Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (5)

ORF8 (5)

ProteinN (2)

ORF1ab (2)

ORF3a (2)


Filter

Genes
Diseases
SARS-CoV-2 Proteins
    displaying 1 - 5 records in total 5
    records per page




    Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

    Authors: Jasdeep Singh; Nasreen Z Ehtesham; Syed Asad Rahman; Yakob G. Tsegay; Daniel S. Abebe; Mesay G. Edo; Endalkachew H. Maru; Wuletaw C. Zewde; Lydia K. Naylor; Dejen F. Semane; Menayit T. Deresse; Bereket B. Tezera; Lovisa Skoglund; Jamil Yousef; Elisa Pin; Wanda Christ; Mikaela Olausson; My Hedhammar; Hanna Tegel; Sara Mangsbo; Mia Phillipson; Anna Manberg; Sophia Hober; Peter Nilsson; Charlotte Thalin; Samuel Bates; Chevaun Morrison-Smith; Benjamin Nicholson; Edmond Wong; Leena El-Mufti; Michael Kann; Anna Bolling; Brooke Fortin; Hayden Ventresca; Wen Zhou; Santiago Pardo; Megan Kwock; Aditi Hazra; Leo Cheng; Rushdy Ahmad; James A. Toombs; Rebecca Larson; Haley Pleskow; Nell Meosky Luo; Christina Samaha; Unnati M. Pandya; Pushpamali De Silva; Sally Zhou; Zakary Ganhadeiro; Sara Yohannes; Rakiesha Gay; Jacqueline Slavik; Shibani S. Mukerji; Petr Jarolim; David R. Walt; Becky C. Carlyle; Lauren L. Ritterhouse; Sara Suliman

    doi:10.1101/2021.01.01.425028 Date: 2021-01-04 Source: bioRxiv

    The SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus MESHD) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 MESHD cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 PROTEIN and nucleocapsid (N) protein PROTEIN of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2 MESHD. SummarySince initial outbreak of COVID-19 MESHD in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab PROTEIN non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N PROTEIN), membrane (M), and envelope (E) proteins PROTEIN. The S protein PROTEIN mediates initial contacts with human hosts while the E and M proteins PROTEIN function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein PROTEIN (Clade G), G251V in ORF3a PROTEIN (Clade V) and L84S in ORF 8 (Clade S) were observed [2-4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness MESHD [5, 6]. As per latest WHO reports on COVID-19 MESHD, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise MESHD in COVID-19 MESHD detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19 MESHD, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.

    Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

    Authors: Vladimir Makarenkov; Bogdan Mazoure; Guillaume Rabusseau; Pierre Legendre; Gustavo Ferrer; Xiaoping Jiang; Ya-Nan Dai; Haiyan Zhao; Lucas Adams; Michael Holtzman; Adam Bailey; James Brett Case; Daved Fremont; Robyn S Klein; Michael Diamond; Adrianus Boon

    doi:10.1101/2020.12.03.410233 Date: 2020-12-03 Source: bioRxiv

    The SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV MESHD and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus MESHD (CoV) strains for the receptor binding (RB) domain of the spike protein PROTEIN. We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-Cov-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV MESHD have been identified in region [1215-1425] of gene S and region [534-727] of gene N PROTEIN. Moreover, some significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV MESHD and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab PROTEIN, S, ORF3a PROTEIN, ORF7a PROTEIN, ORF8 PROTEIN and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab PROTEIN, S and N forming the first cluster, gene phylogenies of ORF3a PROTEIN, E, M, ORF6 PROTEIN, ORF7a PROTEIN, ORF7b PROTEIN and ORF8 PROTEIN forming the second cluster, and phylogeny of gene ORF10 PROTEIN forming the third cluster. The results of our horizontal gene transfer and recombination analysis suggest that SARS-Cov-2 could not only be a chimera resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of SARS-CoV-2.

    LL-37 HGNC fights SARS-CoV-2: The Vitamin D-Inducible Peptide LL-37 HGNC Inhibits Binding of SARS-CoV-2 Spike PROTEIN Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 HGNC In Vitro

    Authors: Annika Roth; Steffen Luetke; Denise Meinberger; Gabriele Hermes; Gerhard Sengle; Manuel Koch; Thomas Streichert; Andreas R. Klatt; Maarja Andaloussi Mae; Lars Muhl; Nicky M. Craig; Samantha J. Griffiths; Jurgen G. Haas; Christine Tait Burkard; Urban Lendahl; Graeme M. Birdsey; Christer Betsholtz; Michela Noseda; Andrew Baker; Anna M Randi; Sofia Palma; Carolina Escobar; Josefina bascunan; Rodrigo Munoz; Monica Pinto; Daniela Cardemil; Marcelo Navarrete; Soledad Reyes; Victoria Espinoza; Nicolas Yanez; Christian Caglevic

    doi:10.1101/2020.12.02.408153 Date: 2020-12-02 Source: bioRxiv

    Objective: Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) is the pathogen accountable for the coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic. Viral entry via binding of the receptor binding domain (RBD) located within the S1 subunit of the SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN ( S) protein PROTEIN to its target receptor angiotensin converting enzyme (ACE) 2 HGNC is a key step in cell infection. The efficient transition of the virus is linked to a unique protein called open reading frame ( ORF MESHD) 8. As SARS-CoV-2 infection MESHD SARS-CoV-2 infection MESHDs can develop into life threatening lower respiratory syndromes, effective therapy options are urgently needed. Several publications propose vitamin D treatment, although its mode of action against COVID-19 MESHD is not fully elucidated. It is speculated that vitamin D's beneficial effects are mediated by up regulating LL-37 HGNC, a well known antimicrobial peptide with antiviral effects. Methods: Recombinantly expressed SARS-CoV-2 S protein PROTEIN, the extended S1 subunit (S1e), the S2 subunit (S2), the receptor binding domain (RBD), and ORF8 PROTEIN were used for surface plasmon resonance ( SPR HGNC) studies to investigate LL-37 HGNC's ability to bind to SARS-CoV-2 proteins MESHD and to localize its binding site within the S protein PROTEIN. Binding competition studies were conducted to confirm an inhibitory action of LL-37 HGNC on the attachment of SARS-CoV-2 S MESHD S protein PROTEIN to its entry receptor ACE2 HGNC. Results: We could show that LL-37 HGNC binds to SARS-CoV-2 S MESHD S protein PROTEIN ( LL-37 HGNC/S-Strep KD = 407 nM, LL-37 HGNC/S-His KD = 414 nM) with the same affinity, as SARS-CoV-2 binds to hACE2 HGNC ( hACE2 HGNC/S-Strep KD = 374 nM, hACE2 HGNC/S-His KD = 368 nM). The binding is not restricted to the RBD of the S protein PROTEIN, but rather distributed along the entire length of the protein. Interaction between LL-37 HGNC and ORF8 PROTEIN was detected with a KD of 294 nM. Further, inhibition of the binding of S-Strep (IC50 = 735 nM), S1e (IC50 = 168 nM), and RBD (IC50 = 126 nM) to hACE2 HGNC by LL-37 HGNC was demonstrated. Conclusions: We have revealed a biochemical link between vitamin D, LL-37 HGNC, and COVID-19 MESHD severity. SPR HGNC analysis demonstrated that LL-37 HGNC binds to SARS-CoV-2 S MESHD S protein PROTEIN and inhibits binding to its receptor hACE2 HGNC, and most likely viral entry into the cell. This study supports the prophylactic use of vitamin D to induce LL-37 HGNC that protects from SARS-CoV-2 infection MESHD, and the therapeutic administration of vitamin D for the treatment of COVID-19 MESHD patients. Further, our results provide evidence that the direct use of LL-37 HGNC by inhalation and systemic application may reduce the severity of COVID-19 MESHD.

    The Discovery of a Recombinant SARS2-like CoV Strain Provides Insight Into SARS and COVID-19 MESHD Pandemics

    Authors: Xin Li; Xiufeng Jin; Shunmei Chen; Liangge Wang; Tung On Yau; Jianyi Yang; Zhangyong Hong; Jishou Ruan; Guangyou Duan; Shan Gao

    doi:10.21203/rs.3.rs-60430/v1 Date: 2020-08-16 Source: ResearchSquare

    Background: In December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2).Results: In the present study, we classified betacoronavirus subgroup B into the SARS-CoV-2, SARS-CoV MESHD and SARS-like CoV clusters, and the ORF8 PROTEIN genes of these three clusters into types 1, 2 and 3, respectively. One important result of our study is that we reported—for the first time—a recombination event of ORF8 PROTEIN at the whole-gene level in a bat, which had been co-infected MESHD by two betacoronavirus strains. This result provides substantial proof for long-existing hypotheses regarding the recombination and biological functions of ORF8 PROTEIN. Based on the analysis of recombination events in the Spike gene, we propose that the Spike protein PROTEIN of SARS-CoV-2 may have more than one specific receptor for its function as gp120 HGNC of HIV has CD4 HGNC and CCR5 HGNC. In the present study, we also found that the ancestor of betacoronavirus had a strong first Internal Ribosome Entry Site (IRES) and at least one furin cleavage site (FCS) in the junction region between S1 and S2 subunits.Conclusions: We concluded that the junction FCS in SARS-CoV-2 may increase the efficiency of its entry into cells, while the type 2 ORF8 PROTEIN acquired by SARS-CoV may increase its replication efficiency. These two most critical events provide the most likely explanation for SARS and COVID-19 pandemic MESHD COVID-19 pandemic MESHDs.

    The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-2019 pandemics

    Authors: Xin Li; Xiufeng Jin; Shunmei Chen; Liangge Wang; Tung On Yau; Jianyi Yang; Zhangyong Hong; Jishou Ruan; Guangyou Duan; Shan Gao

    doi:10.1101/2020.07.22.213926 Date: 2020-07-22 Source: bioRxiv

    In December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2). In the present study, we classified betacoronavirus subgroup B into the SARS-CoV-2, SARS-CoV MESHD and SARS-like CoV clusters, and the ORF8 PROTEIN genes of these three clusters into types 1, 2 and 3, respectively. One important result of our study is that the recently reported strain RmYN02 was identified as a recombinant SARS2-like CoV strain that belongs to the SARS-CoV-2 cluster MESHD, but has an ORF8 PROTEIN from a SARS-like CoV. This result provides substantial proof for long-existing hypotheses regarding the recombination and biological functions of ORF8 PROTEIN. Based on the analysis of recombination events in the Spike gene, we propose that the Spike protein PROTEIN of SARS-CoV-2 may have more than one specific receptor for its function as gp120 HGNC of HIV has CD4 HGNC and CCR5 HGNC. We concluded that the furin protease cleavage site acquired by SARS-CoV-2 may increase the efficiency of viral entry into cells, while the type 2 ORF8 PROTEIN acquired by SARS-CoV may increase its replication efficiency. These two most critical events provide the most likely explanation for SARS and COVID-2019 pandemics.

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.