Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (49)

ProteinN (10)

NSP5 (10)

ComplexRdRp (8)

ProteinE (7)


SARS-CoV-2 Proteins
    displaying 41 - 50 records in total 2073
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    Molecular Epidemiology of SARS-CoV-2 in Cyprus

    Authors: Jan Richter; Pavlos Fanis; Christina Tryfonos; Dana Koptides; George Krashias; Stavros Bashiardes; Andreas Hadjisavvas; Maria Loizidou; Anastasis Oulas; Denise Alexandrou; Olga Kalakouta; Mihalis I Panayiotidis; George M Spyrou; Christina Christodoulou

    doi:10.1101/2021.03.16.21252974 Date: 2021-03-24 Source: medRxiv

    Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 MESHD were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths MESHD were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.

    Forecasting the Epidemiological Impact of Coronavirus Disease MESHD ( COVID-19 MESHD): Pre-vaccination Era

    Authors: Saheed Oladele Amusat

    doi:10.1101/2021.03.17.21253791 Date: 2021-03-24 Source: medRxiv

    Background: During this pandemic, many studies have been published on the virology, diagnosis, prevention, and control of the novel coronavirus. However, fewer studies are currently available on the quantitative future epidemiological impacts. Therefore, the purpose of this study is to forecast the COVID-19 MESHD morbidities and associated-mortalities among the top 20 countries with the highest number of confirmed COVID-19 MESHD cases globally prior to vaccination intervention. Method: We conducted a secondary data analysis of the prospective geographic distribution of COVID-19 MESHD cases data worldwide as of 10 April 2020. The historical data was forecasted using Exponential-Smoothing to detect seasonality patterns and confidence intervals surrounding each predicted value in which 95 percent of the future points are expected to fall based on the forecast. Results: The total mean forecasted cases and deaths MESHD were 99,823 and 8,801. Interestingly, the US has the highest forecasted cases, deaths, and percentage cases-deaths ratio of 45,338, 2 358, and 5.20% respectively. China has the lowest cases, deaths, and percentage cases-deaths ratio -267, -2, and 0.75% respectively. In addition, France has the highest forecasted percentage cases-deaths ratio of 26.40% with forecasted cases, and deaths of 6,246, and 1,649 respectively. Conclusion Our study revealed the possibility of higher COVID-19 MESHD morbidities and associated-mortalities worldwide.

    Background rates of all-cause mortality, hospitalizations, and emergency department visits among nursing home residents in Ontario, Canada to inform COVID-19 MESHD vaccine safety assessments

    Authors: Maria Sundaram; Sharifa Nasreen; Andrew Calzavara; Siyi He; Hannah Chung; Susan E Bronskill; Sarah A Buchan; Mina Tadrous; Peter Tanuseputro; Kumanan Wilson; Sarah Wilson; Jeff Kwong; - Canadian Immunization Research Network (CIRN) Investigators

    doi:10.1101/2021.03.17.21253290 Date: 2021-03-24 Source: medRxiv

    Background. Nursing home (NH) residents have been disproportionately affected by the coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic and are prioritized for vaccination. NH residents are generally at increased risk of poor outcomes due to advanced age, frailty, and complex health conditions. We report monthly incidence rates of deaths MESHD, hospitalizations, and emergency department (ED) visits during ten pre-pandemic years (2010-2019) and 2020 to provide context for assessments of COVID-19 MESHD vaccine safety in NH residents. Methods. We observed deaths, hospitalizations, and ED visits among all Ontarians living in NHs using health administrative databases. Monthly incidence rates were calculated by month, by sex, and by age group. Direct comparisons between months were assessed using one-sample t-tests; direct comparisons by age and sex were assessed using chi-squared tests. Results. From January 1, 2010 through December 31, 2019, there were, on average, 83,453 (SD: 652.4) Ontarians living in NHs in any given month, with an average of 2.3 (SD: 0.28) deaths, 3.1 (SD: 0.16) hospitalizations, and 3.6 (SD: 0.17) ED visits per 100 residents per month. Mortality rates were higher for men (p<0.001) and residents aged [≥]80 years (p<0.001). Hospitalization and ED visit rates were higher for men but were lower for residents aged [≥]80 years. From January to October 2020, the number of NH residents declined markedly. Mortality rates were increased in 2020 compared to 2010-2019, but hospitalization and ED visit rates were reduced in 2020 compared to 2010-2019 (p<0.001). Conclusion. We identified relatively consistent monthly mortality, hospitalization, and ED visit rates during ten pre-pandemic years. Marked differences in these rates were observed during 2020, coinciding with heightened COID-19 infection rates and restrictions. These results provide context to the assessment of COVID-19 MESHD vaccine safety outcomes in this high-risk population.

    Mortality in individuals treated with COVID-19 MESHD convalescent plasma varies with the geographic provenance of donors

    Authors: Katie L Kunze; Patrick W Johnson; Noud van Helmond; Jonathon W Senefeld; Molly M Petersen; Stephen A Klassen; Chad C Wiggins; Allan M Klompas; Katelyn A Bruno; John R Mills; Elitza S Theel; Matthew R Buras; Michael A Golafshar; Matthew A Sexton; Juan C Diaz Soto; Sarah E Baker; John R.A. Shepherd; Nicole C Verdun; Peter Marks; Nigel S Paneth; DeLisa Fairweather; R. Scott Wright; Camille M van Buskirk; Jeffrey L Winters; James R Stubbs; Robert F Rea; Vitaly Herasevich; Emily R Whelan; Andrew J Clayburn; Kathryn F Larson; Juan G Ripoll; Kylie J Andersen; Elizabeth R Lesser; Matthew N.P. Vogt; Joshua J Dennis; Riley J Regimbal; Philippe R Bauer; Janis E Blair; Arturo Casadevall; Rickey E Carter; Michael J Joyner

    doi:10.1101/2021.03.19.21253975 Date: 2021-03-22 Source: medRxiv

    Treatment and prevention of coronavirus disease 2019 MESHD ( COVID-19 MESHD) have attempted to harness the immune response to severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) including the development of successful COVID-19 MESHD vaccines and therapeutics (e.g., Remdesivir, convalescent plasma [CP]). Evidence that SARS-CoV-2 exists as quasispecies evolving locally suggests that immunological differences may exist that could impact the effectiveness of antibody-based treatments and vaccines. Regional variants of SARS-CoV-2 were reported in the USA beginning in November 2020 but were likely present earlier. There is available evidence that the effectiveness of CP obtained from donors infected with earlier strains in the pandemic may be reduced when tested for neutralization against newer SARS-Cov-2 variants. Using data from the Expanded Access Program to convalescent plasma, we used a gradient-boosting machine to identify predictors of 30-day morality and a series of regression models to estimate the relative risk of death MESHD at 30 days post-transfusion for those receiving near sourced plasma (defined as plasma transported [≤] 150 miles) vs. distantly sourced plasma (> 150 miles). Our results show a lower risk of death MESHD at 30 days post-transfusion for near sourced plasma. Additional analyses stratified by disease severity, time to treatment, and donor region further supported these findings. The results of this study suggest that near sourced plasma is superior to distantly sourced plasma, which has implications for interpreting the results of clinical studies and designing effective treatment of COVID-19 MESHD patients as additional local variant are likely to emerge.

    Lives Saved from Age-Prioritised COVID-19 MESHD Vaccination

    Authors: Joshua R Goldstein; Ayesha Mahmud; Thomas Cassidy

    doi:10.1101/2021.03.19.21253991 Date: 2021-03-22 Source: medRxiv

    BACKGROUND The criteria used to allocate scarce COVID-19 MESHD vaccines are hotly contested. While some are pushing just to get vaccines into arms as quickly as possible, others advocate prioritization in terms of risk. OBJECTIVE Our aim is to use demographic models to show the enormous potential of vaccine risk-prioritization in saving lives. METHODS We develop a simple mathematical MESHD model that accounts for the age distribution of the population and of COVID-19 MESHD mortality. This model considers only the direct live-savings for those who receive the vaccine, and does not account for possible indirect effects of vaccination. We apply this model to the United States, Japan, and Bangladesh. RESULTS In the United States, we find age-prioritization would reduce deaths MESHD during a vaccine campaign by about 93 percent relative to no vaccine and 85 percent relative to age-neutral vaccine distribution. In countries with younger age structures, such as Bangladesh, the benefits of age-prioritization are even greater. CONTRIBUTION For policy makers, our findings give additional support to risk-prioritized allocation of COVID-19 MESHD vaccines. For demographers, our results show how the age-structures of the population and of disease mortality combine into an expression of risk concentration that shows the benefits of prioritized allocation. This measure can also be used to study the effects of prioritizing other dimensions of risk such as underlying health conditions.

    Live imaging of SARS-CoV-2 infection MESHD in mice reveals neutralizing antibodies require Fc function for optimal efficacy

    Authors: Irfan Ullah; Jeremie Prevost; Mark S. Ladinsky; Helen Stone; Maolin Lu; Sai Priya Anand; Guillaume Beaudoin-Bussieres; Mehdi Benlarbi; Shilei Ding; Romain Gasser; Corby Fink; Yaozong Chen; Alexandra Tauzin; Guillaume Goyette; Catherine Bourassa; Halima Medjahed; Matthias Mack; Kunho Chung; Craig B Wilen; Gregory A Dekaban; Jimmy D Dikeakos; Emily A Bruce; Daniel E Kaufmann; Leonidas Stamatatos; Andrew McGuire; Jonathan Richard; Marzena Pazgier; Pamela Bjorkman; Walther Mothes; Andres Finzi; Priti Kumar; Pradeep D Uchil

    doi:10.1101/2021.03.22.436337 Date: 2021-03-22 Source: bioRxiv

    Neutralizing antibodies (NAbs) are effective in treating COVID-19 MESHD but the mechanism of immune protection is not fully understood. Here, we applied live bioluminescence imaging (BLI) to monitor the real-time effects of NAb treatment in prophylaxis and therapy of K18- hACE2 HGNC mice intranasally infected with SARS-CoV-2-nanoluciferase. We visualized sequential spread of virus from the nasal cavity to the lungs followed by systemic spread to various organs including the brain, culminating in death MESHD. Highly potent NAbs from a COVID-19 MESHD convalescent subject prevented, and also effectively resolved, established infection when administered within three days of infection. In addition to direct neutralization, in vivo efficacy required Fc effector functions of NAbs, with contributions from monocytes, neutrophils and natural killer cells, to dampen inflammatory responses and limit immunopathology. Thus, our study highlights the requirement of both Fab and Fc effector functions for an optimal in vivo efficacy afforded by NAbs against SARS-CoV-2.

    COVID-19 MESHD and Scientific Research Interests and Findings in Epidemiology and Social Sciences: A Systematic Review

    Authors: Bruno Enagnon Lokonon; Marcel Gbaguidi Alia; Romain Glèlè Kakaï

    id:10.20944/preprints202103.0509.v1 Date: 2021-03-22 Source:

    The emergence of COVID-19 MESHD has prompted an unprecedented scientic publication with the aim of better understanding this new disease. This study assessed the scientic impact and disciplinary priorities of the published papers on the pandemic by comparing epidemiological (EP) and social sciences (SS) research interests. Papers were identified via keywords searching using Google Scholar and Scopus databases. From an initial 1720 papers, we identified 597 relevant articles, of which 347 were for EP researches and 250 for SS studies. We extracted information, such as authors' countries, and research thematic related to EP and SS. The results revealed that most papers were authored by Asian (37.5%), European (30.5%) and American (19.6%) scientists. Only 10.1% and 2.3% of authors were aliated with African and Oceanian institutions, respectively, indicating that the regions most affected by the pandemic mainly contributed to the scientic publications. In total, 26 research themes were recorded from both EP and SS studies. There was a high signicant dierence among themes in both research fields (Chi-square = 1204.3, df = 1, p-value < 0.001). EP papers mostly dealt with clinical trials (54.5%) and diagnosis (53.3%). These papers assessed the incidence and epidemiological characteristics of the disease (incubation period, symptomatic period, recovering or death MESHD), testing tests developed, drugs and vaccines used. SS papers were mainly concerned with the sociocultural analyses (78%) and economic impact (55.6%) of the pandemic. They mainly focused on behavioral changes induced by the pandemic and strategies developed to mitigate its impacts. This study highlights the difference between regions and gaps between scientific disciplines concerning the proposed responses to control the pandemic. It is important to promote collaborative and interdisciplinary studies for health emergencies.

    Adapting French COVID-19 MESHD vaccination campaign duration to variant dissemination

    Authors: Simon Pageaud; Nicolas Ponthus; Romain Gauchon; Catherine Pothier; Christophe Rigotti; Anne Eyraud-Loisel; Jean-Pierre Bertoglio; Alexis Bienven&uumle; Fran&ccedilois Gueyffier; Philippe Vanhems; Nicolas Leboisne; Jean Iwaz; St&eacutephane Loisel; Pascal Roy

    doi:10.1101/2021.03.17.21253739 Date: 2021-03-20 Source: medRxiv

    Background The outbreak of SARS-CoV-2 virus has caused a major international health crisis with serious consequences in terms of public health and economy. In France, two lockdown periods were decided in 2020 to avoid the saturation of intensive care units (ICU) and an increase in mortality. The rapid dissemination of variant SARS-CoV-2 VOC 202012/01 has strongly influenced the course of the epidemic. Vaccines have been rapidly developed. Their efficacy against the severe forms of the disease has been established, and their efficacy against disease transmission is under evaluation. The aim of this paper is to compare the efficacy of several vaccination strategies in the presence of variants in controlling the COVID-19 MESHD epidemic through population immunity. Methods An agent-based model was designed to simulate with different scenarios the evolution of COVID-19 pandemic MESHD in France over 2021 and 2022. The simulations were carried out ignoring the occurrence of variants then taking into account their diffusion over time. The expected effects of three Non-Pharmaceutical Interventions (Relaxed-NPI, Intensive-NPI, and Extended-NPI) to limit the epidemic extension were compared. The expected efficacy of vaccines were the values recently estimated in preventing severe forms of the disease (75% and 94%) for the current used vaccines in France (Pfizer-BioNTech and Moderna since January 11, 2021, and AstraZeneca since February 2, 2021). All vaccination campaigns reproduced an advanced age-based priority advised by the Haute Autorit[c] de Sant[c]. Putative reductions of virus transmission were fixed at 0, 50, 75 and 90%. The effects of four vaccination campaign durations (6-month, 12-month, 18-month and 24-month) were compared. Results In the absence of vaccination, the presence of variants led to reject the Relaxed-NPI because of a high expected number of deaths (170 to 210 thousands) and the significant overload of ICUs from which 35 thousand patients would be deprived. In comparison with the situation without vaccination, the number of deaths was divided by 7 without ICU saturation with a 6-month vaccination campaign. A 12-month campaign would divide the number of deaths by 3 with Intensive-NPI and by 6 with Extended-NPI (the latter being necessary to avoid ICU saturation). With 18-month and 24-month vaccination campaigns without Extended-NPI, the number of deaths MESHD and ICU admissions would explode. Conclusion Among the four compared strategies the 6-month vaccination campaign seems to be the best response to changes in the dynamics of the epidemic due to the variants. The race against the COVID-19 MESHD epidemic is a race of vaccination strategy. Any further vaccination delay would increase the need of strengthened measures such as Extended-NPI to limit the number of deaths MESHD and avoid ICU saturation.

    Integrated immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 MESHD mortality

    Authors: Elsa Brunet-Ratnasingham; Sai Priya Anand; Pierre Gantner; Gaël Moquin-Beaudry; Alina Dyachenko; Nathalie Brassard; Guillaume Beaudoin-Bussières; Amelie Pagliuzza; Romain Gasser; Mehdi Benlarbi; Floriane Point; Jérémie Prévost; Annemarie Laumaea; Julia Nießl; Manon Nayrac; Gérémy Sannier; Marianne Boutin; Jade Descôteaux-Dinelle; Gabrielle Gendron; Catherine Orban; Guillaume Butler-Laporte; David Morrison; Sirui Zhou; Tomoko Nakanishi; Laetitia Laurent; Jonathan Richard; Mathieu Dubé; Rémi Fromentin; Rose-Marie Rébillard; Nathalie Arbour; Alexandre Prat; Catherine Larochelle; Madeleine Durand; Brent Richards; Michaël Chassé; Martine Tétreault; Nicolas Chomont; Andrés Finzi; Daniel E. Kaufmann

    doi:10.1101/2021.03.18.21253907 Date: 2021-03-20 Source: medRxiv

    Despite advances in COVID-19 MESHD management, it is unclear how to recognize patients who evolve towards death MESHD. This would allow for better risk stratification and targeting for early interventions. However, the explosive increase in correlates of COVID-19 MESHD severity complicates biomarker prioritisation. To identify early biological predictors of mortality, we performed an immunovirological assessment (SARS-CoV-2 viral RNA, cytokines and tissue injury markers, antibody responses) on plasma samples collected from 144 hospitalised COVID-19 MESHD patients 11 days after symptom onset and used to test models predicting mortality within 60 days of symptom onset. In the discovery cohort (n=61, 13 fatalities), high SARS-CoV-2 vRNA HGNC, low RBD-specific IgG levels, low SARS-CoV-2-specific antibody-dependent cellular cytotoxicity MESHD, and elevated levels of several cytokines and lung injury MESHD markers were strongly associated with increased mortality in the entire cohort and the subgroup on mechanical ventilation. Model selection revealed that a three-variable model of vRNA HGNC, age and sex was very robust at identifying patients who will succumb to COVID-19 MESHD (AUC=0.86, adjusted HR for log-transformed vRNA HGNC=3.5; 95% CI: 2.0-6.0). This model remained robust in an independent validation cohort (n=83, AUC=0.85). Quantification of plasma SARS-CoV-2 RNA can help understand the heterogeneity of disease trajectories and identify patients who may benefit from new therapies.

    Sarcopenic obesity MESHD and the risk of hospitalisation or death from COVID-19 MESHD: findings from UK Biobank

    Authors: Thomas Wilkinson; Thomas Yates; Luke A Baker; Francesco Zaccardi; Alice C Smith

    doi:10.1101/2021.03.19.21253945 Date: 2021-03-20 Source: medRxiv

    Background Coronavirus disease-2019 ( COVID-19 MESHD) is an infectious disease MESHD caused by severe acute respiratory syndrome coronavirus 2 MESHD (SARS;CoV-2 virus). The role of skeletal muscle mass in modulating immune response is well documented. Whilst obesity MESHD is well-established as a key factor in COVID-19 MESHD infection and outcome, no study has examined the influence of both sarcopenia MESHD (low muscle mass) and obesity MESHD, termed sarcopenic obesity MESHD on COVID-19 MESHD risk. Methods This study uses data from UK Biobank. Probable sarcopenia MESHD was defined as low handgrip strength. Sarcopenic obesity MESHD was mutually exclusively defined as the presence of obesity MESHD and low muscle mass (based on two established criteria: appendicular lean mass (ALM) adjusted for either: 1) height and 2) body mass index (BMI)). Severe COVID-19 MESHD was defined by a positive test result in a hospital setting or death MESHD with a primary cause reported as COVID-19 MESHD. Fully adjusted logistic regression models were used to analyse the associations between sarcopenic status MESHD and severe COVID-19 MESHD. This work was conducted under UK Biobank application number 52553. Results We analysed data from 490,301 UK Biobank participants. 2203 (0.4%) had severe COVID-19 infection MESHD. Individuals with probable sarcopenia were 64% more likely to have had severe COVID-19 MESHD infection (odds ratio (OR) 1.638; P

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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