Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event.
Identifieur interne : 000586 ( PubMed/Curation ); précédent : 000585; suivant : 000587Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event.
Auteurs : D. Paraskevis [Grèce] ; E G Kostaki [Grèce] ; G. Magiorkinis [Grèce] ; G. Panayiotakopoulos [Grèce] ; G. Sourvinos [Grèce] ; S. Tsiodras [Grèce]Source :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [ 1567-7257 ] ; 2020.
Abstract
A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.
DOI: 10.1016/j.meegid.2020.104212
PubMed: 32004758
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Electronic address: dparask@med.uoa.gr.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author><author><name sortKey="Kostaki, E G" sort="Kostaki, E G" uniqKey="Kostaki E" first="E G" last="Kostaki">E G Kostaki</name><affiliation wicri:level="1"><nlm:affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author><author><name sortKey="Magiorkinis, G" sort="Magiorkinis, G" uniqKey="Magiorkinis G" first="G" last="Magiorkinis">G. Magiorkinis</name><affiliation wicri:level="1"><nlm:affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author><author><name sortKey="Panayiotakopoulos, G" sort="Panayiotakopoulos, G" uniqKey="Panayiotakopoulos G" first="G" last="Panayiotakopoulos">G. Panayiotakopoulos</name><affiliation wicri:level="1"><nlm:affiliation>National Public Health Organization (NPHO), Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>National Public Health Organization (NPHO), Athens</wicri:regionArea></affiliation></author><author><name sortKey="Sourvinos, G" sort="Sourvinos, G" uniqKey="Sourvinos G" first="G" last="Sourvinos">G. Sourvinos</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion</wicri:regionArea></affiliation></author><author><name sortKey="Tsiodras, S" sort="Tsiodras, S" uniqKey="Tsiodras S" first="S" last="Tsiodras">S. Tsiodras</name><affiliation wicri:level="1"><nlm:affiliation>Medical School, National and Kapodistrian University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32004758</idno><idno type="pmid">32004758</idno><idno type="doi">10.1016/j.meegid.2020.104212</idno><idno type="wicri:Area/PubMed/Corpus">000586</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000586</idno><idno type="wicri:Area/PubMed/Curation">000586</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000586</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event.</title><author><name sortKey="Paraskevis, D" sort="Paraskevis, D" uniqKey="Paraskevis D" first="D" last="Paraskevis">D. Paraskevis</name><affiliation wicri:level="1"><nlm:affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece. Electronic address: dparask@med.uoa.gr.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author><author><name sortKey="Kostaki, E G" sort="Kostaki, E G" uniqKey="Kostaki E" first="E G" last="Kostaki">E G Kostaki</name><affiliation wicri:level="1"><nlm:affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author><author><name sortKey="Magiorkinis, G" sort="Magiorkinis, G" uniqKey="Magiorkinis G" first="G" last="Magiorkinis">G. Magiorkinis</name><affiliation wicri:level="1"><nlm:affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author><author><name sortKey="Panayiotakopoulos, G" sort="Panayiotakopoulos, G" uniqKey="Panayiotakopoulos G" first="G" last="Panayiotakopoulos">G. Panayiotakopoulos</name><affiliation wicri:level="1"><nlm:affiliation>National Public Health Organization (NPHO), Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>National Public Health Organization (NPHO), Athens</wicri:regionArea></affiliation></author><author><name sortKey="Sourvinos, G" sort="Sourvinos, G" uniqKey="Sourvinos G" first="G" last="Sourvinos">G. Sourvinos</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion</wicri:regionArea></affiliation></author><author><name sortKey="Tsiodras, S" sort="Tsiodras, S" uniqKey="Tsiodras S" first="S" last="Tsiodras">S. Tsiodras</name><affiliation wicri:level="1"><nlm:affiliation>Medical School, National and Kapodistrian University of Athens, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea></affiliation></author></analytic><series><title level="j">Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</title><idno type="eISSN">1567-7257</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">A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32004758</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1567-7257</ISSN><JournalIssue CitedMedium="Internet"><Volume>79</Volume><PubDate><Year>2020</Year><Month>04</Month></PubDate></JournalIssue><Title>Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</Title><ISOAbbreviation>Infect. Genet. Evol.</ISOAbbreviation></Journal><ArticleTitle>Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event.</ArticleTitle><Pagination><MedlinePgn>104212</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1567-1348(20)30044-7</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.meegid.2020.104212</ELocationID><Abstract><AbstractText Label="BACKGROUND">A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.</AbstractText><AbstractText Label="METHODS">Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods.</AbstractText><AbstractText Label="RESULTS">Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5'-part spanning the first 11,498 nucleotides and the last 3'-part spanning 24,341-30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3'-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch.</AbstractText><AbstractText Label="CONCLUSIONS">The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Paraskevis</LastName><ForeName>D</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece. Electronic address: dparask@med.uoa.gr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kostaki</LastName><ForeName>E G</ForeName><Initials>EG</Initials><AffiliationInfo><Affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magiorkinis</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Panayiotakopoulos</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>National Public Health Organization (NPHO), Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sourvinos</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tsiodras</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Medical School, National and Kapodistrian University of Athens, Athens, Greece.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Infect Genet Evol</MedlineTA><NlmUniqueID>101084138</NlmUniqueID><ISSNLinking>1567-1348</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Genomic sequence analysis</Keyword><Keyword MajorTopicYN="Y">Molecular epidemiology</Keyword><Keyword MajorTopicYN="Y">Novel coronavirus</Keyword><Keyword MajorTopicYN="Y">Origin</Keyword><Keyword MajorTopicYN="Y">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="Y">Recombination</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest All authors report no conflict of interest related to the submitted work.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>01</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>01</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32004758</ArticleId><ArticleId IdType="pii">S1567-1348(20)30044-7</ArticleId><ArticleId IdType="doi">10.1016/j.meegid.2020.104212</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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