Corpus overview


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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (289)

ProteinN (99)

NSP5 (59)

ComplexRdRp (26)

NSP3 (17)


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SARS-CoV-2 Proteins
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    Understanding and Addressing Vaccine Hesitancy in the Context of COVID-19 MESHD: Development of a Digital intervention

    Authors: Holly Knight; Ru Jia; Kieran Ayling; Katherine Bradbury; Katherine Baker; Trudie Chalder; Joanne R Morling; Lindy Durrant; Tony Avery; Jonathan Ball; Caroline Barker; Robert Bennett; Tricia McKeever; kavita vedhara

    doi:10.1101/2021.03.24.21254124 Date: 2021-03-26 Source: medRxiv

    Background Severe Acute Respiratory Coronavirus MESHD 2 (SARS-CoV-2) was identified in late 2019, spreading to over 200 countries and resulting in almost two million deaths worldwide. The emergence of safe and effective vaccines provides a route out of the pandemic, with vaccination uptake of 75-90% needed to achieve population protection. Vaccine hesitancy is problematic for vaccine rollout; global reports suggest only 73% of the population may agree to being vaccinated. As a result, there is an urgent need to develop equitable and accessible interventions to address vaccine hesitancy at the population level. Method We report the development of a scalable digital intervention seeking to address COVID-19 MESHD vaccine hesitancy and enhance uptake of COVID-19 MESHD vaccines. Guided by motivational interviewing ( MI MESHD) principles, the intervention includes a series of therapeutic dialogues addressing 10 key concerns of vaccine hesitant individuals. Development of the intervention occurred linearly across four stages. During stage 1, we identified common reasons for COVID-19 MESHD vaccine hesitancy through analysis of existing survey data, a rapid systematic literature review, and public engagement workshops. Stage 2 comprised qualitative interviews with medical, immunological, and public health experts. Rapid content and thematic analysis of the data provided evidence-based responses to common vaccine concerns. Stage 3 involved the development of therapeutic dialogues through workshops with psychological MESHD and digital behaviour change experts. Dialogues were developed to address concerns using MI principles, including embracing resistance and supporting self-efficacy. Finally, stage 4 involved digitisation of the dialogues and pilot testing with members of the public. Discussion The digital intervention provides an evidence-based approach to addressing vaccine hesitancy through MI principles. The dialogues are user-selected, allowing exploration of relevant issues associated with hesitancy in a non-judgmental context. The text-based content and digital format allow for rapid modification to changing information and scalability for wider dissemination.

    Sudden rise in COVID-19 MESHD case fatality among young and middle-aged adults in the south of Brazil after identification of the novel B.1.1.28.1 ( P.1 HGNC) SARS-CoV-2 strain: analysis of data from the state of Parana

    Authors: Maria Helena Santos de Oliveira; Giuseppe Lippi; Brandon Michael Henry

    doi:10.1101/2021.03.24.21254046 Date: 2021-03-26 Source: medRxiv

    Brazil is currently suffering a deadly surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections MESHD, which has been attributed to the spread of a new strain known as P.1 HGNC (B.1.1.28.1). In this investigation, we analyzed coronavirus disease 2019 MESHD ( COVID-19 MESHD) public health data from Parana, the largest state in southern half of Brazil, between September 1, 2020 and March 17, 2021, to evaluate recent trends in case fatality rates in different age groups. A total of 553,518 cases of SARS-CoV-2, 8,853 currently registered as fatal, were finally included in our analysis. All age groups showed either decline or stabilization of the case fatality rates (CFRs) between September 2020 and January 2021. In February 2021, an increase in CFR for almost all age groups could be instead observed. All groups above 20 years of age showed statistically significant increases in CFR when diagnosed in February 2021 as opposed to January 2021. Patients aged 20-29 years experienced a tripling of their CFR, from 0.04% to 0.13%, while those aged 30-39, 40-49, 50-59 experienced approximate CFR doubling. Individuals between 20 and 29 years of age whose diagnosis was made in February 2021 had an over 3-fold higher risk of death MESHD compared to those diagnosed in January 2021 (Risk Ratio (RR): 3.15 [95%CI: 1.52-6.53], p<0.01), while those aged 30-39, 40-49, 50-59 years experienced 93% (1.93 [95%CI:1.31-2.85], p<0.01), 110% (RR: 2.10 [95%CI:1.62-2.72], p<0.01), and 80% (RR: 1.80 [95%CI:1.50-2.16], p<0.01) increases in risk of death MESHD, respectively. Notably, the observed CFR increase coincided with the second consecutive month of declining number of diagnosed SARS-CoV-2 cases. Taken together, these preliminary findings suggest significant increases in CFR in young and middle-aged adults after identification of a novel SARS-CoV-2 strain circulating in Brazil, and this should raise public health alarms, including the need for more aggressive local and regional public health interventions and faster vaccination.

    Sulforaphane exhibits in vitro and in vivo antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses MESHD

    Authors: Alvaro A Ordonez; Cynthia K Bullen; Andres F Villabona-Rueda; Elizabeth A Thompson; Mitchell L Turner; Stephanie L Davis; Oliver Komm; Jonathan D Powell; Robert H Yolken; Sanjay K Jain; Lorraine Jones-Brando

    doi:10.1101/2021.03.25.437060 Date: 2021-03-25 Source: bioRxiv

    Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 MESHD ( COVID-19 MESHD), has incited a global health crisis. Currently, there are no orally available medications for prophylaxis for those exposed to SARS-CoV-2 and limited therapeutic options for those who develop COVID-19 MESHD. We evaluated the antiviral activity of sulforaphane ( SFN HGNC), a naturally occurring, orally available, well-tolerated, nutritional supplement present in high concentrations in cruciferous vegetables with limited side effects. SFN inhibited in vitro replication of four strains of SARS-CoV-2 as well as that of the seasonal coronavirus HCoV-OC43. Further, SFN and remdesivir interacted synergistically to inhibit coronavirus infection MESHD in vitro. Prophylactic administration of SFN to K18- hACE2 HGNC mice prior to intranasal SARS-CoV-2 infection MESHD significantly decreased the viral load in the lungs and upper respiratory tract and reduced lung injury MESHD and pulmonary pathology compared to untreated infected mice. SFN treatment diminished immune cell activation in the lungs, including significantly lower recruitment of myeloid cells and a reduction in T cell activation and cytokine production. Our results suggest that SFN is a promising treatment for prevention of coronavirus infection MESHD or treatment of early disease.

    DCcov: Repositioning of Drugs and Drug Combinations for SARS-CoV-2 Infected MESHD Lung through Constraint-Based Modelling

    Authors: Ali Kishk; Maria Pires Pacheco; Thomas Sauter

    id:2103.13844v1 Date: 2021-03-25 Source: arXiv

    The 2019 coronavirus disease MESHD ( COVID-19 MESHD) became a worldwide pandemic with currently no effective antiviral drug except treatments for symptomatic therapy. Flux balance analysis is an efficient method to analyze metabolic networks. It allows optimizing for a metabolic function and thus e.g., predicting the growth rate of a specific cell or the production rate of a metabolite of interest. Here flux balance analysis was applied on human lung cells infected with severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) to reposition metabolic drugs and drug combinations against the replication of the SARS-CoV-2 virus within the host tissue. Making use of expression data sets of infected lung MESHD tissue, genome-scale COVID-19 MESHD-specific metabolic models were reconstructed. Then host-specific essential genes and gene-pairs were determined through in-silico knockouts that permit reducing the viral biomass production without affecting the host biomass. Key pathways that are associated with COVID-19 MESHD severity in lung tissue are related to oxidative stress, as well as ferroptosis, sphingolipid metabolism, cysteine metabolism, and fat digestion. By in-silico screening of FDA approved drugs on the putative disease-specific essential genes and gene-pairs, 45 drugs and 99 drug combinations were predicted as promising candidates for COVID-19 MESHD focused drug repositioning (https://github.com/sysbiolux/DCcov). Among the 45 drug candidates, six antiviral drugs were found and seven drugs that are being tested in clinical trials against COVID-19 MESHD. Other drugs like gemcitabine, rosuvastatin and acetylcysteine, and drug combinations like azathioprine-pemetrexed might offer new chances for treating COVID-19 MESHD.

    A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants

    Authors: Aaron J. Schmitz; Jackson S. Turner; Zhuoming Liu; Ishmael D. Aziati; Rita E. Chen; Astha Joshi; Traci L. Bricker; Tamarand L. Darling; Daniel C. Adelsberg; Wafaa B. Al Soussi; James Brett Case; Tingting Lei; Mahima Thapa; Fatima Amanat; Pei-Yong Shi; Rachel M. Presti; Florian Krammer; Goran Bajic; Sean P.J. Whelan; Michael S. Diamond; Adrianus C.M. Boon

    doi:10.1101/2021.03.24.436864 Date: 2021-03-25 Source: bioRxiv

    The emergence of antigenically distinct severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) variants with increased transmissibility is a public health threat. Some of these variants show substantial resistance to neutralization by SARS-CoV-2 infection MESHD- or vaccination-induced antibodies, which principally target the receptor binding domain (RBD) on the virus spike glycoprotein PROTEIN. Here, we describe 2C08, a SARS-CoV-2 mRNA vaccine-induced germinal center B cell-derived human monoclonal antibody that binds to the receptor binding motif within the RBD. 2C08 broadly neutralizes SARS-CoV-2 variants with remarkable potency and reduces lung inflammation MESHD, viral load, and morbidity in hamsters challenged with either an ancestral SARS-CoV-2 strain or a recent variant of concern. Clonal analysis identified 2C08-like public clonotypes among B cell clones responding to SARS-CoV-2 infection MESHD or vaccination in at least 20 out of 78 individuals. Thus, 2C08-like antibodies can be readily induced by SARS-CoV-2 vaccines MESHD and mitigate resistance by circulating variants of concern.

    Efficacy of a Broadly Neutralizing SARS-CoV-2 Ferritin MESHD Nanoparticle Vaccine in Nonhuman Primates

    Authors: Michael G. Joyce; Hannah A.D. King; Ines Elakhal Naouar; Aslaa Ahmed; Kristina K. Peachman; Camila M. Cincotta; Caroline Subra; Rita E. Chen; Paul V. Thomas; Wei-Hung Chen; Rajeshwer S. Sankhala; Agnes Hajduczki; Elizabeth J. Martinez; Caroline E. Peterson; William C. Chang; Misook Choe; Clayton Smith; Parker J. Lee; Jarrett A. Headley; Mekdi G. Taddese; Hanne A. Elyard; Anthony Cook; Alexander Anderson; Kathryn McGuckin-Wuertz; Ming Dong; Isabella Swafford; James B. Case; Jeffrey R. Currier; Kerri G. Lal; Sebastian Molnar; Manoj S. Nair; Vincent Dussupt; Sharon P. Daye; Xiankun Zeng; Erica K. Barkei; Hilary M. Staples; Kendra Alfson; Ricardo Carrion; Shelly J. Krebs; Dominic Paquin-Proulx; Nicos Karasavva; Victoria R. Polonis; Linda L. Jagodzinski; Mihret F. Amare; Sandhya Vasan; Paul T. Scott; Yaoxing Huang; David D Ho; Natalia de Val; Michael S. Diamond; Mark G. Lewis; Mangala Rao; Gary R. Matyas; Gregory D. Gromowski; Sheila A. Peel; Nelson L. Michael; Diane L. Bolton; Kayvon Modjarrad

    doi:10.1101/2021.03.24.436523 Date: 2021-03-25 Source: bioRxiv

    The emergence of novel severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) variants stresses the continued need for next-generation vaccines that confer broad protection against coronavirus disease 2019 MESHD ( COVID-19 MESHD). We developed and evaluated an adjuvanted SARS-CoV-2 Spike PROTEIN SARS-CoV-2 Spike MESHD Ferritin Nanoparticle (SpFN) vaccine in nonhuman primates. High-dose (50 mcg) SpFN vaccine, given twice within a 28 day interval, induced a Th1-biased CD4 T cell helper response and a peak neutralizing antibody geometric mean titer of 52,773 against wild-type virus, with activity against SARS-CoV-1 and minimal decrement against variants of concern. Vaccinated animals mounted an anamnestic response on high-dose SARS-CoV-2 respiratory challenge that translated into rapid elimination of replicating virus in their upper and lower airways and lung parenchyma. The potent and broad immunogenicity profile of this vaccine and its resulting efficacy in NHPs supports its utility as a candidate platform for SARS-like betacoronaviruses.

    SARS-CoV-2 prevalence and transmission in swimming activities: results from a retrospective cohort study

    Authors: Martin Brink Termansen; Ask Vest Christiansen; Sebastian Frische

    doi:10.1101/2021.03.19.21253351 Date: 2021-03-24 Source: medRxiv

    There is an urgent need for research on the epidemiology of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) causing corona virus disease MESHD 2019 ( COVID-19 MESHD), as the transmissibility differs between settings and populations. Here we report on a questionnaire-based retrospective cohort study of the prevalence and transmission of SARS-CoV-2 among participants in swimming activities in Denmark in the last five months of 2020 during the COVID-19 pandemic MESHD. Eight of 162 swimming activities with a SARS-CoV-2 positive participant led to transmission to 23 other participants. Overall, the percentage of transmission episodes was 4.9% (competitive swimming 8.9%; recreational swimming 1.3%). Overall, the incidence rate of transmission was 19.5 participants per 100.000 pool activity hours (corresponding values: 43.5 and 4.7 for competitive and recreational swimming, respectively). Compliance with precautionary restrictions was highest regarding hand hygiene (98.1%) and lowest in distancing personal sports bags (69.9%). Due to low statistical power, the study showed no significant effect of restrictions. Insight into the risk of transmission of SARS-CoV-2 during indoor swimming is needed to estimate the efficiency of restrictive measures on this and other sports and leisure activities. Only when we know how the virus spreads through various settings, optimal strategies to handle the COVID-19 pandemic MESHD can be developed.

    SARS-CoV-2 spike PROTEIN protein gene variants with N501T and G142D mutation dominated infections in minks in the US

    Authors: Hugh Y Cai; Allison Cai

    doi:10.1101/2021.03.18.21253734 Date: 2021-03-24 Source: medRxiv

    Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) have infected human and animals world wide. Since the first SARS-CoV-2 sequences identified from samples collected in December 2019, the virus has been evolving. Now, in the GISAID database of SARS-CoV-2 genomes as of March 17, 2021, 95.7% (758,684 of 792,388) of the SARS-CoV-2 genome has the D614G mutation in the spike protein PROTEIN gene; and 22% (178,186 of 792.388) had N501Y mutation which occurred in the more virulent UK variants, South Africa variant and Brazil variant. Large number of minks were infected with the virus which containing the Y453F mutation in Europe, causing zoonosis concerns. To evaluate the genetic characteristics of the US mink-derived SARS-CoV-2 sequences, we analyzed all animal-derived (977), all Canadian (19,529) and US (173,277) SARS-CoV-2 sequences deposited in GISAID from December 2019 to March 12, 2021, and identified 2 dominant novel variants, the N501T-G142D variant and N501T-G142D-F486L variant, in the US mink-derived SARS-CoV-2 sequences. These variants were not found in minks from Canada or other countries. The Y453F mutation was not identified in the mink-derive sequences in the US and Canada. The N501T mutation occurred two months earlier in the human than in the minks in the US. The results of our study highlighted the importance of on going monitoring the mutations of the SARS-CoV-2 virus in animals.

    Within-Day Variability of SARS-CoV-2 RNA in Municipal Wastewater Influent During Periods of Varying COVID-19 MESHD Prevalence and Positivity

    Authors: Aaron Bivins; Devin North; Zhenyu Wu; Marlee Shaffer; Warish Ahmed; Kyle James Bibby

    doi:10.1101/2021.03.16.21253652 Date: 2021-03-24 Source: medRxiv

    Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) RNA is being used to monitor Coronavirus Disease 2019 MESHD ( COVID-19 MESHD) trends in communities; however, within-day variation in primary influent concentrations of SARS-CoV-2 RNA remain largely uncharacterized. In the current study, grab sampling of primary influent was performed every 2 hours over two different 24-hour periods at two wastewater treatment plants (WWTPs) in northern Indiana, USA. In primary influent, uncorrected, recovery-corrected, and pepper mild mottle virus (PMMoV)-normalized SARS-CoV-2 RNA concentrations demonstrated ordinal agreement with increasing clinical COVID-19 MESHD positivity, but not COVID-19 MESHD cases. Primary influent SARS-CoV-2 RNA concentrations exhibited greater variation than PMMoV RNA concentrations as expected for lower shedding prevalence. The bovine respiratory syncytial virus (BRSV) process control recovery efficiency was low (mean: 0.91%) and highly variable (coefficient of variation: 51% - 206%) over the four sampling events with significant differences between the two WWTPs (p <0.0001). The process control recovery was similar to the independently assessed SARS-CoV-2 RNA recovery efficiency, which was also significantly different between the two WWTPs (p <0.0001). Recovery-corrected SARS-CoV-2 RNA concentrations better reflected within-day changes in primary influent flow rate and fecal content, as indicated by PMMoV concentrations. These observations highlight the importance of assessing the process recovery efficiency, which is highly variable, using an appropriate process control. Despite large variations, both recovery-corrected and PMMoV-normalized SARS-CoV-2 RNA concentrations in primary influent demonstrate potential for monitoring COVID-19 MESHD positivity trends in WWTPs serving peri-urban and rural areas.

    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.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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