A database resource and online analysis tools for coronaviruses on a historical and global scale

Zhu, Zhenglin; Meng, Kaiwen; Liu, Gexin; Meng, Geng

doi:10.1093/database/baaa070

Cited by 19 publications

(15 citation statements)

References 60 publications

(40 reference statements)

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“…We collected genomic sequences and related information of coronavirus from GISAID ( www.gisaid.org ), NCBI, CoVdb ( Zhu et al. 2020 ) and ViralZone ( Hulo et al.…”

Section: Methodsmentioning

confidence: 99%

Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis

Zhu

Liu

Meng

et al. 2021

Genome Biology and Evolution

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The novel coronavirus (SARS-CoV-2) has become a pandemic and is threatening human health globally. Here, we report 9 newly evolved SARS-CoV-2 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (7 cases) or decrease (2 cases) in their frequency for 30% ∼ 80% in the initial four months, which are further confirmed by intra-host single nucleotide variation (iSNV) analysis using raw sequence data including 8217 samples. The 9 SNPs are mostly (8/9) located in the coding region and are mainly (6/9) nonsynonymous substitutions. The 9 SNPs show a complete linkage in SNP pairs and belong to 3 different linkage groups, named LG_1 to LG_3. Analyses in population genetics show signatures of adaptive selection towards the mutants in LG_1, but no signal of selection for LG_2. Population genetic analysis results on LG_3 show geological differentiation. Analyses on geographic COVID-19 cases and published clinical data provide evidence that the mutants in LG_1 and LG_3 benefit virus replication and those in LG_1 have a positive correlation with the disease severity in COVID-19 infected patients. The mutants in LG_2 show a bias towards mildness of the disease based on available public clinical data. Our findings may be instructive for epidemiological surveys and disease control of COVID-19 in the future.

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“…We collected genomic sequences and related information of coronavirus from GISAID ( www.gisaid.org ), NCBI, CoVdb ( Zhu et al. 2020 ) and ViralZone ( Hulo et al.…”

Section: Methodsmentioning

confidence: 99%

Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis

Zhu

Liu

Meng

et al. 2021

Genome Biology and Evolution

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“…Several databases and online resources have been developed to aid the fight against the deadly COVID-19 pandemic. Databases like EpiCoV TM platform from GISAID ( GISAID, 2020 ), NCBI-SARS-CoV2 resources ( NCBI-SARS-CoV2 Resources, 2020 ), COVID-19 data portal ( EMBL-EBI, 2020 ), Virus Pathogen Database and Analysis Resource (ViPR) ( Pickett et al, 2012 ), GESS ( Fang et al, 2021 ), CovDB ( Zhu et al, 2020 ), and ViruSurf ( Canakoglu et al, 2021 ) systematically categorized thousands of nCoV2 genome sequences deposited from all over the world. Similarly, resources like Cov3D ( Gowthaman et al, 2021 ), SWISS-MODEL SARS-CoV2 portal ( Swiss-Model, 2020 ), and Zhang lab COVID-19 resource ( Zhang Lab, 2020 ) developed 3D models for SARS-CoV2 proteins for structural characterizations, whereas exhaustive experimental characterization of host protein interactions was revealed by works from Gordon et al (2020a , b) .…”

Section: Discussionmentioning

confidence: 99%

Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients

et al. 2021

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The novel coronavirus 2 (nCoV2) outbreaks took place in December 2019 in Wuhan City, Hubei Province, China. It continued to spread worldwide in an unprecedented manner, bringing the whole world to a lockdown and causing severe loss of life and economic stability. The coronavirus disease 2019 (COVID-19) pandemic has also affected India, infecting more than 10 million till 31st December 2020 and resulting in more than a hundred thousand deaths. In the absence of an effective vaccine, it is imperative to understand the phenotypic outcome of the genetic variants and subsequently the mode of action of its proteins with respect to human proteins and other bio-molecules. Availability of a large number of genomic and mutational data extracted from the nCoV2 virus infecting Indian patients in a public repository provided an opportunity to understand and analyze the specific variations of the virus in India and their impact in broader perspectives. Non-structural proteins (NSPs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) virus play a major role in its survival as well as virulence power. Here, we provide a detailed overview of the SARS-CoV2 NSPs including primary and secondary structural information, mutational frequency of the Indian and Wuhan variants, phylogenetic profiles, three-dimensional (3D) structural perspectives using homology modeling and molecular dynamics analyses for wild-type and selected variants, host-interactome analysis and viral–host protein complexes, and in silico drug screening with known antivirals and other drugs against the SARS-CoV2 NSPs isolated from the variants found within Indian patients across various regions of the country. All this information is categorized in the form of a database named, Database of NSPs of India specific Novel Coronavirus (DbNSP InC), which is freely available at http://www.hpppi.iicb.res.in/covid19/index.php.

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“…The established platform provides PCA, linear regression, differential expression analysis, and cluster analysis by heatmap based on the author’s own data. Zhu et al developed an online coronavirus genomic, proteomic, and evolutionary analysis platform 10 . Dannon Baker et al integrated the available SARS-CoV-2 sequence data and published their results on the public Galaxy platform in order to promote the exchange of data between different laboratories 11 .…”

Section: Introductionmentioning

confidence: 99%

Integrative web-based analysis of omics data for study of drugs against SARS-CoV-2

Wang

Huang

et al. 2021

Sci Rep

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Research on drugs against SARS-CoV-2 (cause of COVID-19) has been one of the major world concerns at present. There have been abundant research data and findings in this field. The interference of drugs on gene expression in cell lines, drug-target, protein-virus receptor networks, and immune cell infiltration of the host may provide useful information for anti-SARS-CoV-2 drug research. To simplify the complex bioinformatics analysis and facilitate the evaluation of the latest research data, we developed OmiczViz (http://medcode.link/omicsviz), a web tool that has integrated drug-cell line interference data, virus-host protein–protein interactions, and drug-target interactions. To demonstrate the usages of OmiczViz, we analyzed the gene expression data from cell lines treated with chloroquine and ruxolitinib, the drug-target protein networks of 48 anti-coronavirus drugs and drugs bound with ACE2, and the profiles of immune cell infiltration between different COVID-19 patient groups. Our research shows that chloroquine had a regulatory role of the immune response in renal cell line but not in lung cell line. The anti-coronavirus drug-target network analysis suggested that antihistamine of promethaziney and dietary supplement of Zinc might be beneficial when used jointly with antiviral drugs. The immune infiltration analysis indicated that both the COVID-19 patients admitted to the ICU and the elderly with infection showed immune exhaustion status, yet with different molecular mechanisms. The interactive graphic interface of OmiczViz also makes it easier to analyze newly discovered and user-uploaded data, leading to an in-depth understanding of existing findings and an expansion of existing knowledge of SARS-CoV-2. Collectively, OmicsViz is web program that promotes the research on medical agents against SARS-CoV-2 and supports the evaluation of the latest research findings.

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A database resource and online analysis tools for coronaviruses on a historical and global scale

Cited by 19 publications

References 60 publications

Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis

Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis

Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients

Integrative web-based analysis of omics data for study of drugs against SARS-CoV-2

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