Full-genome sequences of the first two SARS-CoV-2 viruses from India.
Identifieur interne : 000376 ( PubMed/Corpus ); précédent : 000375; suivant : 000377Full-genome sequences of the first two SARS-CoV-2 viruses from India.
Auteurs : Pragya D. Yadav ; Varsha A. Potdar ; Manohar Lal Choudhary ; Dimpal A. Nyayanit ; Megha Agrawal ; Santosh M. Jadhav ; Triparna D. Majumdar ; Anita Shete-Aich ; Atanu Basu ; Priya Abraham ; Sarah S. CherianSource :
- The Indian journal of medical research [ 0971-5916 ] ; 2020.
Abstract
: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.
DOI: 10.4103/ijmr.IJMR_663_20
PubMed: 32242873
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Full-genome sequences of the first two SARS-CoV-2 viruses from India.</title><author><name sortKey="Yadav, Pragya D" sort="Yadav, Pragya D" uniqKey="Yadav P" first="Pragya D" last="Yadav">Pragya D. Yadav</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Potdar, Varsha A" sort="Potdar, Varsha A" uniqKey="Potdar V" first="Varsha A" last="Potdar">Varsha A. Potdar</name><affiliation><nlm:affiliation>Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Choudhary, Manohar Lal" sort="Choudhary, Manohar Lal" uniqKey="Choudhary M" first="Manohar Lal" last="Choudhary">Manohar Lal Choudhary</name><affiliation><nlm:affiliation>Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Nyayanit, Dimpal A" sort="Nyayanit, Dimpal A" uniqKey="Nyayanit D" first="Dimpal A" last="Nyayanit">Dimpal A. Nyayanit</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Agrawal, Megha" sort="Agrawal, Megha" uniqKey="Agrawal M" first="Megha" last="Agrawal">Megha Agrawal</name><affiliation><nlm:affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Jadhav, Santosh M" sort="Jadhav, Santosh M" uniqKey="Jadhav S" first="Santosh M" last="Jadhav">Santosh M. Jadhav</name><affiliation><nlm:affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Majumdar, Triparna D" sort="Majumdar, Triparna D" uniqKey="Majumdar T" first="Triparna D" last="Majumdar">Triparna D. Majumdar</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Shete Aich, Anita" sort="Shete Aich, Anita" uniqKey="Shete Aich A" first="Anita" last="Shete-Aich">Anita Shete-Aich</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Basu, Atanu" sort="Basu, Atanu" uniqKey="Basu A" first="Atanu" last="Basu">Atanu Basu</name><affiliation><nlm:affiliation>Electron Microscopy, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Abraham, Priya" sort="Abraham, Priya" uniqKey="Abraham P" first="Priya" last="Abraham">Priya Abraham</name><affiliation><nlm:affiliation>ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Cherian, Sarah S" sort="Cherian, Sarah S" uniqKey="Cherian S" first="Sarah S" last="Cherian">Sarah S. Cherian</name><affiliation><nlm:affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32242873</idno><idno type="pmid">32242873</idno><idno type="doi">10.4103/ijmr.IJMR_663_20</idno><idno type="wicri:Area/PubMed/Corpus">000376</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000376</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Full-genome sequences of the first two SARS-CoV-2 viruses from India.</title><author><name sortKey="Yadav, Pragya D" sort="Yadav, Pragya D" uniqKey="Yadav P" first="Pragya D" last="Yadav">Pragya D. Yadav</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Potdar, Varsha A" sort="Potdar, Varsha A" uniqKey="Potdar V" first="Varsha A" last="Potdar">Varsha A. Potdar</name><affiliation><nlm:affiliation>Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Choudhary, Manohar Lal" sort="Choudhary, Manohar Lal" uniqKey="Choudhary M" first="Manohar Lal" last="Choudhary">Manohar Lal Choudhary</name><affiliation><nlm:affiliation>Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Nyayanit, Dimpal A" sort="Nyayanit, Dimpal A" uniqKey="Nyayanit D" first="Dimpal A" last="Nyayanit">Dimpal A. Nyayanit</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Agrawal, Megha" sort="Agrawal, Megha" uniqKey="Agrawal M" first="Megha" last="Agrawal">Megha Agrawal</name><affiliation><nlm:affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Jadhav, Santosh M" sort="Jadhav, Santosh M" uniqKey="Jadhav S" first="Santosh M" last="Jadhav">Santosh M. Jadhav</name><affiliation><nlm:affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Majumdar, Triparna D" sort="Majumdar, Triparna D" uniqKey="Majumdar T" first="Triparna D" last="Majumdar">Triparna D. Majumdar</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Shete Aich, Anita" sort="Shete Aich, Anita" uniqKey="Shete Aich A" first="Anita" last="Shete-Aich">Anita Shete-Aich</name><affiliation><nlm:affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Basu, Atanu" sort="Basu, Atanu" uniqKey="Basu A" first="Atanu" last="Basu">Atanu Basu</name><affiliation><nlm:affiliation>Electron Microscopy, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Abraham, Priya" sort="Abraham, Priya" uniqKey="Abraham P" first="Priya" last="Abraham">Priya Abraham</name><affiliation><nlm:affiliation>ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author><author><name sortKey="Cherian, Sarah S" sort="Cherian, Sarah S" uniqKey="Cherian S" first="Sarah S" last="Cherian">Sarah S. Cherian</name><affiliation><nlm:affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</nlm:affiliation></affiliation></author></analytic><series><title level="j">The Indian journal of medical research</title><idno type="ISSN">0971-5916</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32242873</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0971-5916</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Mar</Month><Day>27</Day></PubDate></JournalIssue><Title>The Indian journal of medical research</Title><ISOAbbreviation>Indian J. Med. Res.</ISOAbbreviation></Journal><ArticleTitle>Full-genome sequences of the first two SARS-CoV-2 viruses from India.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.4103/ijmr.IJMR_663_20</ELocationID><Abstract><AbstractText Label="Background & objectives" NlmCategory="UNASSIGNED">: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.</AbstractText><AbstractText Label="Methods" NlmCategory="UNASSIGNED">: Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.</AbstractText><AbstractText Label="Results" NlmCategory="UNASSIGNED">: Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.</AbstractText><AbstractText Label="Interpretation & conclusions" NlmCategory="UNASSIGNED">: The two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yadav</LastName><ForeName>Pragya D</ForeName><Initials>PD</Initials><AffiliationInfo><Affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Potdar</LastName><ForeName>Varsha A</ForeName><Initials>VA</Initials><AffiliationInfo><Affiliation>Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Choudhary</LastName><ForeName>Manohar Lal</ForeName><Initials>ML</Initials><AffiliationInfo><Affiliation>Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nyayanit</LastName><ForeName>Dimpal A</ForeName><Initials>DA</Initials><AffiliationInfo><Affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Agrawal</LastName><ForeName>Megha</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jadhav</LastName><ForeName>Santosh M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Majumdar</LastName><ForeName>Triparna D</ForeName><Initials>TD</Initials><AffiliationInfo><Affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shete-Aich</LastName><ForeName>Anita</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Basu</LastName><ForeName>Atanu</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Electron Microscopy, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Abraham</LastName><ForeName>Priya</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cherian</LastName><ForeName>Sarah S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>India</Country><MedlineTA>Indian J Med Res</MedlineTA><NlmUniqueID>0374701</NlmUniqueID><ISSNLinking>0971-5916</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Epitope - genomes - India - Kerala - next-generation sequencing - phylogeny - real-time reverse transcription-polymerase chain reaction - severe acute respiratory syndrome coronavirus 2</Keyword></KeywordList><CoiStatement>None</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32242873</ArticleId><ArticleId IdType="pii">281471</ArticleId><ArticleId IdType="doi">10.4103/ijmr.IJMR_663_20</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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