Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins


SARS-CoV-2 Proteins
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    Comparative studies of the seven human coronavirus envelope proteins PROTEIN using topology prediction and molecular modelling to understand their pathogenicity

    Authors: Dewald Schoeman; Ruben Cloete; Burtram Fielding

    doi:10.1101/2021.03.08.434384 Date: 2021-03-08 Source: bioRxiv

    Human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 are less virulent and cause mild, self-limiting respiratory tract infections, while SARS-CoV MESHD, MERS-CoV, and SARS-CoV-2, are more virulent and have caused severe outbreaks. The CoV envelope (E) protein PROTEIN, an important contributor to the pathogenesis of severe hCoVs infections MESHD, may provide insight into this disparate severity of the disease. Topology prediction programs and 3D modelling software was used to predict and visualize structural aspects of the hCoV E protein PROTEIN related to its functions. All seven hCoV E proteins PROTEIN largely adopted different topologies, with some distinction between the more virulent and less virulent ones. The 3D models refined this distinction, showing the PDZ-binding motif (PBM) of SARS-CoV MESHD, MERS-CoV, and SARS-CoV-2 to be more flexible than the PBM of hCoVs 229E, NL63, OC43, and HKU1. We speculate that the increased flexibility of the PBM may provide the more virulent hCoVs with a greater degree of freedom, which can allow them to bind to different host proteins and can contribute to a more severe form of the disease. This is the first paper to predict the topologies and model 3D structures of all seven hCoVs E proteins PROTEIN, providing novel insights for possible drug and/or vaccine development.

    Rapid environmental monitoring, capture, and destruction activities of SARS-CoV-2 during the Covid-19 MESHD health emergency

    Authors: Roberto Marchetti; Martina Stella; Debjyoti Talukdar; Rosaria Erika Pileci

    doi:10.1101/2020.11.24.20237040 Date: 2020-11-27 Source: medRxiv

    SARS-CoV-2 pandemic is a health emergency for occupational healthcare workers at COVID19 MESHD hospital wards in Italy. The objective of the study was to investigate if U-Earth AIRcel bioreactors were effective in monitoring and improving air quality via detection, capture, and destruction of the SARS-CoV-2 virus, reducing the risk of transmission among healthcare workers. U-Earth AIRcel bioreactors are a demonstrated effective biomonitoring system. We implemented a methodological approach wherein they were placed at various hospitals treating COVID-19 MESHD patients in Italy. The detection of the SARS-CoV-2 virus was achieved through rapid biomonitoring testing of the solutes from the AIRcel bioreactors via SARS-CoV-2 rapid test antigen and consecutive reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) and the Real-Time PCR Rotor-Gene. The marked presence of the SARS-CoV-2 virus was found in multiple water samples via the detection of ORF1ab PROTEIN + N and/or E gene PROTEIN involved in gene expression and cellular signaling of the SARS-CoV virus MESHD. The AIRcel bioreactors were able to neutralize the virus effectively as traces of the viruses were no longer found in multiple solute samples after an overnight period. Transmission of COVID-19 MESHD via bio-aerosols, transmitted by infected MESHD patients, remains a viable threat for health workers. AIRcel bioreactors allow for rapid biomonitoring testing for early virus detection within the environment, reducing the risk of exponential contagion exposure and maintaining good air quality without endangering health workers. This same protocol can also be extended to public spaces as a bio-monitoring tool for hotpots early detection.

    Identification of key genes and pathways in the hPSC-derived lungs infected by the SARS-CoV-2

    Authors: Hanming Gu; Gongsheng Yuan

    doi:10.21203/ Date: 2020-11-23 Source: ResearchSquare

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is caused by the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), which has led to numerous infections MESHD and deaths MESHD in the world. Our research is to explore the differentially expressed genes (DEGs) and signaling pathways in hPSC-derived lungs by using a bioinformatics method to clarify their potential pathogenesis. The gene expression profile of GSE155241 dataset was originally created by using an Illumina NovaSeq 6000 (Homo sapiens) platform. Functional categories and significant pathways were identified by the KEGG and GO analysis. The results suggested that brain disorders MESHD and mitochondrial dysfunctions MESHD are the main signaling pathways affected by the SARS-CoV-2 infection MESHD. Furthermore, key genes e PROTEIN.g. CDC20 HGNC, NCBP1 HGNC and inhibitors e.g. MEK1 HGNC-2-inhibitor, tivozanib may paly critical roles in COVID-19 MESHD. Therefore, our study provides insights into the treatment of COVID-19 MESHD and related disorders.

    Gene Expression Meta-Analysis Identifies Molecular Changes Associated with SARS-CoV Infection in Lungs

    Authors: Amber Park; Laura Harris; Tanushka Doctor; Neda Nasheri; Hua Wang; Xuemei Feng; Gennadiy Zelinskyy; Mirko Trilling; Kathrin Sutter; Mengji Lu; Baoju Wang; Dongliang Yang; Xin Zheng; Jia Liu; Davey Smith; Daniela Weiskopf; Alessandro Sette; Shane Crotty; Jian Jin; Xian Chen; Andrew Pekosz; Sabra Klein; Irina Burd

    doi:10.1101/2020.11.14.382697 Date: 2020-11-16 Source: bioRxiv

    Background: Severe Acute Respiratory Syndrome MESHD (SARS) corona virus ( SARS-CoV) infections MESHD are a serious public health threat because of their pandemic-causing potential. This work uses mRNA expression data to predict genes associated with SARS-CoV infection MESHD through an innovative meta-analysis examining gene signatures (i. e., gene PROTEIN lists ranked by differential gene expression between SARS and mock infection MESHD). Methods: This work defines 29 gene signatures representing SARS infection MESHD across seven strains with established mutations that vary virulence (infectious clone SARS (icSARS), Urbani, MA15, {Delta} ORF6 PROTEIN, BAT-SRBD, {Delta} NSP16 PROTEIN, and ExoNI) and host (human lung cultures and/or mouse lung samples) and examines them through Gene Set Enrichment Analysis (GSEA). To do this, first positive and negative icSARS gene panels were defined from GSEA-identified leading-edge genes between 500 genes from positive or negative tails of the GSE47960-derived icSARSvsmock signature and the GSE47961-derived icSARSvsmock signature, both from human cultures. GSEA then was used to assess enrichment and identify leading-edge icSARS panel genes in the other 27 signatures. Genes associated with SARS-CoV infection MESHD are predicted by examining membership in GSEA-identified leading-edges across signatures. Results: Significant enrichment (GSEA p<0.001) was observed between GSE47960-derived and GSE47961-derived signatures, and those leading-edges defined the positive (233 genes) and negative (114 genes) icSARS panels. Non-random (null distribution p<0.001) significant enrichment (p<0.001) was observed between icSARS panels and all verification icSARSvsmock signatures derived from human cultures, from which 51 over- and 22 under-expressed genes were shared across leading-edges with 10 over-expressed genes already being associated with icSARS infection MESHD. For the icSARSvsmock mouse signature, significant, non-random enrichment (both p<0.001) held for only the positive icSARS panel, from which nine genes were shared with icSARS infection MESHD in human cultures. Considering other SARS strains, significant (p<0.01), non-random (p<0.002) enrichment was observed across signatures derived from other SARS strains for the positive icSARS panel. Five positive icSARS panel genes, CXCL10, OAS3, OASL, IFIT3, and XAF1, were found in mice and human signatures. Conclusion: The GSEA-based meta-analysis approach used here identified genes with and without reported associations with SARS-CoV infections MESHD, highlighting this approachs predictability and usefulness in identifying genes that have potential as therapeutic targets to preclude or overcome SARS infections MESHD.

    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.

    SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP

    Authors: Steffen Klein; Thorsten G. Mueller; Dina Khalid; Vera Sonntag-Buck; Anke-Mareil Heuser; Baerbel Glass; Matthias Meurer; Ivonne Morales; Angelika Schillak; Andrew Freistaedter; Ina Ambiel; Sophie L. Winter; Liv Zimmermann; Tamara Naumoska; Felix Bubeck; Daniel Kirrmaier; Stephanie Ullrich; Isabel Barreto-Miranda; Simon Anders; Dirk Grimm; Paul Schnitzler; Michael Knop; Hans-Georg Kraeusslich; Viet Loan Dao Thi; Kathleen Boerner; Petr Chlanda

    doi:10.1101/2020.07.08.20147561 Date: 2020-07-11 Source: medRxiv

    Rapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection MESHD is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and alternative, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric RT- LAMP HGNC using N primers, as well as RT-qPCR using E gene PROTEIN primers showing that the here presented RNA extraction protocol can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot.

    No SARS-CoV-2 detected in the vermiform appendix of a COVID-19 MESHD patient with appendicitis: a case report 

    Authors: Benjamin Wolf; Corinna Pietsch; Marc-Philip Radosa; Lars-Christian Horn; Uwe G. Liebert; Bahriye Aktas

    doi:10.21203/ Date: 2020-06-28 Source: ResearchSquare

    Background:SARS-CoV-2, the virus causing corona virus disease 2019 ( COVID-19 MESHD), has been demonstrated to i nfect the gastrointestinal MESHDtract and might therefore be a source of infection for the surgical team during abdominal operations. One of the most common surgical procedures performed is appendectomy. However, reports of virologic testing of appendiceal tissue specimens in COVID-19 MESHD patients are lacking. We sought to determine whether SARS-CoV-2 is present in the appendectomy specimen of a patient with COVID-19 MESHD. Case presentation:A female patient presented to the emergency department of our tertiary care academic hospital with lower a bdominal pain, MESHD f ever, MESHD n ausea, MESHD and v omiting. MESHD She was admitted to the gynecological floor because of suspected p elvic inflammatory disease. MESHD Due to worsening symptoms, a laparoscopy was performed the next day and a severely inflamed appendix was detected. Laparoscopic appendectomy was performed without complications. A few hours postoperatively, the patient was tested positive for c orona virus disease MESHD2019 (COVID 19). Real-time reverse transcription polymerase chain reaction analysis targeting the SARS-CoV-2 E-gene PROTEIN was performed on the appendectomy specimen. SARS-CoV-2 could not be detected. During her hospital stay, the patient developed mild respiratory symptoms while the postoperative course was otherwise uncomplicated. Conclusions:The absence of SARS-CoV-2 in the appendectomy specimen of our case adds to the preliminary available evidence indicating that appendectomy in COVID-19 MESHD patients with mild disease carries probably a low risk of i nfection MESHDby aerosols generated during the procedure. 

    Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

    Authors: Lucas Maldonado Sr.; Laura Kamenetzky

    doi:10.1101/2020.06.23.167072 Date: 2020-06-25 Source: bioRxiv

    In December 2019 rising pneumonia MESHD cases caused by a novel {beta}-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern therefore several scientists are dedicated to the study of the new virus. Since human viruses have codon usage biases that match highly expressed proteins in the tissues they infect MESHD and depend on host cell machinery for replication and co-evolution, we selected the genes that are highly expressed in the tissue of human lungs to perform computational studies that permit to compare their molecular features with SARS, SARS-CoV-2 and MERS genes. In our studies, we analysed 91 molecular features for 339 viral genes and 463 human genes that consisted of 677873 codon positions. Hereby, we found that A/T bias in viral genes could propitiate the viral infection MESHD favoured by a host dependant specialization using the host cell machinery of only some genes. The envelope protein E PROTEIN, the membrane glycoprotein M PROTEIN and ORF7 could have been further benefited by a high rate of A/T in the third codon position. Thereby, the mistranslation or de-regulation of protein synthesis could produce collateral effects, as a consequence of viral occupancy of the host translation machinery due tomolecular similarities with viral genes. Furthermore, we provided a list of candidate human genes whose molecular features match those of SARS-CoV-2, SARSand MERS genes, which should be considered to be incorporated into genetic population studies to evaluate thesusceptibility to respiratory viral infections MESHD caused by these viruses. The results presented here, settle the basis for further research in the field of human genetics associated with the new viral infection, COVID-19 MESHD, caused by SARS-CoV-2 and for the development of antiviral preventive methods.

    Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India

    Authors: Sudipti Arora; Aditi Nag; Jasmine Sethi; Jayana Rajvanshi; Sonika Saxena; Sandeep Kumar Shrivastava; Akhilendra Bhushan Gupta

    doi:10.1101/2020.06.18.20135277 Date: 2020-06-20 Source: medRxiv

    The infection with SARS-CoV-2 is reported to be accompanied by the shedding of the virus in stool samples of infected MESHD patients. Earlier reports have suggested that COVID-19 MESHD agents can be present in the fecal and sewage samples and thus it can be a good indication of the pandemic extent in a community. However, no such studies have been reported in the Indian context so far. Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. Samples from different local municipal WWTPs and hospital wastewater samples were collected and wastewater based epidemiology (WBE) studies for the presence of SARS-CoV-2 were carried out using the RT-PCR technique to confirm the presence of different COVID-19 MESHD target genes namely S gene, E PROTEIN gene, ORF1ab PROTEIN gene, RdRp PROTEIN gene and N PROTEIN gene in the viral load of wastewater samples. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 MESHD positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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