutant R735X alters actin fiber organization and cell mechanical stiffness. Also showed that SARS-CoV-2 Nsp1 protein acts similarly to this known pathogenic R735X mutant, altering the actomyosin component distribution on cardiac cells. Data reveals that Nsp1 hijacks PKP2 into the cytoplasm and mimics the effect of delocalized R735X mutant.   These results demonstrate that cytoplasmic PKP2 drives actomyosin deregulation and structural collapse, validating a critical role of PKP2 localization in the regulation of actomyosin architecture. The fact that Nsp1 and R735X share similar phenotypes also suggests that direct SARS-CoV-2 heart infection could induce a transient ACM-like disease in COVID-19 patients, which may contribute to right ventricle dysfunction, observed in patients with poor prognosis.
Resurgence of BK Virus following Covid-19 in kidney transplant recipients	Masset,  C,  Ville, et al	Transpl Infect Dis	Clinical data| Données cliniques Immunology | Immunologie	Herein, we report two cases of BKV replication after non-severe SARS-CoV-2 infection. The first case was a 59-year-old man, transplanted 3 months ago, with recent history of slight BKV viremia (3.3 log(10) DNA copies/ml). Despite strong reduction of maintenance immunosuppression (interruption of mycophenolic acid and important decrease of calcineurin inhibitors), BKV replication largely increased after Covid-19 and viremia persisted at 4.5 log copy/ml few months later. The second case was a 53-year-old woman, transplanted 15 years ago. She had recent history of BKV cystitis, which resolved with decrease of MPA dosage. Few weeks after SARS-CoV-2 infection, she presented recurrence of lower urinary tract symptoms.
COVID-19 outbreak, social distancing and mass testing in Kenya - Insights from a mathematical model	Mbogo,  Rachel Waema,  Oddhiambo, et al	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Transmission Public health interventions*| Interventions de santé publique	Employed a SEIHCRD delay differential mathematical transmission model with reported Kenyan data on cases of COVID -19 to estimate how transmission varies over time and which population to target for mass testing. The model is concise in structure, and successfully captures the course of the COVID -19 outbreak, and thus sheds light on understanding the trends of the outbreak and the vulnerable populations. The results from the model gives insights to the government on the population to target for mass testing.
COVID-19 outbreak and control in Kenya- Insights from a mathematical model	Mbogo,  Rachel Waema,  Orwa, et al	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Transmission Public health interventions*| Interventions de santé publique	This study used a SEIHCRD mathematical transmission model with reported Kenyan data on cases of COVID -19 to estimate how transmission varies over time. The model is concise in structure, and successfully captures the course of the COVID -19 outbreak, and thus sheds light on understanding the trends of the outbreak. The next generation matrix approach was adopted to calculate the basic reproduction number ( $R_0$ ) from the model to assess the factors driving the infection. The results show that non-pharmaceutical interventions over a relatively long period is needed to effectively get rid of the COVID -19 epidemic otherwise the rate of infection will continue to increase despite the increased rate of recovery.
Heterogeneous antibodies against SARS-CoV-2 spike receptor binding domain and nucleocapsid with implications for COVID-19 immunity	McAndrews,  KM,  Dowlatshahi, et al	JCI Insight	Epidemiology| Épidémiologie Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes Immunology | Immunologie	Here, we generated a quantitative serological ELISA using recombinant S-RBD and N-protein for the detection of circulating antibodies in 138 serial serum samples from 30 reverse transcription PCR–confirmed, SARS-CoV-2–hospitalized patients, as well as 464 healthy and non–COVID-19 serum samples. Our studies show that detection of N-protein–binding antibodies does not always correlate with presence of S-RBD–neutralizing antibodies and caution against the extensive use of N-protein–based serology testing for determination of potential COVID-19 immunity.
Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing	Meyer,  Bjoern,  Chiaravalli, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	This study examined the proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. Identified multiple previously unknown cleavage sites in multiple viral proteins, including major antigenic proteins S and N, which are the main targets for vaccine and antibody testing efforts. Discovered significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. Showed that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and the Ser/Thr kinase MYLK/MLCK, showed a dose-dependent reduction in SARS-CoV-2 titres.
Immunogenicity and protective efficacy of BBV152: a whole virion inactivated SARS CoV-2 vaccine in the Syrian hamster model	Mohandas,  Sreelekshmy,  Yadav, et al	Research Square prepub	Vaccine Research| Recherche sur les vaccins Immunology | Immunologie Animal model | Modèle animal	Here, we have developed and assessed the immunogenicity and protective efficacy of an inactivated SARS-CoV-2 vaccine (BBV152) in hamsters. Three dose vaccination regime with three formulations of BBV152 induced significant titres of SARS-CoV-2 specific IgG and neutralizing antibodies. The protection of the hamsters was evident by the rapid clearance of the virus from lower respiratory tract, reduced virus load in upper respiratory tract, absence of lung pathology and robust humoral immune response.
Metabolic Consequences Of Obesity On The Hypercoagulable State Of Polycystic Ovary Syndrome: A Risk For Severe SARS-Cov-2 Infection?	Moin,  ASM,  S	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques	Olycystic ovary syndrome (PCOS) women have a hypercoagulable state and are also at high risk for severe COVID-19 leading to thromboembolic complications and increased mortality. We determined plasma coagulation pathway protein levels in PCOS (n=146) and control (n=97) women recruited to a PCOS biobank. In a multivariate analysis accounting for inflammation, insulin resistance and BMI, there was no correlation of PCOS with any of the coagulation proteins. The hypercoagulable State in PCOS can be fully accounted for by BMI, inflammation and insulin resistance suggesting that only obese PCOS women would be predisposed to an enhanced risk for severe COVID-19-related disease.
Comparison of Clinical Outcomes in Patients with ST Elevation Myocardial Infarction with Percutaneous Coronary Intervention and the Use of a Telemedicine App Before and After the COVID-19 Pandemic at a Center in Beijing, China, from August 2019 to March 2	Nan,  J,  Meng, et al	Med Sci Monit	Healthcare Response | Réponse des soins de santé	This study compared outcomes in patients with STEMI who had percutaneous coronary intervention (PCI) and the use of a telemedicine app from August 2019 to March 2020 at a single center in Beijing, China. The time from symptom onset to calling an ambulance (SCT), door to balloon time (DTB), and total ischemia time (TIT) were significantly prolonged in patients after the pandemic. Patients who used the app had shorter SCT, DTB, and TIT before and after the pandemic compared to those who did not. Adverse clinical outcomes were significantly higher after compared with before the pandemic, despite the incidence rate of stroke, any revascularization, and stent thrombosis. However, there was no significant difference in short-term adverse clinical outcomes between patients who used the app and those who did not before and after the pandemic.
Effect of Arbidol on COVID-19: A Randomized Controlled Trial	Nojomi,  Marzieh,  Yasin, et al	Research Square prepub	Clinical data| Données cliniques Therapeutics| Thérapeutique RCT	This study aimed to determine the effect of Arbidol on COVID-19 disease. One hundred eligible patients with diagnosis of Covid-19 recruited in the study and assigned randomly to two groups of either Hydroxychloroquine followed by Kaletra (Lopinavir-ritonavir) or Hydroxychloroquine followed by ARB. Without any drop out, 100 patients were entered to final analysis with significant level of 0.05. The duration of hospitalization in ARB group was less than Kaletra arm significantly (7.2 versus 9.6 days; P=0.02). Time to relief fever was almost similar across two groups (2.7 versus 3.1 days in ARB and Kaletra arms respectively). Peripheral oxygen saturation rate was different after seven days of admission across two groups signi¦cantly (94% versus 92% in ARB and Kaletra groups respectively) (P=0.02). Based on multiple linear regression analysis, IHD, Na level and oxygen saturation at the time of admission and type of therapy were the independent adjusted variables that determined the duration of hospitalization in patients with COVID-19. Arbidol, compared to Kaletra, significantly contributes to clinical and laboratory improvements, including peripheral oxygen saturation, requiring ICU admissions, duration of hospitalization, chest CT involvements, WBC, and ESR.
The effect of the COVID-19 pandemic on skin cancer surgery in the United Kingdom: a national, multi-centre, prospective cohort study and survey of Plastic Surgeons	Nolan,  GS,  Dunne, et al	Br J Surg	Healthcare Response | Réponse des soins de santé	Throughout ‘lockdown’ (March 16th – June 14th 2020) a prospective cohort of patients undergoing non‐melanoma skin cancer (NMSC) surgery was undertaken. Retrospective data was collected on melanoma surgery. Data from immediately prior to lockdown (March 16th – 22nd) served as a control as normal NHS activities were undertaken during this time. Consecutive monthly surveys of Plastic Surgeons confirmed trends. The median number of general anaesthetic (GA) lists per week per institution fell from 3 pre‐lockdown to 0·5 in April (p < 0·0001) and did not reach pre‐lockdown levels in June.  The number of NMSC treated per week fell by 27‐47% throughout April and May. Excision of Squamous cell carcinomas (SCCs) was prioritised over basal cell carcinomas (BCCs), and at the pandemics' peak SCCs comprised 71% of excisions. This study demonstrates all skin cancer treatment was negatively affected by the COVID‐19 pandemic.
The enzymatic activity of the nsp14 exoribonuclease is critical for replication of MERS-CoV and SARS-CoV-2	Ogando,  NS,  Zevenhoven-Dobbe, et al	J Virol	Coronavirology| Coronavirologie	We established in vitro assays with purified recombinant MERS-CoV nsp14 to monitor its ExoN and N7-MTase activities. All ExoN knockout mutations that proved lethal in reverse genetics were found to severely decrease ExoN activity, while not affecting N7-MTase activity. Our study strongly suggests CoV nsp14 ExoN to have an additional function, which apparently is critical for primary viral RNA synthesis and thus differs from the proofreading function that - based on previous MHV and SARS-CoV studies - was proposed to boost longer-term replication fidelity.
A fractional order approach to modeling and simulations of the novel COVID-19	Owusu-Mensah,  Isaac	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Transmission Public health interventions*| Interventions de santé publique	Introduce a fractional type Susceptible-Exposed-Infected-Recovered (SEIR) model to gain insight into the ongoing pandemic of COVID-19. Our proposed model incorporates transmission rate, testing rates, and transition rate (from asymptomatic to symptomatic population groups) for a holistic study of the coronavirus disease. The simulation results confirm that fractional calculus is an appropriate tool in modeling the spread of a complex infectious disease such as the novel COVID-19. In the absence of vaccine and treatment, our analysis strongly supports the significance reduction in the transmission rate as valuable strategy to curb the spread of the virus.  Tracing and moving testing reduces the number of infected individuals in the general public and thereby reduce the spread of the pandemic. Once the infected individuals are identified and isolated, the interaction between susceptible and infected individuals diminishes and transmission reduces. Furthermore, aggressive testing is also highly recommended.
Perceived risk, anxiety and protective health behaviours during the early phase of coronavirus (COVID-19) pandemic in Nigeria	Oyetunji,  Tosin Philip,  Oyelakin, et al	Research Square prepub	Public Health response| Interventions de santé publique	This study aims to assess perceived risk, anxiety and protective health behaviours of the general public during the early phase of the coronavirus (COVID-19) pandemic in Nigeria. This was a cross-sectional study among 1197 respondents aged 18 years and above between April 27th to May 16th, 2020. More than half (61.9%) of the respondents have high risk perception towards COVID-19. Using the seven-item Generalized Anxiety Disorder (GAD-7) scale, 37.2% of participants had high anxiety levels. Male gender (OR=1.38,CI=1.09-1.74), being employed (OR=1.53,CI = 1.21- 1.95) and high risk perception (OR=1.33, CI = 1.05-1.69) were positively associated with observance of more than one protective measure against COVID-19. Having not more than 12 years of education (OR=0.51, CI=0.32-0.81) was negatively associated with observance of more than one protective behaviour. High risk perception (OR=1.82; CI=1.42-2.34), having not more than 12 years of education (OR=1.73; CI= 1.13-2.64), and being employed (OR =1.29; CI=1.01-1.64) were positively associated with anxiety. Participants aged 25-34 years (OR=0.34; CI =0.12-0.94) and aged 35-54 years (OR=0.30; CI=0.10-0.85) were found to be protective against developing COVID-19- related anxiety.
Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey	Pavel,  STI,  Yetiskin, et al	PLoS One	Clinical data| Données cliniques Coronavirology| Coronavirologie	We isolated SARS-CoV-2 from the nasopharyngeal sample of a patient in Turkey with confirmed COVID-19. We determined that the Vero E6 and MA-104 cell lines are suitable for supporting SARS-CoV-2 that supports viral replication, development of cytopathic effect (CPE) and subsequent cell death. Phylogenetic analyses of the whole genome sequences showed that the hCoV-19/Turkey/ERAGEM-001/2020 strain clustered with the strains primarily from Australia, Canada, England, Iran and Kuwait and that the cases in the nearby clusters were reported to have travel history to Iran and to share the common unique nucleotide substitutions.
[Provisioning of personal protective equipment in hospitals in preparation for a pandemic]	Pfenninger,  EG,  Kaisers, et al	Anaesthesist	Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI) Healthcare Response | Réponse des soins de santé	The aim of this study was to develop a tool to predict the necessary amount of PPE to be in stock at a transregional university hospital for a certain period of time during a pandemic. In April 2020 PPE consisting of 18 different items were kept in stock at Ulm University Hospital and in total 1,995,500 individual items were used. 22 intensive care patients with 257 nursing days and in the infection ward 39 patients with 357 nursing days were treated for COVID-19 disease, leading to a total of 603.2 man-days. A total of 34,550 KN95 masks, 1,558,780 gloves and 1100 goggles or protective visors were used, with a daily average of 49 NK95 masks and 2216 gloves required per ICU patient. In May 2020, 6 ICU patients and 19 patients in infection wards were treated for COVID-19 with 34 nursing days in intensive care and 201 nursing days in infection wards. The use of PPE material was 39% lower than in the previous month but in absolute terms 82% and on average 39% higher than calculated.
The COVID-19 pandemic: Psychological and behavioral responses to the shutdown of the beauty industry	Pikoos,  TD,  Buzwell, et al	Int J Eat Disord	Public Health response| Interventions de santé publique	The current study explored the relationship between engagement in appearance-focused behaviors and distress regarding beauty service closure. Participants with high and low levels of dysmorphic concern were compared to determine whether COVID-19 restrictions may affect these groups differently. An online survey was completed by 216 participants living in Australia. Appearance-focused behaviors decreased in the low DCQ group (n = 163) during the COVID-19 pandemic, while such behaviors in the high DCQ group (n = 53) remained unchanged. Individuals who were living alone, younger, reported higher dysmorphic concern and greater distress over beauty service closure engaged in more frequent appearance-focused behaviors (R(2) = .57, p < .001). The high DCQ group reported greater distress over beauty service closure and increased desire to obtain future beauty treatments.
Targeting RNA G-quadruplex in SARS-CoV-2: A Promising Therapeutic Target for COVID-19?	Qu,  X,  Zhao, et al	Angew Chem Int Ed Engl	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	COVID-19 pandemic caused by SARS-CoV-2 has become a global threat. Understanding the underlying mechanisms and developing innovative treatments are extremely urgent. G-quadruplexes (G4s) are important non-canonical nucleic acids structures with distinct biofunctions. Here, we studied four putative G4-forming sequences (PQSs) in SARS-CoV-2 genome. One of them (namely RG-1), which locates in the coding sequence (CDS) region of SARS-CoV-2 nucleocapsid phosphoprotein (N), has been verified to form stable RNA G4 structure in live cells. G4-specific compounds, such as PDP, can stabilize RG-1 G4 and significantly reduce the protein levels of SARS-CoV-2 N by inhibiting its translation bothin vitro andin vivo. To our knowledge, this is the first evidence that PQSs in SARS-CoV-2 can form G4 structures in live cells, and their biofunctions can be regulated by G4-specific stabilizer. We expect this finding will provide new insights into developing novel antiviral drugs against COVID-19.
ECIEN-2020 Study: the effect of COVID-19 on admissions for NON-COVID diseases	Ramos-Lacuey,  Beatriz	Research Square prepub	Healthcare Response | Réponse des soins de santé	The objective of this study is to analyze and describe the epidemiology of admissions for non-covid pathologies, in a pediatric hospital during the first wave of COVID-19 and compare it with the same period in 2019. The pandemic has significantly decreased pediatric admissions for NON-COVID diseases by 33%, with a 48% reduction in patients admitted for pulmonary diseases. The percentage of patients admitted among those seen in the emergency department rose from 5.1% in 2019 to 10.9% in 2020, whereas the total number of consultations in the emergency department decreased a 68%.
High COVID-19 attack rate among attendees of wedding events in Bali, Indonesia, March 2020	Ravindran,  B,  Hogarth, et al	Commun Dis Intell (2018)	Epidemiology| Épidémiologie	We investigated a cluster of COVID-19 cases in returning Australian residents who attended wedding events in Bali, Indonesia, during 15–21 March 2020. We conducted a retrospective cohort study of the 41 attendees. COVID-19 was identified in 56% of attendees (23/41), with illness onset between 21 March and 2 April 2020. One secondary case was identified in a household contact of an attendee. The median age of cases was 31 years (range 3–64). One case was hospitalised and did not require critical care. There were no deaths. No cases occurred among six attendees who left prior to the actual wedding day. Attack rates ranged from 64% to 87% for different exposures. We could not identify a single risk exposure that accounted for all cases; it is therefore likely there were multiple episodes of transmission.
Incidence of “new-onset” constipation and associated factors during lockdown due to the coronavirus-19 pandemic	Remes-Troche,  Jose	Research Square prepub	Public Health response| Interventions de santé publique	The objective is to examine the appearance of symptoms of constipation and its associated factors during the COVID-19 pandemic. A cross-sectional and descriptive study was conducted on an open population, applying an electronic survey (4 weeks after lockdown due to COVID-19 in Mexico) to evaluate: demographic characteristics, physical activity, water and fiber intake, appearance of constipation symptoms (including stool consistency), and quality of life. Out of 678 subjects evaluated, 170 (25%, 95% CI 21.7-28.4) developed symptoms of “new-onset” constipation, with a significant decrease in the number of daily bowel movements (p<0.05) and hardness of stool consistency (p<0.05) during lockdown. The multivariate analysis (logistic regression) showed that female sex (p=0.001), water intake (p=0.039), and physical activity (p=0.012) were associated with “new-onset” constipation.
In silico investigation of spice molecules as potent inhibitor of SARS-CoV-2	Rout,  J,  Swain, et al	J Biomol Struct Dyn	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	In this work, the molecular docking of 30 selected spice molecules (screened through ADME property) was performed to identify the potential inhibitors for the RBD Spro and Mpro of SARS-CoV-2. We have found that though all the molecules bind actively with the SARS-CoV-2 RBD Spro and Mpro, but Piperine has the highest binding affinity among the 30 screened molecules. Besides, the comparative study between Piperine and currently used drugs show that Piperine is more effective. The interaction of Piperine with receptor-binding domain (RBD) Spro and Mpro is further validated by the molecular dynamics (MD) simulation studies.
Time-varying auto-regressive models for count time-series	Roy,  Arkaprava,  Karmakar, et al	arXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie Public health interventions*| Interventions de santé publique	We propose a Bayesian framework to study time-varying semiparametric AR(p) model for count and then extend it to propose a time-varying INGARCH model considering the rapid changes in the spread. We calculate posterior contraction rates of the proposed Bayesian methods with respect to average Hellinger metric. Our proposed structures of the models are amenable to Hamiltonian Monte Carlo (HMC) sampling for efficient computation. We analyze the daily time series data of newly confirmed cases to study its spread through different government interventions.
Bromelain Inhibits SARS-CoV-2 Infection in VeroE6 Cells	Sagar,  Satish,  Rathinavel, et al	bioRxiv	Coronavirology| Coronavirologie Therapeutics| Thérapeutique Animal model | Modèle animal	This study expressed a GFP-tagged SARS-CoV-2 S-Ectodomain in Tni insect cells. That contained sialic acid-enriched N- and O-glycans. Surface resonance plasmon (SPR) and Luminex assay showed that the purified S-Ectodomain binding to human ACE-2 and immunoreactivity with COVID-19 positive samples. We demonstrate that bromelain (isolated from pineapple stem and used as a dietary supplement) treatment diminishes the expression of ACE-2 and Transmembrane Serine Protease 2 (TMPRSS2) in VeroE6 cells and dramatically lowers the expression of S-Ectodomain. Importantly, bromelain treatment reduced the interaction between S-Ectodomain and VeroE6 cells. Most importantly, bromelain treatment significantly diminished the SARS-CoV-2 infection in VeroE6 cells.
Radiology Departments as COVID-19 entry-door might improve healthcare efficacy and efficiency, and Emergency Department safety	Santos,  José María García,  Martínez, et al	Research Square prepub	Infection Prevention and Control/ Prévention et contrôle des infections (IPAC/PCI) Healthcare Response | Réponse des soins de santé	We aimed to assess the efficiency of a primary care high-resolution radiology service (pcHRRS) for ppCOVID-19 in terms of time consumed at the hospital and decision reliability. We assessed 849 consecutive ppCOVID-19 patients, 418 appointed by general practitioners to the pcHRRS (home-confined ppCOVID-19 cases with negative –group-1- and positive -group-2- X-ray results) and 431 arriving at the ED by themselves (group-3). The pcHRRS halved ED respiratory patients (49.2%), allowed faster decisions and prompted admission in most cases (84/93, 90.3%). A Radiology Department pcHRRS may be a more efficient entry-door for ppCOVID-19 by decreasing ED patients and making expedited decisions while guaranteeing social distance.
Antibody potency, effector function and combinations in protection from SARS-CoV-2 infection in vivo</em&gt	Schäfer,  Alexandra,  Muecksch, et al	bioRxiv	Therapeutics| Thérapeutique Animal model | Modèle animal	This study examined the properties of highly potent human monoclonal antibodies (hu-mAbs) in a mouse adapted model of SARS-CoV-2 infection (SARS-CoV-2 MA). In vitro antibody neutralization potency did not uniformly correlate with in vivo activity, and some hu-mAbs were more potent in combination in vivo. Analysis of antibody Fc regions revealed that binding to activating Fc receptors is essential for optimal protection against SARS-CoV-2 MA. The data indicate that hu-mAb protective activity is dependent on intact effector function and that in vivo testing is required to establish optimal hu-mAb combinations for COVID-19 prevention
Mouse model for testing SARS-CoV-2 antivirals: Pharmacokinetics	Scherf-Clavel,  Oliver,  Kinzig, et al	bioRxiv	Therapeutics| Thérapeutique Animal model | Modèle animal	In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 (the resulting main metabolite of remdesivir) and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness.  High tissue to plasma ratios for GS-441 524 and HCQ were found, indicating a significant distribution into the examined tissue, except for the central nervous system and fat. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. For HCQ, relatively high in vitro EC50 values are reported, which were not reached in all tissues. Facing its slow tissue distribution, HCQ might not lead to sufficient tissue saturation for a reliable antiviral effect.
High levels of SARS-CoV-2 specific T-cells with restricted functionality in severe course of COVID-19	Schub,  D,  Klemis, et al	JCI Insight	Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie	In this study, SARS-CoV-2 specific T-cells and antibodies were characterized in uninfected controls and patients with different COVID-19 related disease severity. SARS-CoV-2 specific T-cells were flow-cytometrically quantified after stimulation with SARS-CoV-2 peptide pools and analyzed for expression of cytokines (IFNγ, IL-2 and TNFα) and markers for activation, proliferation and functional anergy. SARS-CoV-2 specific IgG and IgA antibodies were quantified using ELISA. Moreover, global characteristics of lymphocyte subpopulations were compared between patient groups and uninfected controlsResults: Despite severe lymphopenia affecting all major lymphocyte subpopulations, patients with severe disease mounted significantly higher levels of SARS-CoV-2 specific T-cells as compared to convalescent individuals. SARS-CoV-2 specific CD4 T-cells dominated over CD8 T-cells and closely correlated with the number of plasmablasts and SARS-CoV-2 specific IgA- and IgG-levels. Unlike in convalescents, SARS-CoV-2 specific T-cells in patients with severe disease showed marked alterations in phenotypical and functional properties, which also extended to CD4 and CD8 T-cells in general.
Covid-19: contribution of clinical characteristics and laboratory features for early detection of patients with high risk of severe evolution	Sepulchre,  E,  Pittie, et al	Acta Clin Belg	Clinical data| Données cliniques	The aim of this study was to identify early clinical and laboratory predictive factors of COVID-19. A retrospective study was conducted on adult patients hospitalized for COVID-19 in our hospital. The cohort was divided into two groups, i.e. a favorable evolution (FE) group and an unfavorable evolution (UFE) group, including intensive care unit (ICU) and deceased patients. A total of 198 patients were enrolled in the study, with 138 FE (70%) and 60 UFE (30%). Older age, male gender, comorbidities and dyspnea at admission constituted significantly worse prognosis factors. Among laboratory features, lymphocyte and platelet counts as well as corrected glomerular filtration rate were significantly lower in UFE patients, while neutrophil to lymphocyte ratio, inflammation biomarkers, creatinine, aspartate aminotransferase, lactate dehydrogenase (LDH), glycemia and D-dimer were significantly higher. Procalcitonin and LDH appeared as the most accurate variables according to receiver operating characteristic curves.
Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design	Sorokina,  M,  J, et al	Sci Data	Coronavirology| Coronavirologie Therapeutics| Thérapeutique	We collected information regarding naturally-occurring variants of the Angiotensin-converting enzyme 2 (ACE2), an epithelial receptor that both SARS-CoV and SARS-CoV-2 use to enter the host cells. We built 242 structural models of variants of human ACE2 bound to the receptor binding domain (RBD) of the SARS-CoV-2 surface spike glycoprotein (S protein) and refined their interfaces with HADDOCK. Our dataset includes 140 variants of human ACE2 representing missense mutations found in genome-wide studies, 39 mutants with reported effects on the recognition of the RBD, and 63 predictions after computational alanine scanning mutagenesis of ACE2-RBD interface residues. This dataset will help accelerate the design of therapeutics against SARS-CoV-2, as well as contribute to prevention of possible future coronaviruses outbreaks.
Being on hemodialysis during the COVID-19 outbreak: A mixed-methods' study exploring the impacts on dialysis adequacy, analytical data, and patients' experiences	Sousa,  H,  Ribeiro, et al	Semin Dial	Public Health response| Interventions de santé publique	This study aimed to explore the impacts of the COVID-19 pandemic in non-COVID-19 patients with ESRD undergoing in-center hemodialysis (HD). A mixed-methods study was conducted with a purposive sample recruited from one dialysis unit in Portugal. Quantitative data were collected retrospectively from patients' medical records from February 2020 (T1-before the outbreak) and from April 2020 (T2-during lockdown). Semi-structured interviews were conducted with 20 patients undergoing HD for an average of 46.1 months in April 2020. Overall results suggested that dialysis adequacy and serum albumin levels decreased significantly at T2, while phosphorus levels increased. The findings from thematic analysis suggested several psychosocial negative impacts and impacts on disease and treatment-related health behaviors, which can partially explain these quantitative results
Investigation of genetic variations of IL6 and IL6R as potential prognostic and pharmacogenetics biomarkers: implications for COVID19 and neuroinflammatory disorders	Strafella,  Claudia,  Caputo, et al	Research Square prepub	Clinical data| Données cliniques	This study aims to investigate the distribution of genetic variations in IL6 and IL6R genes, which may be employed as prognostic and pharmacogenetic biomarkers for COVID-19 and neurodegenerative diseases. The study was performed on 271 samples representative of the Italian general population and identified seven variants (rs140764737, rs142164099, rs2069849, rs142759801, rs190436077, rs148171375, rs13306435) in IL6 and five variants (rs2228144, rs2229237, rs2228145, rs28730735, rs143810642) within IL6R, respectively. The Ingenuity Pathway Analysis (IPA) showed that IL6 and IL6R appeared to be implicated in several pathogenetic mechanisms associated with COVID19 severity and mortality as well as with neurodegenerative diseases mediated by neuroinflammation. The availability of IL6-IL6R-related biomarkers for COVID19 disease may be helpful to counteract harmful complications and prevent multi-organ failure. IL6-IL6R-related biomarkers could also be useful for assessing the susceptibility and progression of neuroinflammatory disorders and undertake the most suitable treatment strategies to improve patients’ prognosis and quality of life.
Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2	Tahir Ul Qamar,  M,  Shahid, et al	Infect Dis Poverty	Vaccine Research| Recherche sur les vaccins	The present study was aimed to design a multiepitope-based subunit vaccine (MESV) against COVID-19. Predicted epitopes suggested high antigenicity, conserveness, substantial interactions with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 88.40%.  The MESV construct was non-allergenic, stable, and highly antigenic. Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3 (TLR3). Furthermore, in silico immune simulation revealed significant immunogenic response of MESV.
Molecular variance analysis (AMOVA) and levels of genetic diversity of complete genome of SARS-CoV-2 virus from of six South American Countries	Teodosio Felix,  Pierre,  da Silva Ramos, et al	Research Square prepub	Epidemiology| Épidémiologie Coronavirology| Coronavirologie	In this work, we evaluated the levels of genetic diversity in 38 complete Genomes of SARS-CoV-2 from six countries in South America.  The analyses showed non-significant evolutionary divergences within and between the six countries, as well as a significant similarity to the time of genetic evolutionary divergence between all populations. The findings can help reduce speculation about the existence of rapid and silent mutations that, although they exist as we have shown in this work, can significantly increase the genetic variability of the virus.
Olfactory bulb and mucosa abnormalities in persistent COVID-19 induced anosmia: a Magnetic Resonance Imaging study	Tsivgoulis,  G,  Fragkou, et al	Eur J Neurol	Epidemiology| Épidémiologie Clinical data| Données cliniques	We performed a pilot case control study on MRI findings in recovered COVID‐19 patients with protracted olfactory dysfunction. Eight patients were evaluated. The bilateral olfactory  bulbs  (OB) height in cases was significantly lower than in controls, indicative of mild to moderate OB atrophy in 88% of the patients. Moreover, MRI demonstrated olfactory  mucosa  (OM) thickening in four cases. One patient (12.5%) had greater enhancement of OM compared to  nasal  mucosa  post-contrast  media  infusion.  Normal  neuroimaging findings of healthy controls are provided for comparison.
Structure Model Analysis Of Phosphorylation Dependent Binding And Sequestration Of SARS-COV-2 Encoded Nucleocapsid Protein By Protein 14-3-3	Tung,  HYL,  Limtung, et al	bioRxiv	Coronavirology| Coronavirologie	Phosphorylation of serines 197 and 206 of SARS-COV-2 Nucleocapsid protein (NCp) enhanced the stability and binding efficiency and sequestration of NCp to Protein 14-3-3 by increasing the Stability Energy (ΔGstability energy) and Binding Energy (ΔΔGbinding energy) from ~545 Kcal/mol to ~616 Kcal/mol, and from 108 Kcal/mol to ~228 Kcal/mol respectively. The calculated Binding Energy Difference (ΔΔGbinding energy difference) between dephospho-NCp-14-3-3 complex and phospho-NCp-13-3-3 complex was ~72 Kcal/mol. Phosphorylations of serines 186, 197, 202 and 206, and threonines 198 and 205 NCp also caused an increase in the Stability Energy (ΔGstability energy) and Binding Energy (ΔΔGbinding energy) from ~545 Kcal/mol to ~617, 616, 583, 580, 574, 564 and 566 Kcal/mol and from ~108 Kcal/mol to ~228, 216, 184, 188, 184, 174 and 112 Kcal/mol respectively. Phosphorylation of NCp on serines 197 and 206 caused a decrease in Stability Energy and Binding Energy from ~698 Kcal/mol to 688 Kcal/mol, and from ~91 Kcal/mol to ~82 Kcal/mol for the dimerization of NCp. These results support the existence of a phosphorylation dependent cellular mechanism to bind and sequester NCp.
Contrastive Cross-site Learning with Redesigned Net for COVID-19 CT Classification	Wang,  Zhao,  Liu, et al	arXiv	Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	This paper proposes a novel joint learning framework to perform accurate COVID-19 identification by effectively learning with heterogeneous datasets with distribution discrepancy. We build a powerful backbone by redesigning the recently proposed COVID-Net in aspects of network architecture and learning strategy to improve the prediction accuracy and learning efficiency. Moreover, we propose to use a contrastive training objective to enhance the domain invariance of semantic embeddings for boosting the classification performance on each dataset. We develop and evaluate our method with two public large-scale COVID-19 diagnosis datasets made up of CT images.
Screening for SARS-CoV-2 antibodies in convalescent plasma in Brazil: Preliminary lessons from a voluntary convalescent donor program	Wendel,  S,  Kutner, et al	Transfusion	Epidemiology| Épidémiologie Clinical data| Données cliniques Immunology | Immunologie	Among 271 donors (41 females, 230 males), 250 presented with neutralizing antibodies. Final RT‐PCR was negative on swab (77.0%) or blood (88.4%; P = .46).  Neutralizing antibody titers of 160 or greater were found in 63.6%. Correlation between IgG signal/cutoff of 5.0 or greater and neutralizing antibody of 160 or greater was 82.4%. Combination of final RT‐PCR –ve with neutralizing antibody ≥160 was 41.3% (112/271). Serial plasma collection showed decline in neutralizing antibody titers and IgA levels (P < .05), probably denoting a “golden period” for convalescent plasma collection (≤28 days after joining the program); IgA might have an important role as neutralizing antibody. Donor's weight, days between disease onset and serial plasma collection, and IgG and IgM levels are important predictors for neutralizing antibody titer.
Clinical characteristics of pediatric cases of SARS-CoV-2 infection in Hunan, China: A retrospective, multi-center case series	Wu,  Lei,  Zhang, et al	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques	The objective of this study was to investigate the epidemiological characteristics, clinical features, treatment and short-term prognosis of SARS-CoV-2 infection in children hospitalized in China. Most children with SARS CoV-2 infection in Hunan province were asymptomatic (23%), mild (31%) or moderate (42%). Severe cases are rare (4%). Close family contact was the main route of infection. The younger the age, the less obvious symptoms for children might be. Epidemiological history, nucleic acid test and chest imaging were important tools for the diagnosis in children.
Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients	Xu,  T,  Wang, et al	Brief Bioinform	Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	We have developed an anchor primer (AP)-based assay to improve viral RNA stability by bioinformatics identification of RNase-binding site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. The improved sensitivity by AP-PCR was demonstrated by detection of SARS-CoV-2 RNA in 70–80% of sputum, nasal, pharyngeal swabs and feces and 36% (4/11) of urine of the confirmed cases (n = 252), 7% convalescent cases (n = 54) and none of 300 negative cases.  The AP dually targeting SARS-CoV-2 RNA and RNase improves molecular detection by preserving SARS-CoV-2 RNA integrity and reveals the prolonged viral loading associated with older age and male gender in COVID-19 patients.
Risk Factors Analysis of COVID-19 Patients with ARDS and Prediction Based on Machine Learning	Xu,  Wan,  Sun, et al	Research Square prepub	Epidemiology| Épidémiologie Clinical data| Données cliniques Diagnostics / Pathogen detection| Diagnostics / Détection d'agents pathogènes	This study aims to analyze the clinical characteristics of COVID-19 acute respiratory distress syndrome (ARDS) in patients and establishes a diagnostic system based on artificial intelligence (AI) method to predict the probability of ARDS in COVID-19 patients. We collected clinical data of 659 COVID-19 patients from 11 regions in China. The clinical characteristics of the two groups were compared and both traditional machine learning algorithms and deep learning-based methods were used to build the prediction models. Results indicated the median age of ARDS patients was 56.5 years old, which was significantly older than those with non-ARDS by 7.5 years. Male and patients with BMI>25 were more likely to develop ARDS. The clinical features of ARDS patients included cough (80.3%), polypnea (59.2%), lung consolidation (53.9%), secondary bacterial infection (30.3%), and comorbidities such as hypertension (48.7%). Abnormal biochemical indicators such as lymphocyte count, leukocyte counting, CK, NLR, AST, LDH, and CRP were all strongly related to the aggravation of ARDS.
Central Venous Catheter Insertion in the Prone Position-A Last Resort in Critically Ill COVID-19 Patients	Yang,  MX,  Ng, et al	J Intensive Care Med	Clinical data| Données cliniques	A 69-year-old male with rapidly declining respiratory status secondary to COVID pneumonia quickly developed acute respiratory distress syndrome, was rapidly intubated, and then placed in the prone position. Patient could not tolerate the supine position even briefly and required a central venous catheter insertion for continuous renal replacement therapy. We kept the patient in the prone position and successfully inserted a central venous catheter in such position with real-time ultrasound guidance and using micropuncture technique.
A New Dynamical Modelling of the Epidemic Diseases to Assessing the Rates of Spread of COVID-19 in Saudi Arabia: SEIRQ Model	Youssef,  Hamdy,  Alghamdi, et al	Research Square prepub	Modelling/ prediction| Modélisation/prédiction Transmission	The aim of this paper is to establish a a new dynamic model using real knowledge on the distribution of COVID-19 in Saudi Arabia for mathematical modeling and dynamic analyses. The reproductive number and detailed stability analysis are provided in the SEIRQ model dynamics. In a Jacobian method of linearization, we will address the domain of the solution and the equilibrium situation based on the SEIRQ model. The equilibrium and its importance have been proven, and a study of the stability of the equilibrium free from diseases has been implemented. The reproduction number was evaluated in accordance with its internal parameters. The Lyapunov theorem of stability has proven the global stability of the current model's equilibrium. The SEIRQ model was contrasted by comparing the results based on the SEIRQ model with the real COVID-19 spread data in Saudi Arabia. The results indicate that the SEIRQ model is a strong model for the study of the spread of epidemics.
Platelets Can Associate with SARS-Cov-2 RNA and Are Hyperactivated in COVID-19	Zaid,  Y,  Puhm, et al	Circ Res	Epidemiology| Épidémiologie Clinical data| Données cliniques	Objective: To evaluate the contribution of platelets to inflammation and thrombosis in COVID-19 patients. Blood was collected from 115 consecutive COVID-19 patients presenting non-severe (n=71) and severe (n=44) respiratory symptoms. Exhaustive assessment of cytokines in plasma and in platelets revealed the modulation of platelet-associated cytokine levels in both non-severe and severe COVID-19 patients, pointing to a direct contribution of platelets to the plasmatic cytokine load. Levels of D-dimers, a marker of thrombosis, failed to correlate with any measured indicators of platelet activation. Functionally, platelets were hyperactivated in COVID-19 subjects presenting non-severe and severe symptoms, with aggregation occurring at suboptimal thrombin concentrations.
Pneumothorax in COVID-19 disease- incidence and clinical characteristics	Zantah,  M,  Dominguez Castillo, et al	Respir Res	Epidemiology| Épidémiologie Clinical data| Données cliniques	METHODS: We performed a retrospective review of COVID-19 cases admitted to our hospital. Patients who were diagnosed with a spontaneous pneumothorax were identified to calculate the incidence of this event. RESULTS:  Six cases of COVID-19 patients who developed spontaneous pneumothorax were identified (0.66%).  4/6 cases were associated with mechanical ventilation. All patients required placement of a chest tube. In all cases, mortality (66.6%) was not directly related to the pneumothorax.Spontaneous pneumothorax is a rare complication of COVID-19 viral pneumonia and may occur in the absence of mechanical ventilation.
Association of Daily Wear of Eyeglasses With Susceptibility to Coronavirus Disease 2019 Infection	Zeng,  W,  Wang, et al	JAMA Ophthalmol	Epidemiology| Épidémiologie Clinical data| Données cliniques	OBJECTIVE: To study the association between the daily wearing of eyeglasses and the susceptibility to COVID-19. DESIGN, SETTING, AND PARTICIPANTS: This cohort study enrolled all inpatients with COVID-19 in Suizhou Zengdu Hospital, Suizhou, China, a designated hospital for COVID-19 treatment in the area, from January 27 to March 13, 2020. COVID-19 was diagnosed according to the fifth edition of Chinese COVID-19 diagnostic guidelines. The proportion of persons with myopia who wore eyeglasses in Hubei province was based on data from a previous study.  MAIN OUTCOMES AND MEASURES: The main outcomes were the proportions of daily wearers of eyeglasses among patients admitted to the hospital with COVID-19 and among the local population. RESULTS:  In this cohort study of patients hospitalized with COVID-19 in Suizhou, China, the proportion of inpatients with COVID-19 who wore glasses for extended daily periods (>8 h/d) was smaller than that in the general population, suggesting that daily wearers of eyeglasses may be less susceptible to COVID-19.
Management of acute type A aortic dissection during COVID-19 outbreak: The Anzhen experience	Zhang,  CH,  Ma, et al	J Card Surg	Healthcare Response | Réponse des soins de santé	OBJECTIVES: We seek to report our management protocol and early outcomes of acute type A aortic dissection (ATAAD) repair during the early phase of coronavirus disease 2019 (COVID-19).  METHODS: From January 23 to April 30, 2020, we performed ATAAD repair for 33 patients, including three with pregnancy-related TAADs. Confirmation of COVID-19 depended on the results of two nucleic acid tests and pulmonary computed tomography scan. CONCLUSIONS: The results of this study show that our management protocol based on testing results and hemodynamic stability in patients with ATAAD during the COVID-19 pandemic was effective and achieved favorable early surgical outcomes.
3D Visualizations of Multiple Coronaviruses on Whole Genomes	Zhang,  Zhongwei,  Duan, et al	Research Square prepub	Coronavirology| Coronavirologie	In this paper, a 3D visualization method is proposed to show the A9 module of the metagenomic analysis system. Seven coronaviruses of genera were illustrated and briefly analyzed. Comparing the visualization results, various SARS-CoV-2 genomes were represented as 2D & 3D maps under different conditions. Through related specific projections, the characteristics of the coronavirus can be observed intuitively from the projection results to provide an effective viewpoint for studying viral genomes.
Spread of SARS-CoV-2 Genomes on Genomic Index Maps of Hierarchy	Zheng,  Jeffrey,  Zhou, et al	Research Square prepub	Epidemiology| Épidémiologie Coronavirology| Coronavirologie	In this paper, a novel projection is proposed to arrange SARS-CoV-2 genomes by genomic indexes to make a structural organization as 2D GIS maps. Complementary visual effects are provided with phylogenetic tree technology. Sample regions and various projections show spread effects of five thousand SARS-CoV-2 genomes in 72 countries, and four special countries are selected on genomic index maps.
High-resolution Spatio-temporal Model for County-level COVID-19 Activity in the U.S	Zhu,  Shixiang,  Bukharin, et al	arXiv	Modelling/ prediction| Modélisation/prédiction Epidemiology| Épidémiologie	We present an interpretable high-resolution spatio-temporal model to estimate COVID-19 deaths together with confirmed cases one-week ahead of the current time, at the county-level and weekly aggregated, in the United States. A feature of our spatio-temporal model is that it considers the (a) temporal auto- and pairwise correlation of the two local time series (confirmed cases and death of the COVID-19), (b) dynamics between locations (propagation between counties), and (c) covariates such as local within-community mobility and social demographic factors. The within-community mobility and demographic factors, such as total population and the proportion of the elderly, are included as important predictors since they are hypothesized to be important in determining the dynamics of COVID-19. To reduce the model's high-dimensionality, we impose sparsity structures as constraints and emphasize the impact of the top ten metropolitan areas in the nation, which we refer (and treat within our models) as hubs in spreading the disease. Our retrospective out-of-sample county-level predictions were able to forecast the subsequently observed COVID-19 activity accurately.
Stepwise anti-inflammatory and anti-SARS-CoV-2 effects following convalescent plasma therapy with full clinical recovery	Zimmerli,  Aurelia,  Monti, et al	Research Square prepub	Clinical data| Données cliniques Therapeutics| Thérapeutique Immunology | Immunologie	We describe a severely immunosuppressed patient following rituximab and chemotherapy for chronic lymphoid leukemia, who became infected by SARS-CoV-2. His prolonged viral disease was successfully cured after four cycles of convalescent plasma. Its immunomodulatory properties led to the rapid improvement of inflammation, pneumonia and blood cell counts, already after the first cycle. Importantly, the cumulative increase in anti-SARS-CoV-2 neutralizing antibodies following each plasma transfusion was associated to progressive viral clearance, resulting in clinical recovery from infection. Our data provide insight into the different modes of action of plasma components.
Leveraging on the genomics and immunopathology of SARS-CoV-2 for vaccines development: prospects and challenges	Abdullahi,  IN,  Emeribe, et al	Hum Vaccin Immunother	Review Literature| Revue de littérature
Clinical effectiveness of drugs in hospitalized patients with COVID-19: a systematic review and meta-analysis	Abeldaño,  Roberto Ariel,  Coca, et al	Research Square prepub	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.
The spectrum of neuropathology in COVID-19	Al-Sarraj,  S,  Troakes, et al	Neuropathol Appl Neurobiol	Review Literature| Revue de littérature
The trend of cutaneous lesions during COVID-19 pandemic: lessons from a meta-analysis and systematic review	Bandhala Rajan,  M,  Kumar, et al	Int J Dermatol	Review Literature| Revue de littérature	SR-MA: etailed literature search was done in PubMed and Embase from December 1, 2019, till May 1, 2020. The estimated prevalence of cutaneous manifestations in COVID‐19 was 5.69%. Other manifestations were urticaria, chilblain‐like lesions, livedo reticularis, and finger/toe gangrene. Although it is premature to conclude the prevalence of the cutaneous manifestations during this ongoing pandemic, our report may be a stimulating factor for the physicians to perform further vigilant streamlined reporting of cutaneous manifestations in COVID‐19 patients to estimate the final prevalence.
SARS-CoV-2 multifaceted interaction with the human host. Part II: Innate immunity response, immunopathology, and epigenetics	Beacon,  TH,  Su, et al	IUBMB life	Review Literature| Revue de littérature
Use of antimicrobial mouthwashes (gargling) and nasal sprays by healthcare workers to protect them when treating patients with suspected or confirmed COVID-19 infection	Burton,  MJ,  Clarkson, et al	Cochrane Database Syst Rev	Review Literature| Revue de littérature
Antimicrobial mouthwashes (gargling) and nasal sprays to protect healthcare workers when undertaking aerosol-generating procedures (AGPs) on patients without suspected or confirmed COVID-19 infection	Burton,  MJ,  Clarkson, et al	Cochrane Database Syst Rev	Review Literature| Revue de littérature
COVID-19 and Diabetes: A Collision and Collusion of Two Diseases	Feldman,  EL,  Savelieff, et al	Diabetes	Review Literature| Revue de littérature
Saliva in the Diagnosis of COVID-19: A Review and New Research Directions	Fernandes,  LL,  Pacheco, et al	J Dent Res	Review Literature| Revue de littérature
Comparison of published guidelines for management of coagulopathy and thrombosis in critically ill patients with COVID 19: implications for clinical practice and future investigations	Flaczyk,  A,  Rosovsky, et al	Crit Care	Review Literature| Revue de littérature
Gender susceptibility to COVID-19: a review of the putative role of sex hormones and X chromosome	Foresta,  C,  Rocca, et al	J Endocrinol Invest	Review Literature| Revue de littérature
PMC7462635; COVID-19 associated atrial fibrillation: Incidence, putative mechanisms and potential clinical implications	Gawałko,  M,  Kapłon-Cieślicka, et al	Int J Cardiol Heart Vasc	Review Literature| Revue de littérature
Investigating the Capabilities of Information Technologies to support Policymaking in COVID-19 Crisis Management; A Systematic Review and Expert opinions	Lagzian,  M,  Dadkhah, et al	Eur J Clin Invest	Review Literature| Revue de littérature	SR
SARS-CoV-2 and the reproductive system: assessment of risk and considerations for infection control in reproductive departments	Li,  G,  Li, et al	Syst Biol Reprod Med	Review Literature| Revue de littérature
Intraoperative aerosol viral transmission in minimally invasive surgery: A scoping review and impact on clinical guidelines and practice during the onset of the COVID-19 pandemic	Mun,  DH,  Pradere, et al	BJU Int	Review Literature| Revue de littérature	ScR: scoping review on PubMed, Cochrane, Embase, clinical trial register, and grey literature repository database.  scoping review of the evidence and an assessment of the benefits and harms together with a survey showed that laparoscopic procedures do not seem to increase the risk of viral transmission.
Pulmonary embolism in patients with coronavirus disease-2019 (COVID-19) pneumonia: a narrative review	Sakr,  Y,  Giovini, et al	Ann Intensive Care	Review Literature| Revue de littérature
Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis	Wang,  Ji-Gan,  Cui, et al	Research Square prepub	Review Literature| Revue de littérature	SR-MA: PubMed, Web of Science, Embase, Johns Hopkins University published data, as well as the Chinese databases CNKI, Wanfang, and Chongqing Weipu data were searched and the retrieval period was from January 1, 2020 to August 10, 2020. Gastrointestinal symptoms in pediatric COVID-19 are relatively common. Attention should be paid to the detection of fecal nucleic acids in children. Fecal nucleic acid-negative status should be considered as one of the desegregation standards.
Crosstalk between coronavirus disease 2019 and cardiovascular disease and its treatment	Ye,  Q,  Lu, et al	ESC Heart Fail	Review Literature| Revue de littérature	SR: search was performed in the electronic databases MEDLINE and EMBASE. Studies have found that there is an interaction between COVID-19 and CVD. Underlying CVD is associated with a high risk of mortality in patients with COVID-19. SARS-CoV-2 infection can also cause new-onset CVD.
Can symptoms of anosmia and dysgeusia be diagnostic for COVID-19?	Zahra,  SA,  Iddawela, et al	Brain Behav	Review Literature| Revue de littérature
Research progress and challenges to coronavirus vaccine development	Zhou,  P,  Li, et al	J Med Virol	Review Literature| Revue de littérature
Important Pharmacogenetic Information for Drugs Prescribed During the SARS-CoV-2 Infection (COVID-19)	Zubiaur,  P,  Koller, et al	Clin Transl Sci	Review Literature| Revue de littérature
The Science of Persuasion Offers Lessons for COVID-19 Prevention	Abbasi,  J	Jama	Commentary/Editorial| Commentaire/Éditorial
Providing pediatric well-care and sick visits in the COVID-19 pandemic era: the recommendations of the Italian pediatric society	Agostiniani,  R,  Bozzola, et al	Ital J Pediatr	Commentary/Editorial| Commentaire/Éditorial
Moving towards online rheumatology education in the era of COVID-19	Ahmed,  S,  Zimba, et al	Clin Rheumatol	Commentary/Editorial| Commentaire/Éditorial
Creating a Colocation Unit for End-of-Life Care during a Pandemic	Apoeso,  O,  Kuwata, et al	J Palliat Med	Commentary/Editorial| Commentaire/Éditorial
Extracorporeal membrane oxygenation in COVID-19: Supplementary considerations	Axiaq,  A,  Haiduc, et al	J Card Surg	Commentary/Editorial| Commentaire/Éditorial
Paediatric critical care referrals of children with diabetic ketoacidosis during the COVID-19 pandemic	Basatemur,  E,  Jones, et al	Arch Dis Child	Commentary/Editorial| Commentaire/Éditorial
The escalating global burden of obesity following the COVID-19 times - Are we ready?	Belančić,  A,  Klobučar Majanović, et al	Clin Obes	Commentary/Editorial| Commentaire/Éditorial
Covid-19 and Health Equity - Time to Think Big	Berkowitz,  SA,  Cené, et al	N Engl J Med	Commentary/Editorial| Commentaire/Éditorial
Immigrants and the Right to Health Care in the Era of COVID-19	Brenes,  F	Hisp Health Care Int	Commentary/Editorial| Commentaire/Éditorial
Editorial Comment on "Multi-Center Study of Temporal Changes and Prognostic Value of a CT Visual Severity Score in Hospitalized Patients with COVID-19"	Brooks,  MA	AJR Am J Roentgenol	Commentary/Editorial| Commentaire/Éditorial
Alveolar Epithelial Cell Type II as main target of SARS-CoV-2 virus and COVID-19 development via NF-Kb pathway deregulation	Carcaterra,  Maurizio,  Caruso, et al	Research Square prepub	Commentary/Editorial| Commentaire/Éditorial
Expanding the BBMRI-ERIC Directory into a Global Catalogue of COVID-19-Ready Collections: A Joint Initiative of BBMRI-ERIC and ISBER	Catchpoole,  DR,  Florindi, et al	Biopreserv Biobank	Commentary/Editorial| Commentaire/Éditorial
COVID-19 & Hydroxychloroquine side-effects: Glucose 6-phosphate dehydrogenase deficiency (G6PD) and acute haemolytic anaemia	Chaney,  S,  Basirat, et al	Qjm	Commentary/Editorial| Commentaire/Éditorial
Emergency management of the COVID-19 pandemic in a vascular surgery department of a large metropolitan hospital in Italy. Preparation, escalation, de-escalation, and normal activity	Chiesa,  R,  Kahlberg, et al	J Card Surg	Commentary/Editorial| Commentaire/Éditorial
Flaws in the development and validation of a covid-19 prediction model	Collins,  GS,  Riley, et al	Clin Infect Dis	Commentary/Editorial| Commentaire/Éditorial
Which are the main assessment tools of functional capacity in post-acute COVID-19 patients admitted to Rehabilitation Units?	Curci,  C,  Pisano, et al	Eur J Phys Rehabil Med	Commentary/Editorial| Commentaire/Éditorial
Mass Events Trigger Malta's Second Peak After Initial Successful Pandemic Suppression	Cuschieri,  S,  Balzan, et al	J Community Health	Commentary/Editorial| Commentaire/Éditorial
[Challenges of the COVID-19 pandemic in gastrointestinal endoscopy: expectations and implementation of recommendations]	Damm,  M,  Garbe, et al	Z Gastroenterol	Commentary/Editorial| Commentaire/Éditorial
Correction: Difference in levels of SARS-CoV-2 S1 and S2 subunits- and nucleocapsid protein-reactive SIgM/IgM, IgG and SIgA/IgA antibodies in human milk	Demers-Mathieu,  V,  Do, et al	J Perinatol	Commentary/Editorial| Commentaire/Éditorial
The Social Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human Health	Domingues,  CPF,  Rebelo, et al	mSphere	Commentary/Editorial| Commentaire/Éditorial
Teaching NeuroImages: Cytotoxic lesions of the corpus callosum (CLOCCs) in encephalopathic patients with COVID-19	Edjlali,  M,  Le Gal, et al	Neurology	Commentary/Editorial| Commentaire/Éditorial
Structural Racism, Social Risk Factors, and Covid-19 - A Dangerous Convergence for Black Americans	Egede,  LE,  Walker, et al	N Engl J Med	Commentary/Editorial| Commentaire/Éditorial
Substance use and related harms in the context of COVID-19: Aa conceptual model	Enns,  A,  Pinto, et al	Health Promot Chronic Dis Prev Can	Commentary/Editorial| Commentaire/Éditorial
A Pandemic within a Pandemic - Intimate Partner Violence during Covid-19	Evans,  ML,  Lindauer, et al	N Engl J Med	Commentary/Editorial| Commentaire/Éditorial
Author Correction: Exploring the coronavirus pandemic with the WashU Virus Genome Browser	Flynn,  JA,  Purushotham, et al	Nat Genet	Commentary/Editorial| Commentaire/Éditorial
Patient Safety Indicators: Inpatient, Outpatient, and COVID 19	Freischlag,  JA	Ann Surg	Commentary/Editorial| Commentaire/Éditorial
Health and Social Precarity Among Americans Receiving Unemployment Benefits During the COVID-19 Outbreak	Gaffney,  AW,  Himmelstein, et al	J Gen Intern Med	Commentary/Editorial| Commentaire/Éditorial
Virtual learning object: an asynchronous solution for virtual learning in dentistry post COVID-19	Gálvez,  DA,  Noal, et al	J Dent Educ	Commentary/Editorial| Commentaire/Éditorial
Improvement in home-staging three-dimensional virtual surgical planning via webinar during the COVID-19 pandemic	Ganry,  L,  Atlan, et al	Surg Today	Commentary/Editorial| Commentaire/Éditorial
Fast coronavirus tests: what they can and can't do	Guglielmi,  G	Nature	Commentary/Editorial| Commentaire/Éditorial
Response to coronavirus 2019 in Veterans Health Administration facilities participating in an implementation initiative to enhance access to medication for opioid use disorder	Gustavson,  AM,  Gordon, et al	Subst Abus	Commentary/Editorial| Commentaire/Éditorial
NeuroCOVID: it's time to join forces globally	Helbok,  Raimund,  Chou, et al	The Lancet Neurology	Commentary/Editorial| Commentaire/Éditorial
PMC7452821; What are the roles of antibodies versus a durable, high quality T-cell response in protective immunity against SARS-CoV-2?	Hellerstein,  M	Vaccine X	Commentary/Editorial| Commentaire/Éditorial
Doctors call for action on racism in wake of covid-19 and death of George Floyd	Iacobucci,  G	Bmj	Commentary/Editorial| Commentaire/Éditorial
Cerebrospinal fluid confirmed COVID-19-associated encephalitis treated successfully	Kamal,  YM,  Abdelmajid, et al	BMJ Case Rep	Commentary/Editorial| Commentaire/Éditorial
An aptamer/ siRNA Chimera against The SARS-CoV-2: A Dual Therapeutic Strategy for The Virus Neutralizing and RNA Interfering	Khanali,  Javad,  Azangou-khyavy, et al	Research Square prepub	Commentary/Editorial| Commentaire/Éditorial
Allaying Post-COVID19 Negative Health Impacts Among Older People: The "Need To Do Something With Others"-Lessons From the Japan Gerontological Evaluation Study	Kimura,  M,  Ojima, et al	Asia Pac J Public Health	Commentary/Editorial| Commentaire/Éditorial
Echocardiographic assessment of the right ventricle in COVID -related acute respiratory syndrome	Lazzeri,  C,  Bonizzoli, et al	Intern Emerg Med	Commentary/Editorial| Commentaire/Éditorial
PMC7184477; COVID-19 Through the Lens of Gerontology	Le Couteur,  DG,  Anderson, et al	J Gerontol A Biol Sci Med Sci	Commentary/Editorial| Commentaire/Éditorial
Impacts of COVID-19 on Dermatologic Practice, Disease Presentation, and Immunomodulator Prescriptions	Leis,  M,  Fleming, et al	J Cutan Med Surg	Commentary/Editorial| Commentaire/Éditorial
Coronavirus disease 2019 and transplantation: tackling the challenges of SARS-CoV-2 infection in waiting list candidates	Mangioni,  D,  Dondossola, et al	Transpl Int	Commentary/Editorial| Commentaire/Éditorial
Eye Protection and the Risk of Coronavirus Disease 2019: Does Wearing Eye Protection Mitigate Risk in Public, Non-Health Care Settings?	Maragakis,  LL	JAMA Ophthalmol	Commentary/Editorial| Commentaire/Éditorial
[Cross glances on the videoconsultation]	Mazouri-Karker,  S,  Karsegard, et al	Rev Med Suisse	Commentary/Editorial| Commentaire/Éditorial
[Telemedicine at the heart of management of the COVID-19 crisis]	Mazouri-Karker,  S,  Percheron Vendeuvre, et al	Rev Med Suisse	Commentary/Editorial| Commentaire/Éditorial
Lessons from a neurology consult service for patients with COVID-19	McAlpine,  LindsayS,  Zubair, et al	The Lancet Neurology	Commentary/Editorial| Commentaire/Éditorial
Experimental Physics Pratice: Application of Scientific Method to Investigate the Pandemic Behavior of COVID-19	Mendes,  RaulGB	arXiv	Commentary/Editorial| Commentaire/Éditorial
Occupational Safety and Health Administration (OSHA) and Worker Safety During the COVID-19 Pandemic	Michaels,  D,  Wagner, et al	Jama	Commentary/Editorial| Commentaire/Éditorial
Role of novel drug delivery systems in coronavirus disease-2019 (covid-19): time to act now	Mittal,  N,  Garg, et al	Curr Drug Deliv	Commentary/Editorial| Commentaire/Éditorial
Containment of COVID-19 in Ethiopia and implications for tuberculosis care and research	Mohammed,  H,  Oljira, et al	Infect Dis Poverty	Commentary/Editorial| Commentaire/Éditorial
PMC7491013; Global health landscape challenges triggered by COVID-19	Nakatani,  H,  Katsuno, et al	Inflamm Regen	Commentary/Editorial| Commentaire/Éditorial
Cardiac surgery in presence of concomitant corona virus disease-2019 infection	Narayan,  P	J Card Surg	Commentary/Editorial| Commentaire/Éditorial
Suboptimal US Response to COVID-19 Despite Robust Capabilities and Resources	Nuzzo,  JB,  Bell, et al	Jama	Commentary/Editorial| Commentaire/Éditorial
David Oliver: Covid-19 has shown the value of local and clinical NHS leadership	Oliver,  D	Bmj	Commentary/Editorial| Commentaire/Éditorial
[Telemedicine in the era of COVID-19: a revolution ? The experience of the University Hospitals of Geneva]	Percheron Vendeuvre,  L,  Lecygne, et al	Rev Med Suisse	Commentary/Editorial| Commentaire/Éditorial
Territories Under Siege: Risks of the Decimation of Indigenous and Quilombolas Peoples in the Context of COVID-19 in South Brazil	Polidoro,  M,  de Assis Mendonça, et al	J Racial Ethn Health Disparities	Commentary/Editorial| Commentaire/Éditorial
PMC7422834; Consequences of coronavirus disease outbreak on paediatric out-of-hospital cardiac arrest in France	Recher,  M,  Baert, et al	Resuscitation	Commentary/Editorial| Commentaire/Éditorial
COVID-19 and geriatric clinical trials research	Rhodus,  EK,  Bardach, et al	Aging Clin Exp Res	Commentary/Editorial| Commentaire/Éditorial
Covid-19: Reward healthcare staff for pandemic work, says BMA	Rimmer,  A	Bmj	Commentary/Editorial| Commentaire/Éditorial
Rationing care in COVID-19: if we must do it, can we do better?	Rockwood,  K	Age Ageing	Commentary/Editorial| Commentaire/Éditorial
Sexual assault examination and COVID-19: risk reduction strategies in conducting forensic medical examinations of a suspected or confirmed COVID-19 positive patient in Melbourne hospital hot zones	Rowse,  Janine,  Cunningham, et al	Research Square prepub	Commentary/Editorial| Commentaire/Éditorial
Audio Interview: Operation Warp Speed and Covid-19 Therapeutics	Rubin,  EJ,  Baden, et al	N Engl J Med	Commentary/Editorial| Commentaire/Éditorial
Investigating Whether Blood Type Is Linked to COVID-19 Risk	Rubin,  R	Jama	Commentary/Editorial| Commentaire/Éditorial
Preparation, escalation, de-escalation, and normal activities	Sadeghipour,  P,  Mohebbi, et al	J Card Surg	Commentary/Editorial| Commentaire/Éditorial
Long-segment arterial cerebral vessel thrombosis after mild COVID-19	Sartoretti,  E,  Sartoretti, et al	BMJ Case Rep	Commentary/Editorial| Commentaire/Éditorial
COVID-19, masks and communication in the operating theatre: the importance of face value	Sharif,  SP,  Blagrove, et al	Psychol Med	Commentary/Editorial| Commentaire/Éditorial
No patient safety without health worker safety	Shaw,  Alexandra,  Flott, et al	The Lancet	Commentary/Editorial| Commentaire/Éditorial
Navigating assisted reproduction treatment in the time of COVID-19: concerns and considerations	Simopoulou,  M,  Sfakianoudis, et al	J Assist Reprod Genet	Commentary/Editorial| Commentaire/Éditorial
Bridging the Digital Divide: A National Survey Assessing Public Readiness for Digital Health Strategies Against COVID-19 within the United Kingdom	Sounderajah,  Viknesh,  Clarke, et al	Research Square prepub	Commentary/Editorial| Commentaire/Éditorial
A short report on an interprofessional mobilizer team: innovation and impact during the COVID-19 pandemic	Stifter,  J,  Terry, et al	J Interprof Care	Commentary/Editorial| Commentaire/Éditorial
PMC7295959; COVID-19 Molecular Testing in Korea: Practical Essentials and Answers From Experts Based on Experiences of Emergency Use Authorization Assays	Sung,  H,  Roh, et al	Ann Lab Med	Commentary/Editorial| Commentaire/Éditorial
Covid 19: Science must come first with vaccine, says former CDC chief	Tanne,  JH	Bmj	Commentary/Editorial| Commentaire/Éditorial
Surgery at the frontline at the time of the COVID-19 outbreak	Testori,  A,  Cioffi, et al	Thorac Cancer	Commentary/Editorial| Commentaire/Éditorial
How the Covid-19 epidemic is challenging our practice in clinical nutrition-feedback from the field	Thibault,  R,  Coëffier, et al	Eur J Clin Nutr	Commentary/Editorial| Commentaire/Éditorial
PMC7490777; Qualitative analysis of the coordination of major system change within the Colombian health system in response to COVID-19: study protocol	Turner,  S,  Niño, et al	Implement Sci Commun	Commentary/Editorial| Commentaire/Éditorial
The 2019-20 bushfires and COVID-19: The ongoing impact on the mental health of people living in rural and farming communities	Usher,  K,  Ranmuthugala, et al	Int J Ment Health Nurs	Commentary/Editorial| Commentaire/Éditorial
Closing the borders: The unmet need of congenital heart surgery during the COVID-19 pandemic	Vervoort,  D	J Card Surg	Commentary/Editorial| Commentaire/Éditorial
Navigating the COVID-19 waters with chronic pelvic pain	Villegas-Echeveri,  J,  Carrillo, et al	Int J Gynaecol Obstet	Commentary/Editorial| Commentaire/Éditorial
Steroids and COVID-19: We Need a Precision Approach, Not One Size Fits All	Waterer,  GW,  Rello, et al	Infect Dis Ther	Commentary/Editorial| Commentaire/Éditorial
High-Performance Mining of COVID-19 Open Research Datasets for Text Classification and Insights in Cloud Computing Environments	Zhao,  Jie,  Rodriguez, et al	arXiv	Commentary/Editorial| Commentaire/Éditorial
Sensor-aided continuous care and self-management: implications for the post-COVID era	Zhao,  Megan,  Wasfy, et al	The Lancet Digital Health	Commentary/Editorial| Commentaire/Éditorial
Tackling bronchopulmonary dysplasia (BPD) to improve preterm health - A call for family-centered care at World Prematurity Day 2020	Zimmermann,  LJI,  Kostenzer, et al	Am J Physiol Lung Cell Mol Physiol	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