Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (146)

ProteinS (40)

ProteinN (33)

ComplexRdRp (17)

ProteinM (17)


Filter

Genes
Diseases
SARS-CoV-2 Proteins
    displaying 141 - 146 records in total 146
    records per page




    Comparative Performance of SARS-CoV-2 Detection Assays using Seven Different Primer/Probe Sets and One Assay Kit

    Authors: Amanda M. Casto; Meei-Li Huang; Arun Nalla; Garrett A. Perchetti; Reigran Sampoleo; Lasata Shrestha; Yulun Wei; Haiying Zhu; Alexander L. Greninger; Keith R. Jerome

    doi:10.1101/2020.03.13.20035618 Date: 2020-03-17 Source: medRxiv

    More than 100,000 people worldwide are known to have been infected with SARS-CoV-2 beginning in December 2019. The virus has now spread to over 93 countries including the United States, with the largest cluster of US cases to date in the Seattle metropolitan area in Washington. Given the rapid increase in the number of local cases, the availability of accurate, high-throughput SARS-CoV-2 testing is vital to efforts to manage the current public health crisis. In the course of optimizing SARS-CoV-2 testing performed by the University of Washington Clinical Virology Lab (UW Virology Lab), we tested assays using seven different primer/probe sets and one assay kit HGNC. We found that the most sensitive assays were those the used the E-gene PROTEIN primer/probe set described by Corman et al. (Eurosurveillance 25(3), 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045) and the N2 set described by the CDC (Division of Viral Diseases MESHD, Centers for Disease Control and Prevention, 2020, https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf). All assays tested were found to be highly specific for SARS-CoV-2, with no cross-reactivity with other respiratory viruses observed in our analyses regardless of the primer/probe set or kit HGNC used. These results will provide invaluable information to other clinical laboratories who are actively developing SARS-CoV-2 testing protocols at a time when increased testing capacity is urgently needed worldwide.

    Predicting COVID-19 MESHD distribution in Mexico through a discrete and time-dependent Markov chain and an SIR-like model

    Authors: Alfonso Vivanco-Lira

    id:2003.06758v1 Date: 2020-03-15 Source: arXiv

    COVID-19 MESHD is an emergent viral infection which rose in December 2019 in a city in the Chinese province of Hubei, Wuhan; the viral aetiology of this infection is now known as COVID-19 MESHD virus, which belongs to the Betacoronavirus genus. This virus produces the syndrome of acute respiratory stress MESHD that h as been witnessed in other coronaviruses, such as that MERS-CoV in Middle East countries or SARS-CoV which was seen in 2002 and 2003 in China. This virus mediates its entry through its spike (S) proteins PROTEIN interacting with ACE2 receptors in lung epithelial cells, and may promote an inflammatory response by means of inflammasome NLRP3 activation and unfolded protein response (these are possibly consequence of the envelope E protein PROTEIN of COVID-19 MESHD virus). Efforts have been made worldwide to prevent further spread of the disease, but in March 2020 the WHO declared it a pandemic emergency and Mexico started to report its first cases. In this paper we attempt to summarize the biological features of the virus and the possible pathophysiological mechanisms of its disease, as well as a stochastic model characterizing the probability distribution of cases in Mexico by states and the estimated number of cases in Mexico through a differential equation model (modified SIR model), thus will we be able to characterize the disease and its course in Mexico in order to display more preparedness and promote more logical actions by both the policy makers as well as the general population.

    Rapid Detection of SARS-CoV-2 Using Reverse transcription RT-LAMP method

    Authors: Weihua Yang; Xiaofei Dang; Qingxi Wang; Mingjie Xu; Qianqian Zhao; Yunying Zhou; Huailong Zhao; Li Wang; Yihui Xu; Jun Wang; Shuyi Han; Min Wang; Fengyan Pei; Yunshan Wang

    doi:10.1101/2020.03.02.20030130 Date: 2020-03-02 Source: medRxiv

    Corona Virus Disease MESHD 2019 ( COVID-19 MESHD) is a recently emerged life-threatening disease caused by SARS-CoV-2. Real- time fluorescent PCR (RT-PCR) is the clinical standard for SARS-CoV-2 nucleic acid detection. To detect SARS-CoV-2 early and control the disease spreading on time, a faster and more convenient method for SARS-CoV-2 nucleic acid detecting, RT-LAMP method (reverse transcription loop-mediated isothermal amplification) was developed. RNA reverse transcription and nucleic acid amplification were performed in one step at 63 isothermal conditions, and the results can be obtained within 30 minutes. ORF1ab PROTEIN gene, E PROTEIN gene and N PROTEIN gene were detected at the same time. ORF1ab PROTEIN gene was very specific and N gene PROTEIN was very sensitivity, so they can guarantee both sensitivity and specificity for SARS-CoV-2. The sensitivity of RT-LAMP assay is similar to RT-PCR, and specificity was 99% as detecting 208 clinical specimens. The RT-LAMP assay reported here has the advantages of rapid amplification, simple operation, and easy detection, which is useful for the rapid and reliable clinical diagnosis of SARS-CoV-2.

    Functional pangenome analysis provides insights into the origin, function and pathways to therapy of SARS-CoV-2 coronavirus

    Authors: Intikhab Alam; Allan K Kamau; Maxat Kulmanov; Stefan T Arold; Arnab T Pain; Takashi Gojobori; Carlos M. Duarte

    doi:10.1101/2020.02.17.952895 Date: 2020-02-21 Source: bioRxiv

    The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S PROTEIN) of this virus enables binding to the human receptor ACE2 HGNC, and hence presents a prime target for vaccines preventing viral entry into host cells1. The S proteins PROTEIN from SARS-CoV-1 and SARS-CoV-2 MESHD are similar2, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-CoV-1-specific neutralizing antibodies to inhibit SARS-CoV-23. Here we used comparative pangenomic analysis of all sequenced Betacoronaviruses to reveal that, among all core gene clusters present in these viruses, the envelope protein E PROTEIN shows a variant shared by SARS and SARS-Cov2 with two completely-conserved key functional features, an ion-channel and a PDZ-binding Motif (PBM). These features trigger a cytokine storm that activates the inflammasome, leading to increased edema MESHD in lungs causing the acute respiratory distress syndrome MESHD ( ARDS MESHD)4-6, the leading cause of death MESHD in SARS-CoV-1 and SARS-CoV-2 infection7 MESHD SARS-CoV-2 infection MESHD7,8. However, three drugs approved for human use may inhibit SARS-CoV-1 and SARS-CoV-2 Protein E PROTEIN, either acting upon the ion channel (Amantadine and Hexamethylene amiloride9,10) or the PBM (SB2035805), thereby potentially increasing the survival of the host, as already demonstrated for SARS-CoV-1in animal models. Hence, blocking the SARS protein E PROTEIN inhibits development of ARDS in vivo. Given that our results demonstrate that the protein E PROTEIN subcluster for the SARS clade is quasi-identical for the key functional regions of SARS-CoV-1 and SARS-CoV-2, we conclude that use of approved drugs shown to act as SARS E protein PROTEIN inhibitors can help prevent further casualties from COVID-2019 while vaccines and other preventive measures are being developed.

    Structural modeling and conserved epitopes prediction against SARS-COV-2 structural proteins for vaccine development

    Authors: Muhammad Tahir ul Qamar; Farah Shahid; Usman Ali Ashfaq; Sidra Aslam; Israr Fatima; Muhammad Mazhar Fareed; Ali Zohaib; Ling-Ling Chen

    doi:10.21203/rs.2.23973/v1 Date: 2020-02-18 Source: ResearchSquare

    Background: Coronavirus disease 2019 MESHD ( COVID-19 MESHD) caused by Severe Acute Respiratory Syndrome MESHD Corona virus 2 (SARS-COV-2) was first diagnosed in December 2019, Wuhan, China. Little is known about this new virus and it has the potential to cause severe illness and pneumonia MESHD in some people, therefore the development of an effective vaccine is highly desired.Methods: Immunoinformatics and statistical approaches were used in this study to forecast B- and T- cell epitopes for the SARS-COV-2 structural proteins (Surface glycoprotein, Envelope protein PROTEIN Envelope protein HGNC, and Membrane glycoprotein PROTEIN) that may play a key role in eliciting immune response against COVID-19 MESHD. Different types of B cell epitopes (linear as well as discontinuous) and T cell (MHC class I and MHC class II) were determined. Moreover, their antigenicity and allergenicity were also estimated.Results: The antigenic B-cell epitopes exposed to the outer surface were screened out and 23 linear B cell epitopes were selected. “SPTKLNDLCFTNVY” had the highest antigenicity score among B cell epitopes. The T-cell epitopes bound to multiple alleles, antigenic, non-allergen, non-toxic, and conserved in the protein sequence were shortlisted. In total, 16 epitopes (9 from MHC class I and 7 from MHC class II) were selected. Among the T-cell epitopes, MHC class I (IPFAMQMAYRFN) and MHC class II (VTLACFVLAAVYRIN) were classified as strongly antigenic. Digestion analysis verified the safety and stability of the peptides predicted during this study. Furthermore, docking analyses of predicted peptides showed significant interactions with the HLA-B7 allele.Conclusion: The putative antigen epitopes identified in this study may serve as vaccine candidates and can help to eliminate/control growing health threat of COVID-19 MESHD.

    Design of multi epitope-based peptide vaccine against E protein PROTEIN of human 2019-nCoV: An immunoinformatics approach

    Authors: Miyssa I. Abdelmageed; Abdelrahman Hamza Abdelmoneim Sr.; Mujahed Ibrahim Mustafa Sr.; Nafisa M. Elfadol; Naseem S. Murshed; Shaza W. Shantier; Abdelrafie M. Makhawi

    doi:10.1101/2020.02.04.934232 Date: 2020-02-11 Source: bioRxiv

    BackgroundNew endemic disease has been spread across Wuhan City, China on December 2019. Within few weeks, the World Health Organization (WHO) announced a novel coronavirus designated as coronavirus disease 2019 MESHD ( COVID-19 MESHD). In late January 2020, WHO declared the outbreak of a "public-health emergency of international concern" due to the rapid and increasing spread of the disease worldwide. Currently, there is no vaccine or approved treatment for this emerging infection MESHD; thus the objective of this study is to design a multi epitope peptide vaccine against COVID-19 MESHD using immunoinformatics approach. MethodSeveral techniques facilitating the combination of immunoinformatics approach and comparative genomic approach were used in order to determine the potential peptides for designing the T cell epitopes-based peptide vaccine using the envelope protein PROTEIN of 2019-nCoV as a target. ResultsExtensive mutations, insertion and deletion were discovered with comparative sequencing in COVID-19 MESHD strain. Additionally, ten peptides binding to MHC class I and MHC class II were found to be promising candidates for vaccine design with adequate world population coverage of 88.5% and 99.99%, respectively. ConclusionT cell epitopes-based peptide vaccine was designed for COVID-19 MESHD using envelope protein PROTEIN as an immunogenic target. Nevertheless, the proposed vaccine is rapidly needed to be validated clinically in order to ensure its safety, immunogenic profile and to help on stopping this epidemic before it leads to devastating global outbreaks.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

Sources


Annotations

All
None
MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


Export subcorpus as...

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.