Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinN (33)

ProteinE (33)

ProteinS (13)

ProteinM (11)

ComplexRdRp (8)


SARS-CoV-2 Proteins
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    Long-read sequencing of SARS-CoV-2 reveals novel transcripts and a diverse complex transcriptome landscape.

    Authors: Jennifer Li-Pook-Than; Selene Banuelos; Alexander Honkala; Malaya K Sahoo; Benjamin A Pinsky; Michael P Snyder

    doi:10.1101/2021.03.05.434150 Date: 2021-03-06 Source: bioRxiv

    Severe Acute Respiratory Syndrome Coronavirus 2 MESHD, SARS-CoV-2 ( COVID-19 MESHD), is a positive single-stranded RNA virus with a 30 kb genome that is responsible for the current pandemic. To date, the genomes of global COVID-19 MESHD variants have been primarily characterized via short-read sequencing methods. Here, we devised a long-read RNA (IsoSeq) sequencing approach to characterize the COVID-19 MESHD transcript landscape and expression of its [~]27 coding regions. Our analysis identified novel COVID-19 MESHD transcripts including a) a short [~]65-70 nt 5-UTR fused to various downstream ORFs encoding accessory proteins such as the envelope PROTEIN, ORF 8, and ORF 9 HGNC ( nucleocapsid) proteins PROTEIN, that are relatively highly expressed, b) novel SNVs that are differentially expressed, whereby a subset are suggestive of partial RNA editing events, and c) SNVs at functional sites, whereby at least one is associated with a differentially expressed spike protein PROTEIN isoform. These previously uncharacterized COVID-19 MESHD isoforms, expressed genes, and gene variants were corroborated using ddPCR. Understanding this transcriptional complexity may help provide insight into the biology and pathogenicity of SARS-CoV-2 compared to other coronaviruses.

    Expression of human ACE2 HGNC N-terminal domain, part of the receptor for SARS-CoV-2, in fusion with maltose binding protein, E PROTEIN. coli ribonuclease I and human RNase A

    Authors: Shuang-yong Xu; Alexey Fomenkov; Tien-Hao Chen; Erbay Yigit; Yinhui Lu; Karl E Kadler

    doi:10.1101/2021.01.31.429007 Date: 2021-02-01 Source: bioRxiv

    The SARS-CoV-2 viral genome contains a positive-strand single-stranded RNA of ~30 kb. Human ACE2 HGNC protein is the receptor for SARS-CoV-2 virus attachment MESHD and initiation of infection MESHD. We propose to use ribonucleases (RNases) as antiviral agents to destroy the viral genome in vitro. In the virions the RNA is protected by viral capsid proteins, membrane proteins and nucleocapsid PROTEIN proteins. To overcome this protection we set out to construct RNase fusion with human ACE2 HGNC receptor N-terminal domain (ACE2NTD). We constructed six proteins expressed in E. coli cells: 1) MBP-ACE2NTD, 2) ACE2NTD-GFP, 3) RNase I (6xHis), 4) RNase III (6xHis), 5) RNase I-ACE2NTD (6xHis), and 6) human RNase A HGNC-ACE2NTD150 (6xHis). We evaluated fusion expression in different E. coli strains, partially purified MBP-ACE2NTD protein from the soluble fraction of bacterial cell lysate, and refolded MBP-ACE2NTD protein from inclusion body. The engineered RNase I-ACE2NTD (6xHis) and hRNase A-ACE2NTD (6xHis) fusions are active in cleaving COVID-19 MESHD RNA in vitro. The recombinant RNase I (6xHis) and RNase III (6xHis) are active in cleaving RNA and dsRNA in test tube. This study provides a proof-of-concept for construction of fusion protein between human cell receptor and nuclease that may be used to degrade viral nucleic acids in our environment.

    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.

    IGI-LuNER: single-well multiplexed RT-qPCR test for SARS-CoV-2

    Authors: Elizabeth C. Stahl; Connor A. Tsuchida; Jennifer R. Hamilton; Enrique Lin-Shiao; Shana L. McDevitt; Erica A. Moehle; Lea B. Witkowsky; C. Kimberly Tsui; Kathleen Pestal; Holly K. Gildea; Matthew McElroy; Amanda Keller; Iman Sylvain; Clara Williams; Ariana Hirsh; Alison Ciling; Alexander J. Ehrenberg; - SARS-CoV-2 consortium; Fyodor D. Urnov; Bradley R. Ringeisen; Petros Giannikopoulos; Jennifer A. Doudna

    doi:10.1101/2020.12.10.20247338 Date: 2020-12-11 Source: medRxiv

    Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost or risk of false-negative results. Currently, no test combines detection of widely used SARS-CoV-2 E- and N-gene PROTEIN targets and a sample control in a single, multiplexed reaction. We developed the IGI-LuNER RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene PROTEIN, E gene PROTEIN, and human RNase P (NER). This combined, cost-effective test can be performed in 384-well plates with detection sensitivity suitable for clinical reporting, and will aid in future sample pooling efforts, thus improving throughput of SARS-CoV-2 detection. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/20247338v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@74929corg.highwire.dtl.DTLVardef@1457971org.highwire.dtl.DTLVardef@2825ddorg.highwire.dtl.DTLVardef@1cde2b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

    Galectin antagonist use in mild cases of SARS-CoV-2 cases; pilot feasibility randomised, open label, controlled trial


    doi:10.1101/2020.12.03.20238840 Date: 2020-12-04 Source: medRxiv

    ImportanceNovel SARS-CoV-2 virus has infected nearly half a billion people across the world and is highly contagious. There is a need for a novel mechanism to block viral entry and stop its replication. BackgroundSpike protein N PROTEIN terminal domain (NTD) of the novel SARS-CoV-2 is essential for viral entry and replication in human cell. Thus the S1 NTD of human coronavirus family, which is similar to a galectin binding site - human galactose binding lectins, is a potential novel target for early treatment in COVID-19 MESHD. ObjectivesTo study the feasibility of performing a definitive trial of using galectin antagonist - Prolectin HGNC-M as treatment for mild, symptomatic, rRT-PCR positive, COVID-19 MESHD. Main outcomes and measuresCycle threshold (Ct) value is number of cycles needed to express fluorescence, on real time reverse transcriptase polymerase chain reaction. Ct values expressed for RNA polymerase (Rd/RP) gene +Nucleocapsid gene and the small envelope ( E) genes PROTEIN determine infectivity of the individual. A digital droplet PCR based estimation of the Nucleocapid genes (N1+N2) in absolute copies/L determines active viral replication. Design and interventionPilot Feasibility Randomised Controlled Open-Label, parallel arm, study. Oral tablets of Prolectin HGNC-M were administered along with the best practice, Standard of Care (SoC) and compared against SoC. Voluntarily, consenting individuals, age >18 years, and able to provide frequent nasopharyngeal and oropharyngeal swabs were randomly allocated by REDCap software. The intervention, Prolectin HGNC-M was administered as a multi dose regime of 4 gram tablets. Each tablet contained 2 grams of (1-6)-Alpha-D-mannopyranosil mixed with 2 grams of dietary fibre. Each participant took a single chewable tablet every hour, to a maximum of 10 hours in a day. Tablets were administered only during the daytime, for total of 5 days. ResultsThis pilot trial demonstrated the feasibility to recruit and randomize participants. By day 7, following treatment with Prolectin HGNC-M, Ct value of Rd/Rp + N gene PROTEIN increased by16.41 points, 95% (CI - 0.3527 to 32.48, p=0.047). Similarly, small envelope ( E) gene PROTEIN also increased by 17.75 points (95% CI;-0.1321 to 35.63, p = 0.05). The expression of N1, N2 genes went below detectable thresholds by day 3 (Mann Whitney U = 0.000, p<0.029). rRT-PCR testing done in the clinic on day 1, 7, and 14 had 3 participants (60%) turn negative by day 7 and all turned negative by day 14 and stayed negative until day 28. In the SoC group 2 participants had zero detectable viral loads at baseline, 2 participants tested negative on day 14, and the last participant tested remained positive on day 28. There were no serious adverse events, and all participants were clinically asymptomatic before day 28 with reactive immunoglobulin G (IgG). Trial relevanceThis pilot study proves that it is feasible and safe to perform a trial using a Galectin antagonist in COVID-19 MESHD. This is a novel mechanism for blocking viral entry and its subsequent replication. Trial RegistrationClinical identifier NCT04512027; CTRI ref. CTRI/2020/09/027833

    Sequence and Structural Analysis of COVID-19 MESHD E and M Protein PROTEIN With MERS Virus E and M Protein PROTEIN – A Comparative Study

    Authors: Ebtisam A. Aldaais; Subha Yegnaswamy; Fatimah Albahrani; Fatima Alsowaiket; Sarah Alramadan

    doi:10.21203/ Date: 2020-11-14 Source: ResearchSquare

    The outbreak of SARS in 2003, MERS in 2012, and now COVID-19 MESHD in 2019 have demonstrated that Coronaviruses are capable of causing primary lethal infections in humans, and the pandemic is now a global concern. The COVID-19 MESHD belongs to the beta coronavirus family encoding 29 proteins, of which 4 are structural, the Spike, Membrane, Envelope, and Nucleocapsid proteins PROTEIN. Here we have analyzed and compared the Membrane (M) and Envelope (E) proteins PROTEIN of COVID-19 MESHD and MERS with SARS and Bat viruses. The sequence analysis of conserved regions of both E and M protein PROTEIN revealed that many regions of COVID-19 MESHD are similar to Bat and SARS viruses while the MERS virus showed variations. The essential binding motifs found in SARS-CoV MESHD appeared in COVID-19 MESHD. Besides, the M protein PROTEIN of COVID- 19 showed a distinct serine phosphorylation site in the C-terminal domain, which looked like a catalytic triad seen in serine proteases. A Dileucine motif occurred many times in the sequence of the M protein PROTEIN of all the four viruses compared. Concerning the structural part, the COVID-19 MESHD E protein PROTEIN showed more similarity to Bat while MERS shared similarity with the SARS virus. The M protein PROTEIN of both COVID-19 MESHD and MERS displayed variations in the structure. The interaction between M and E protein PROTEIN was also studied to know the additional binding regions. Our study highlights the critical motifs and structural regions to be considered for further research to design better inhibitors for the infection caused by these viruses.

    The Structure of the Membrane Protein of SARS-CoV-2 Resembles the Sugar Transporter semiSWEET

    Authors: Sunil Thomas

    id:10.20944/preprints202004.0512.v6 Date: 2020-10-19 Source:

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 MESHD that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. People with diabetes MESHD are at risk of the disease. As yet we do not know why the virus is highly successful in causing the pandemic within 3 months of its first report. The structural proteins of SARS include, membrane glycoprotein (M PROTEIN), envelope protein (E PROTEIN), nucleocapsid protein (N PROTEIN) and the spike protein (S PROTEIN). The structure and function of the most abundant structural protein of SARS-CoV-2, the membrane (M) glycoprotein PROTEIN is not fully understood. Using in silico analyses we determined the structure and potential function of the M protein PROTEIN. The M protein PROTEIN of SARS-CoV-2 is 98.6% similar to the M protein PROTEIN of bat SARS-CoV MESHD, maintains 98.2% homology with pangolin SARS-CoV MESHD, and has 90% homology with M protein PROTEIN of SARS-CoV MESHD; whereas, the similarity was only 38% with the M protein PROTEIN of MERS-CoV. In silico analyses showed that the M protein PROTEIN of SARS-CoV-2 has a triple helix bundle, form a single 3-transmembrane domain (TM), and are homologous to the prokaryotic sugar transport protein semiSWEET. SemiSWEETs are related to the PQ-loop family that function as cargo receptors in vesicle transport, mediates movement of basic amino acids across lysosomal membranes, and is also involved in phospholipase flippase function. The advantage and role of the M protein PROTEIN having a sugar transport-like structure is not clearly understood. The M protein PROTEIN of SARS-CoV-2 interacts with S, E and N protein PROTEIN. The S protein PROTEIN of the virus is glycosylated. It could be hypothesized that the sugar transporter-like structure of the M protein PROTEIN influences glycosylation of the S protein PROTEIN. Endocytosis is critical for the internalization and maturation of RNA viruses, including SARS-CoV-2. Sucrose is involved in endosome and lysosome maturation and may also induce autophagy, pathways that help in the entry of the virus. Overall, it could be hypothesized that the semiSWEET sugar transporter-like structure of the M protein PROTEIN may be involved in multiple functions that may aid in the rapid proliferation, replication and immune evasion of the SARS-CoV-2 virus. Biological experiments would validate the presence and function of the semiSWEET sugar transporter.

    Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin

    Authors: Kanika Bansal; Prabhu B Patil; Vyacheslav A. Dibrova; Yulia V. Dibrova; Volodymyr M. Vasylyk; Mykhailo Y. Novikov; Nataliia V. Shults; Sergiy G. Gychka; Scott Lee; Zhaohui Cui; Adebola Adebayo; Tiffiany Aholou; Minal Amin; Peter Aryee; Cindy Castaneda; Trudy Chambers; Amy Fleshman; Christin Goodman; Tony Holmes; Asha Ivey-Stephenson; Emiko Kamitani; Susan Katz; Jennifer Knapp; Maureen Kolasa; Maranda Lumsden; Erin Mayweather; Asfia Mohammed; Anne Moorman; Alpa Patel-Larson; Lara Perinet; Mark Pilgard; Deirdre Pratt; Shanica Railey; Jaina Shah; Dawn Tuckey; Emilio Dirlikov; Dale Rose; Julie Villanueva; Alicia Fry; Aron Hall; Hannah Kirking; Jacqueline Tate; Cherie Drenzek; Tatiana Lanzieri; Rebekah Stewart

    doi:10.1101/2020.10.12.335521 Date: 2020-10-12 Source: bioRxiv

    Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is a driving force in its evolution. Systematic analysis of CUP of replicase ( rdrp PROTEIN), spike, envelope (E), membrane glycoprotein (M PROTEIN), and nucleocapsid (N PROTEIN) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. At the same time, our analysis suggests that dogs are not a source of SARS-CoV-2. Interestingly, CUP of rdrp PROTEIN displays conservation with two bat SARS isolates RaTG13 and RmYN02. CUP of the SARS-CoV-2 E gene PROTEIN is also conserved with bat and pangolin isolates with variations for a few amino acids. This suggests role allele replacement in these two genes involving SARS strains of least two hosts. At the same time, a relatively conserved CUP pattern in replicase and envelope across hosts suggests them it to be an ideal target in antiviral development for SARS-CoV-2.

    Phylogenetic analysis of variable and conserved genomic regions in severe acute respiratory syndrome coronavirus 2 ( COVID-19 MESHD)

    Authors: Abeer F. El Nahas; Nasema M. Elkatatny; Haitham G. Abo-Al-Ela

    doi:10.21203/ Date: 2020-10-05 Source: ResearchSquare

    SARS-CoV-2 has rapidly spread around the world. Several mutations have been detected in its genome, but they do not seem to affect the abilities of the virus to spread or infect MESHD. We aimed to explore the conserved genomic regions in coronavirus that could contain the key strengths of the virus. SARS-CoV-2 sequence data were retrieved from Genbank from the period of December 2019 to March 2020. Phylogenetic analyses were conducted for 207 sequences using MEGAX compared with the reference sequence (MN908947.3- CHN-Wuhan Dec-2019). The analysis included seven important genomic regions, the ORF1ab PROTEIN gene (21,290 bp), S gene (3,822 bp), Orf3a PROTEIN gene (827 bp), E gene PROTEIN (227 bp), M gene (669 bp), and N gene PROTEIN (1,259 bp), which play critical roles in virus invasion and replication. Furthermore, the variant nucleotides and amino acids were detected by MEGAX and BLAST. Through the phylogenetic analysis and amino acid substitution, the ORF1ab PROTEIN gene showed 11 conserved regions and also several variable sites. The E and M genes were mainly conserved, and all sequences were included in one clade, with one or two amino acid variants. Orf3a PROTEIN and the N gene PROTEIN have four conserved sites distributed along the genes. The S gene has 12 mutations and four main large conserved regionsWe conclude that the favored occurrence of mutations at the ORFab and Orf3a PROTEIN genes during the SARS-CoV epidemic is an important mechanism for virus pathogenesis. The E and M proteins PROTEIN have an almost conserved structure, whereas the S and N genes PROTEIN have many conserved regions, which could serve as possible targets for vaccine design for SARS-CoV MESHD.

    RT qLAMP--Direct Detection of SARS-CoV-2 in Raw Sewage

    Authors: Jerry E Ongerth; Richard E Danielson

    doi:10.1101/2020.10.01.20205492 Date: 2020-10-04 Source: medRxiv

    The project purpose was to examine ability of a loop-mediated isothermal amplification (LAMP) assay to quantify SARS-CoV-2 in raw sewage, directly, using no preliminary sample processing for virus concentration and RNA extraction. An objective was to take advantage of extensive recently published work to facilitate process development, principally primer selection, and to use readily available off the shelf materials with conventional lab procedure and equipment. Well-developed and referenced primers for ORF1a PROTEIN, E, and N-gene PROTEIN targets were selected and applied, using commercially available synthetic RNA standards, and raw sewage from a local wastewater agency serving 650,000. County health department monitoring provided current COVID-19 MESHD data. Testing defined performance characteristics for each primer set, with significant differences between them. Specific amplification of SARS-CoV-2 RNA was observed using each of the primer sets, with E-gene PROTEIN and N-gene PROTEIN primers most effective. Positive analysis results from all raw sewage samples corresponded to calculated concentrations of virus in 5-10 L raw sewage aliquots for 25 L reactions. Results show that even at low reported case rates e.g. 1-10/100,000, SARS-CoV-2 is present in raw sewage at > 1-5/ L, permitting direct LAMP-based detection. Use of RT qLAMP will facilitate wastewater-based epidemiology as an important component for COVID-19 MESHD control.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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