Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (54)

NSP5 (11)

ProteinN (10)

ComplexRdRp (8)

ProteinE (7)


SARS-CoV-2 Proteins
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    Pharmacovigilance Analysis on Cerebrovascular Accidents MESHD and Coronavirus disease 2019 MESHD Vaccines

    Authors: Pushkar Aggarwal

    doi:10.1101/2021.04.19.21255768 Date: 2021-04-27 Source: medRxiv

    Introduction: Recently, there have been reports of cerebrovascular accidents MESHD ( CVA MESHD) occurring in individuals who have received the Coronavirus disease 2019 MESHD ( COVID-19 MESHD) vaccine. Objective: The objective of this analysis was to determine if a statistically significant signal exists in post-marketing safety reports between CVA MESHD and the three COVID-19 MESHD vaccines being administered in the United States of America (Pfizer, Moderna, Janssen). Methods: A pharmacovigilance disproportionality analysis on adverse events reported with COVID-19 MESHD vaccines was conducted using data from Vaccine Adverse Event Reporting System. Results: A statistically significant signal was found between CVA MESHD events and each of the three COVID-19 MESHD vaccines (Pfizer/BioNTechs, Modernas and Janssens) in the VAERS database. Females and individuals of age 65 or older had higher number of case reports of CVA MESHD events with the COVID-19 MESHD vaccines. Females had also more COVID-19 MESHD adverse event reports in which a CVA MESHD was reported and resulted in the patient having permanent disability or death MESHD. Limitations: Randomized controlled trials are needed to further analyze this signal. Conclusion: Patients should be made aware of the risk-benefit and symptoms to watch out for that may indicate the onset of a CVA MESHD and informed to seek medical care as soon as possible if they develop these symptoms.

    A Generalizable Data Assembly Algorithm for Infectious Disease MESHD Outbreaks

    Authors: Maimuna S. Majumder; Sherri Rose

    doi:10.1101/2021.04.21.21255862 Date: 2021-04-27 Source: medRxiv

    Background & Objective: During infectious disease outbreaks, health agencies often share text-based information about cases and deaths MESHD. This information is usually text-based and rarely machine-readable, thus creating challenges for outbreak researchers. Here, we introduce a generalizable data assembly algorithm that automatically curates text-based, outbreak-related information and demonstrate its performance across three outbreaks. Methods: After developing an algorithm with regular expressions, we automatically curated data from health agencies via three information sources: formal reports, email newsletters, and Twitter. A validation data set was also curated manually for each outbreak. Findings: When compared against the validation data sets, the overall cumulative missingness and misidentification of the algorithmically curated data were [≤]2% and [≤]1%, respectively, for all three outbreaks. Conclusions: Within the context of outbreak research, our work successfully addresses the need for generalizable tools that can transform text-based information into machine-readable data across varied information sources and infectious diseases MESHD.

    Evaluation of Different Types of Face Masks to Limit the Spread of SARS CoV 2, A Modeling Study

    Authors: Brian M. Gurbaxani; Andrew N. Hill; Prabasaj Paul; Pragati V. Prasad; Rachel B. Slayton

    doi:10.1101/2021.04.21.21255889 Date: 2021-04-27 Source: medRxiv

    We updated a published mathematical model of SARS-CoV-2 transmission with laboratory-derived source and wearer protection efficacy estimates for a variety of face masks to estimate their impact on COVID-19 MESHD incidence and related mortality in the United States. When used at already-observed population rates of 80% for those [≥]65 years and 60% for those <65 years, face masks are associated with 69% (cloth) to 78% (medical procedure mask) reductions in cumulative COVID-19 MESHD infections and 82% (cloth) to 87% (medical procedure mask) reductions in related deaths MESHD over a 6 month timeline in the model. If cloth or medical procedure masks' source control and wearer protection efficacies are boosted about 30% each to 84% and 60% by cloth over medical procedure masking, fitters, or braces, the COVID-19 MESHD basic reproductive number of 2.5 could decrease to an effective reproductive number [≤] 1.0, and from 4.0 to {approx} 1.6 for the B.1.1.7 variant.

    A SARS CoV-2 nucleocapsid vaccine protects against distal viral dissemination

    Authors: Jacob Class; Tanushree Dangi; Justin Richner; Pablo Penaloza-MacMaster

    doi:10.1101/2021.04.26.440920 Date: 2021-04-26 Source: bioRxiv

    The SARS CoV-2 pandemic has killed millions of people. This viral infection can also result in substantial morbidity, including respiratory insufficiency MESHD and neurological manifestations, such as loss of smell and psychiatric diseases MESHD. Most SARS CoV-2 vaccines are based on the spike antigen, and although they have shown extraordinary efficacy at preventing severe lung disease MESHD and death MESHD, they do not always confer sterilizing immune protection. We performed studies in K18- hACE2 HGNC mice to evaluate whether the efficacy of SARS CoV-2 vaccines could be augmented by incorporating nucleocapsid as a vaccine antigen. We vaccinated mice with adenovirus-based vaccines encoding spike antigen alone, nucleocapsid antigen alone, or combined spike and nucleocapsid antigens. Mice were then challenged intranasally with SARS CoV-2, and acute viral loads were quantified at a proximal site of infection (lung) and a distal site of infection (brain). Interestingly, the spike-based vaccine conferred acute protection in the lung, but not in the brain. The spike-based vaccine conferred acute protection in the brain only if combined with the nucleocapsid-based vaccine. These findings suggest that nucleocapsid-specific immunity is important for the distal control of SARS CoV-2, warranting the inclusion of nucleocapsid in next-generation COVID-19 MESHD vaccines.

    Conserved in 186 countries the RBD fraction of SARS CoV-2 S-protein PROTEIN with in-silicoT500S mutation strongly blocks ACE2 rejecting the viral spike; A Molecular-docking analysis.

    Authors: Amrita Banerjee; Mehak Kanwar; Dipannita Santra; Smarajit Maiti

    doi:10.1101/2021.04.25.441361 Date: 2021-04-26 Source: bioRxiv

    SARS-CoV-2 developed global-pandemic with millions of infections/deaths MESHD. Blocker/inhibitor of ACE2 and viral-spikes Receptor-Binding-Domain RBD-blockers are helpful. Here, conserved RBD (CUTs) from 186-countries were compared with WUHAN-Hu-1 wild-type by CLUSTAL-X2 and Structural-alignment using Pymol. The RBD of ACE2-bound nCOV2 crystal-structure (2.68)6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the following locations (Y489S/Y453S/T500S/T500Y)/(Y489S,Y453S/Y489S,T500S/Y489S,T500Y/Y453S,T500S/Y453S,T500Y)/ (Y489S,Y453S,T500S/Y489S,Y453S,T500Y) of CUT4 (most-effective) were tested with Swiss-Model-Expacy. Blind-docking of mutated-CUTs to ACE2 (6VW1) by Haddock-Hawkdock was performed and optimally complete-rejection of nCOV2 to ACE2 was noticed. Further, competitive-docking/binding-analyses were done by PRODIGY. Present results suggest that compared to the wild-spike, CUT4 showed extra LYS31-PHE490/GLN42-GLN498 bonding and lack of TYR41-THR500 interaction (in wild H-bond:2.639) with ACE2 RBD. Mutated-CUT4 strongly binds with the ACE2-RBD, promoting TYR41-T500S (H-bond: 2.0 and 1.8)/T500Y (H-bond:2.6) interaction and complete inhibition of ACE2 RBD-nCOV2. Mutant combinations T500S,Y489S,T500S and Y489S,Y453S,T500Y mostly blocked ACE2. Conclusively, CUT4-mutant rejects whole glycosylated-nCoV2 pre-dock/post-dock/competitive-docking conditions.

    County-Level Estimates of Excess Mortality associated with COVID-19 MESHD in the United States

    Authors: Calvin Ackley; Dielle J. Lundberg; Irma T. Elo; Samuel H. Preston; Andrew C Stokes

    doi:10.1101/2021.04.23.21255564 Date: 2021-04-25 Source: medRxiv

    The coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic in the US has been largely monitored on the basis of death certificates containing reference to COVID-19 MESHD. However, prior analyses reveal that a significant fraction of excess deaths associated with the pandemic were not directly assigned to COVID-19 MESHD on the death certificate. The percent of excess deaths not assigned to COVID-19 MESHD is also known to vary across US states. However, few studies to date provide information on patterns of excess mortality and excess deaths not assigned to COVID-19 MESHD for US counties, despite the importance of this information for health policy and planning. In the present study, we develop and validate a generalized linear model of expected mortality in 2020 based on historical trends in deaths by county of residence between 2011 and 2019. We use the results of the model to generate county estimates of excess mortality and excess deaths not assigned to COVID-19 MESHD for each county in the US along with bootstrapped prediction intervals. Overall, the proportion of excess deaths assigned to COVID-19 MESHD was 81%, meaning that 19% of excess deaths were not assigned to COVID-19 MESHD. The proportion assigned to COVID-19 MESHD was lower in the South (76%) and West (75%) as compared to counties in the Midwest (81%) and Northeast (94%). Across US Census Divisions, the proportion was especially low in the East South Central Division (67%). Rural counties across all divisions (67%) reported lower proportions of excess deaths assigned to COVID-19 MESHD than urban areas (83%). For instance, in the Middle Atlantic and Pacific Divisions respectively, only 47% and 39% of excess deaths were assigned to COVID-19 MESHD in nonmetro areas. In contrast, the New England Census Division stood out as the only division where directly assigned COVID-19 MESHD deaths actually exceeded excess deaths, meaning there were 1.23 directly assigned COVID-19 MESHD deaths for every 1 excess death. However, this finding did not extend to nonmetro areas within New England where only 64% of excess deaths were assigned to COVID-19 MESHD. The finding that metro areas in New England reported higher direct COVID-19 MESHD mortality than excess mortality suggests that reductions in mortality from other causes of death MESHD may have occurred in these areas, at least among some populations. Across individual counties, the percentage of excess deaths not assigned to COVID-19 MESHD varied substantially, with some counties' direct COVID-19 MESHD tallies capturing only a small fraction of total excess deaths MESHD, whereas in other counties the direct COVID-19 MESHD death rate far exceeded the number of estimated excess deaths MESHD. Taken together, our results suggest that regional inequalities in the mortality burden associated with COVID-19 MESHD are not fully revealed by data at the state level and that consideration of excess deaths across US counties is critical for a full accounting of the disparate regional effects of the pandemic on US mortality.

    Estimating the total morbidity burden of COVID-19 MESHD

    Authors: Maia Phillips Smith

    doi:10.1101/2021.04.20.21255818 Date: 2021-04-24 Source: medRxiv

    Background Calculations of disease burden of COVID-19 MESHD are used to allocate scarce resources and historically have focused on mortality, with little attention to morbidity such as postviral post-COVID, similar to chronic fatigue syndrome MESHD ( CFS MESHD), which strikes 4 and 16% of male and female survivors. This paper quantifies post-COVID disability burden and combines it with case fatality to estimate total morbidity per COVID-19 MESHD case. Methods Healthy life years lost per COVID-19 MESHD case were computed as the sum of (incidence*disability weight*remaining lifespan) for death MESHD and post-COVID (modeled as CFS MESHD) by sex and 10-year age category. In addition to death, the main model considered lifelong mild, moderate or severe CFS MESHD; Model 2, CFS MESHD which resolved in ten years; Model 3, no CFS MESHD but 10% risk of death MESHD 10 years later. Results In all models, acute mortality was only a small share of total morbidity. For lifelong moderate CFS MESHD symptoms, healthy years lost per COVID-19 MESHD case ranged from 0.92 (male in his 30s) to 5.71 (girl under 10) and were 3.5 and 3.6 for the oldest females and males. At higher symptom severities, young people and females bore larger shares of total morbidity; if symptoms were persistent or survivors had later increased mortality, young people of both sexes were at highest risk. Conclusions Compared to post-COVID, acute mortality contributes only a small share of total COVID-19 MESHD morbidity. Total burden falls heavily on the young, who are currently deprioritized for preventive interventions such as vaccines. To fairly allocate scarce resources, decisionmakers should consider all morbidity.

    Protection of previous SARS-CoV-2 infection MESHD is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel

    Authors: Yair Goldberg; Micha Mandel; Yonatan Woodbridge; Ronen Fluss; Ilya Novikov; Rami Yaari; Arnona Ziv; Laurence Freedman; Amit Huppert

    doi:10.1101/2021.04.20.21255670 Date: 2021-04-24 Source: medRxiv

    Worldwide shortage of vaccination against SARS-CoV-2 infection MESHD while the pandemic is still uncontrolled leads many states to the dilemma whether or not to vaccinate previously infected persons. Understanding the level of protection of previous infection compared to that of vaccination is critical for policy making. We analyze an updated individual-level database of the entire population of Israel to assess the protection efficacy of both prior infection MESHD and vaccination in preventing subsequent SARS-CoV-2 infection MESHD, hospitalization with COVID-19 MESHD, severe disease, and death MESHD due to COVID-19 MESHD. Vaccination was highly effective with overall estimated efficacy for documented infection of 92.8% (CI: [92.6, 93.0]); hospitalization 94.2% (CI: [93.6, 94.7]); severe illness 94.4% (CI: [93.6, 95.0]); and death 93.7% (CI: [92.5, 94.7]). Similarly, the overall estimated level of protection from prior SARS-CoV-2 infection MESHD for documented infection is 94.8% (CI: [94.4, 95.1]); hospitalization 94.1% (CI: [91.9, 95.7]); and severe illness 96.4% (CI: [92.5, 98.3]). Our results question the need to vaccinate previously-infected individuals.

    Clinical Trends Among U.S. Adults Hospitalized with COVID-19 MESHD, March-December 2020

    Authors: Shikha Garg, MD, MPH; Kadam Patel, MPH; Huong Pham, MPH; Pam Daily Kirley, MPH; Breanna Kawasaki, MPH; Kimberly Yousey-Hindes, MPH; Evan J. Anderson, MD; Andrew Weigel, MSW; Patricia A. Ryan, MS; Libby Reeg, MPH; Kathryn Como-Sabetti, MPH; Sarah Shrum Davis, MPH; Alison Muse, MPH; Nancy M. Bennett, MD, MS; Laurie Billing, MPH; Melissa Sutton, MD, MPH; H. Keipp Talbot, MD; Mary Hill, MPH; Jonathan Wortham, MD; Lindsay Kim, MD; Fiona Havers, MD, MHS; - COVID-NET Surveillance Team

    doi:10.1101/2021.04.21.21255473 Date: 2021-04-23 Source: medRxiv

    Background: The COVID-19 pandemic MESHD has caused substantial morbidity and mortality. Objectives: To describe monthly demographic and clinical trends among adults hospitalized with COVID-19 MESHD Design: Pooled cross-sectional Setting: 99 counties within 14 states participating in the Coronavirus Disease 2019 MESHD-Associated Hospitalization Surveillance Network (COVID-NET) Patients: U.S. adults (aged [≥]18 years) hospitalized with laboratory-confirmed COVID-19 MESHD during March 1 HGNC-December 31, 2020 Measurements: Monthly trends in weighted percentages of interventions and outcomes including length of stay (LOS), intensive care unit admissions (ICU), invasive mechanical ventilation (IMV), vasopressor use and in-hospital death ( death MESHD). Monthly hospitalization, ICU and death MESHD rates per 100,000 population. Results: Among 116,743 hospitalized adults, median age was 62 years. Among 18,508 sampled adults, median LOS decreased from 6.4 (March) to 4.6 days (December). Remdesivir and systemic corticosteroid use increased from 2% and 19% (March) to 54% and 74% (December), respectively. Frequency of ICU decreased from 38% (March) to 21% (December). IMV (28% to 9%), vasopressors (23% to 9%) and deaths MESHD (14% to 9%) decreased from March to October; however, percentages of these interventions and outcomes leveled out or increased in November and December. Percentage of deaths significantly decreased over time for non-Hispanic White patients (p-value <0.01) but not non-Hispanic Black or Hispanic patients. Rates of hospitalization (105.3 per 100,000), ICU (20.2) and death MESHD (11.7) were highest during December. Limitations: COVID-NET covers approximately 10% of the U.S. population; findings may not be generalizable to the entire country. Conclusions: After initial improvement during April-October 2020, trends in interventions and outcomes worsened during November-December, corresponding with the 3rd peak of the U.S. pandemic. These data provide a longitudinal assessment of trends in COVID-19 MESHD-associated outcomes prior to widespread COVID-19 MESHD vaccine implementation.

    Mild and severe SARS-CoV-2 infection MESHD induces respiratory and intestinal microbiome changes in the K18- hACE2 HGNC transgenic mouse model

    Authors: Brittany A Seibert; Joaquin Caceres; Stivalis Cardenas-Garcia; Silvia Carnaccini; Ginger Geiger; Daniela Rajão; Elizabeth A Ottesen; Daniel R. Perez

    doi:10.1101/2021.04.20.440722 Date: 2021-04-23 Source: bioRxiv

    Transmission of the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), has resulted in millions of deaths MESHD and declining economies around the world. K18- hACE2 HGNC mice develop disease resembling severe SARS-CoV-2 infection MESHD in a virus dose-dependent manner. The relationship between SARS-CoV-2 and the intestinal or respiratory microbiome is not fully understood. In this context, we characterized the cecal and lung microbiome of SARS-CoV-2 challenged K18- hACE2 HGNC transgenic mice in the presence or absence of treatment with the Mpro PROTEIN inhibitor GC376. Cecum microbiome showed decreased Shannon and Inv Simpson diversity index correlating with SARS-CoV-2 infection MESHD dosage and a difference of Bray-Curtis MESHD dissimilarity distances among control and infected mice. Bacterial phyla such as Firmicutes, particularly Lachnospiraceae and Oscillospiraceae, were significantly less abundant while Verrucomicrobiota, particularly the family Akkermansiaceae, were increasingly more prevalent during peak infection in mice challenged with a high virus dose. In contrast to the cecal microbiome, the lung microbiome showed similar microbial diversity among the control, low and high challenge virus groups, independent of antiviral treatment. Bacterial phyla in the lungs such as Bacteroidota decreased while Firmicutes and Proteobacteria were significantly enriched in mice challenged with a high dose of SARS-CoV-2. In summary, we identified changes in the cecal and lung microbiome of K18- hACE2 HGNC mice with severe clinical signs of SARS-CoV-2 infection MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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