CovidFranceV1, Main, Exploration, bibRecord, 000F02

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

Identifieur interne : 000F02 ( Main/Exploration ); précédent : 000F01; suivant : 000F03

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

Auteurs : M Rafiul Islam [Bangladesh] ; M Nazmul Hoque [Bangladesh] ; M Shaminur Rahman [Bangladesh] ; A S M Rubayet Ul Alam [Bangladesh] ; Masuda Akther [Bangladesh] ; J Akter Puspo [Bangladesh] ; Salma Akter [Bangladesh] ; Munawar Sultana [Bangladesh] ; Keith A. Crandall [États-Unis] ; M Anwar Hossain [Bangladesh]

Source :

Scientific reports [ 2045-2322 ] ; 2020.

RBID : pubmed:32814791

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (genetics), Antibodies, Neutralizing (immunology), Base Pair Mismatch (MeSH), Base Sequence (genetics), Betacoronavirus (classification), Betacoronavirus (genetics), Climate (MeSH), Coronavirus Infections (epidemiology), Coronavirus Infections (virology), Genetic Heterogeneity (MeSH), Genome, Viral (genetics), Genome-Wide Association Study (methods), Global Health (MeSH), Humans (MeSH), Open Reading Frames (genetics), Pandemics (MeSH), Peptidyl-Dipeptidase A (metabolism), Phylogeny (MeSH), Pneumonia, Viral (epidemiology), Pneumonia, Viral (virology), Protein Domains (genetics), Protein Domains (immunology), Sequence Deletion (MeSH), Spike Glycoprotein, Coronavirus (chemistry), Spike Glycoprotein, Coronavirus (genetics), Spike Glycoprotein, Coronavirus (metabolism).
MESH :
- chemical , chemistry : Spike Glycoprotein, Coronavirus.
- chemical , genetics : Spike Glycoprotein, Coronavirus.
- chemical , immunology : Antibodies, Neutralizing.
- classification : Betacoronavirus.
- epidemiology : Coronavirus Infections, Pneumonia, Viral.
- genetics : Amino Acid Sequence, Base Sequence, Betacoronavirus, Genome, Viral, Open Reading Frames, Protein Domains.
- immunology : Protein Domains.
- chemical , metabolism : Peptidyl-Dipeptidase A, Spike Glycoprotein, Coronavirus.
- methods : Genome-Wide Association Study.
- virology : Coronavirus Infections, Pneumonia, Viral.
- Base Pair Mismatch, Climate, Genetic Heterogeneity, Global Health, Humans, Pandemics, Phylogeny, Sequence Deletion.

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.

DOI: 10.1038/s41598-020-70812-6
PubMed: 32814791
PubMed Central: PMC7438523

Affiliations:

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Le document en format XML

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<front><div type="abstract" xml:lang="en">Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.</div>
</front>
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<DateCompleted><Year>2020</Year>
<Month>09</Month>
<Day>09</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>09</Month>
<Day>09</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>10</Volume>
<Issue>1</Issue>
<PubDate><Year>2020</Year>
<Month>08</Month>
<Day>19</Day>
</PubDate>
</JournalIssue>
<Title>Scientific reports</Title>
<ISOAbbreviation>Sci Rep</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.</ArticleTitle>
<Pagination><MedlinePgn>14004</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-020-70812-6</ELocationID>
<Abstract><AbstractText>Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Islam</LastName>
<ForeName>M Rafiul</ForeName>
<Initials>MR</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hoque</LastName>
<ForeName>M Nazmul</ForeName>
<Initials>MN</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Rahman</LastName>
<ForeName>M Shaminur</ForeName>
<Initials>MS</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Alam</LastName>
<ForeName>A S M Rubayet Ul</ForeName>
<Initials>ASMRU</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Akther</LastName>
<ForeName>Masuda</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
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<ForeName>J Akter</ForeName>
<Initials>JA</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Akter</LastName>
<ForeName>Salma</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Sultana</LastName>
<ForeName>Munawar</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Crandall</LastName>
<ForeName>Keith A</ForeName>
<Initials>KA</Initials>
<AffiliationInfo><Affiliation>Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hossain</LastName>
<ForeName>M Anwar</ForeName>
<Initials>MA</Initials>
<AffiliationInfo><Affiliation>Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh. hossaina@du.ac.bd.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Jashore University of Science and Technology, Jashore, 7408, Bangladesh. hossaina@du.ac.bd.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2020</Year>
<Month>08</Month>
<Day>19</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Sci Rep</MedlineTA>
<NlmUniqueID>101563288</NlmUniqueID>
<ISSNLinking>2045-2322</ISSNLinking>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D057134">Antibodies, Neutralizing</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D064370">Spike Glycoprotein, Coronavirus</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C000657845">spike protein, SARS-CoV-2</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>EC 3.4.15.1</RegistryNumber>
<NameOfSubstance UI="D007703">Peptidyl-Dipeptidase A</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>EC 3.4.17.-</RegistryNumber>
<NameOfSubstance UI="C413524">angiotensin converting enzyme 2</NameOfSubstance>
</Chemical>
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<SupplMeshList><SupplMeshName Type="Disease" UI="C000657245">COVID-19</SupplMeshName>
<SupplMeshName Type="Organism" UI="C000656484">severe acute respiratory syndrome coronavirus 2</SupplMeshName>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D057134" MajorTopicYN="N">Antibodies, Neutralizing</DescriptorName>
<QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020137" MajorTopicYN="N">Base Pair Mismatch</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName>
<QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D002980" MajorTopicYN="N">Climate</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="Y">epidemiology</QualifierName>
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<MeshHeading><DescriptorName UI="D014943" MajorTopicYN="Y">Global Health</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
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<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
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<MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName>
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<MeshHeading><DescriptorName UI="D017384" MajorTopicYN="N">Sequence Deletion</DescriptorName>
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<MeshHeading><DescriptorName UI="D064370" MajorTopicYN="N">Spike Glycoprotein, Coronavirus</DescriptorName>
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Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

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