Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus
Identifieur interne : 000048 ( Ncbi/Curation ); précédent : 000047; suivant : 000049Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus
Auteurs : X. W. Zhang [République populaire de Chine] ; Y. L. Yap [République populaire de Chine] ; A. Danchin [France]Source :
- Archives of Virology [ 0304-8608 ] ; 2004.
Descripteurs français
- KwdFr :
- Alignement de séquences, Bases de données génétiques, Biologie informatique, Coronavirus (génétique), Coronavirus (physiologie), Génome viral, Phylogénie, Recombinaison génétique, Similitude de séquences d'acides aminés, Syndrome respiratoire aigu sévère (virologie), Virus du SRAS (génétique), Virus du SRAS (physiologie).
- MESH :
- génétique : Coronavirus, Virus du SRAS.
- physiologie : Coronavirus, Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- Alignement de séquences, Bases de données génétiques, Biologie informatique, Génome viral, Phylogénie, Recombinaison génétique, Similitude de séquences d'acides aminés.
English descriptors
- KwdEn :
- MESH :
- genetics : Coronavirus, SARS Virus.
- physiology : Coronavirus, SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Computational Biology, Databases, Genetic, Genome, Viral, Phylogeny, Recombination, Genetic, Sequence Alignment, Sequence Homology, Amino Acid.
Abstract
The origin of severe acute respiratory syndrome-associated corona-virus (SARS-CoV) is still a matter of speculation, although more than one year has passed since the onset of the SARS outbreak. In this study, we implemented a 3-step strategy to test the intriguing hypothesis that SARS-CoV might have been derived from a recombinant virus. First, we blasted the whole SARS-CoV genome against a virus database to search viruses of interest. Second, we employed 7 recombination detection techniques well documented in successfully detecting recombination events to explore the presence of recombination in SARS-CoV genome. Finally, we conducted phylogenetic analyses to further explore whether recombination has indeed occurred in the course of coronaviruses history predating the emergence of SARS-CoV. Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). Thus, our analyses substantiate the presence of recombination events in history that led to the SARS-CoV genome. Like the other coronaviruses used in the analysis, SARS-CoV is also a mosaic structure.
Url:
DOI: 10.1007/s00705-004-0413-9
PubMed: 15480857
PubMed Central: 7087341
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000182
- to stream Pmc, to step Curation: Pour aller vers cette notice dans l'étape Curation :000182
- to stream Pmc, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000995
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000D64
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :000D64
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000D41
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000048
Links to Exploration step
PMC:7087341Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus</title>
<author><name sortKey="Zhang, X W" sort="Zhang, X W" uniqKey="Zhang X" first="X. W." last="Zhang">X. W. Zhang</name>
<affiliation wicri:level="1"><nlm:aff id="A1"><institution-wrap><institution-id institution-id-type="GRID">grid.194645.b</institution-id>
<institution-id institution-id-type="ISNI">0000000121742757</institution-id>
<institution>HKU-Pasteur Research Centre,</institution>
</institution-wrap>
Hong Kong, P.R. China</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country>
<wicri:regionArea>Hong Kong</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Yap, Y L" sort="Yap, Y L" uniqKey="Yap Y" first="Y. L." last="Yap">Y. L. Yap</name>
<affiliation wicri:level="1"><nlm:aff id="A1"><institution-wrap><institution-id institution-id-type="GRID">grid.194645.b</institution-id>
<institution-id institution-id-type="ISNI">0000000121742757</institution-id>
<institution>HKU-Pasteur Research Centre,</institution>
</institution-wrap>
Hong Kong, P.R. China</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country>
<wicri:regionArea>Hong Kong</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Danchin, A" sort="Danchin, A" uniqKey="Danchin A" first="A." last="Danchin">A. Danchin</name>
<affiliation wicri:level="1"><nlm:aff id="A2"><institution-wrap><institution-id institution-id-type="GRID">grid.428999.7</institution-id>
<institution-id institution-id-type="ISNI">0000000123536535</institution-id>
<institution>Pasteur Institute, Unit Genetics of Bacterial Genomes,</institution>
</institution-wrap>
Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Paris</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">15480857</idno>
<idno type="pmc">7087341</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087341</idno>
<idno type="RBID">PMC:7087341</idno>
<idno type="doi">10.1007/s00705-004-0413-9</idno>
<date when="2004">2004</date>
<idno type="wicri:Area/Pmc/Corpus">000182</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000182</idno>
<idno type="wicri:Area/Pmc/Curation">000182</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000182</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000995</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000995</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:15480857</idno>
<idno type="wicri:Area/PubMed/Corpus">000D64</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D64</idno>
<idno type="wicri:Area/PubMed/Curation">000D64</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000D64</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000D41</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000D41</idno>
<idno type="wicri:Area/Ncbi/Merge">000048</idno>
<idno type="wicri:Area/Ncbi/Curation">000048</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus</title>
<author><name sortKey="Zhang, X W" sort="Zhang, X W" uniqKey="Zhang X" first="X. W." last="Zhang">X. W. Zhang</name>
<affiliation wicri:level="1"><nlm:aff id="A1"><institution-wrap><institution-id institution-id-type="GRID">grid.194645.b</institution-id>
<institution-id institution-id-type="ISNI">0000000121742757</institution-id>
<institution>HKU-Pasteur Research Centre,</institution>
</institution-wrap>
Hong Kong, P.R. China</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country>
<wicri:regionArea>Hong Kong</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Yap, Y L" sort="Yap, Y L" uniqKey="Yap Y" first="Y. L." last="Yap">Y. L. Yap</name>
<affiliation wicri:level="1"><nlm:aff id="A1"><institution-wrap><institution-id institution-id-type="GRID">grid.194645.b</institution-id>
<institution-id institution-id-type="ISNI">0000000121742757</institution-id>
<institution>HKU-Pasteur Research Centre,</institution>
</institution-wrap>
Hong Kong, P.R. China</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country>
<wicri:regionArea>Hong Kong</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Danchin, A" sort="Danchin, A" uniqKey="Danchin A" first="A." last="Danchin">A. Danchin</name>
<affiliation wicri:level="1"><nlm:aff id="A2"><institution-wrap><institution-id institution-id-type="GRID">grid.428999.7</institution-id>
<institution-id institution-id-type="ISNI">0000000123536535</institution-id>
<institution>Pasteur Institute, Unit Genetics of Bacterial Genomes,</institution>
</institution-wrap>
Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Paris</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Archives of Virology</title>
<idno type="ISSN">0304-8608</idno>
<idno type="eISSN">1432-8798</idno>
<imprint><date when="2004">2004</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology</term>
<term>Coronavirus (genetics)</term>
<term>Coronavirus (physiology)</term>
<term>Databases, Genetic</term>
<term>Genome, Viral</term>
<term>Phylogeny</term>
<term>Recombination, Genetic</term>
<term>SARS Virus (genetics)</term>
<term>SARS Virus (physiology)</term>
<term>Sequence Alignment</term>
<term>Sequence Homology, Amino Acid</term>
<term>Severe Acute Respiratory Syndrome (virology)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences</term>
<term>Bases de données génétiques</term>
<term>Biologie informatique</term>
<term>Coronavirus (génétique)</term>
<term>Coronavirus (physiologie)</term>
<term>Génome viral</term>
<term>Phylogénie</term>
<term>Recombinaison génétique</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Syndrome respiratoire aigu sévère (virologie)</term>
<term>Virus du SRAS (génétique)</term>
<term>Virus du SRAS (physiologie)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term>
<term>SARS Virus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term>
<term>Virus du SRAS</term>
</keywords>
<keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Coronavirus</term>
<term>Virus du SRAS</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Coronavirus</term>
<term>SARS Virus</term>
</keywords>
<keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term>
<term>Databases, Genetic</term>
<term>Genome, Viral</term>
<term>Phylogeny</term>
<term>Recombination, Genetic</term>
<term>Sequence Alignment</term>
<term>Sequence Homology, Amino Acid</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term>
<term>Bases de données génétiques</term>
<term>Biologie informatique</term>
<term>Génome viral</term>
<term>Phylogénie</term>
<term>Recombinaison génétique</term>
<term>Similitude de séquences d'acides aminés</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><title>Summary.</title>
<p>The origin of severe acute respiratory syndrome-associated corona-virus (SARS-CoV) is still a matter of speculation, although more than one year has passed since the onset of the SARS outbreak. In this study, we implemented a 3-step strategy to test the intriguing hypothesis that SARS-CoV might have been derived from a recombinant virus. First, we blasted the whole SARS-CoV genome against a virus database to search viruses of interest. Second, we employed 7 recombination detection techniques well documented in successfully detecting recombination events to explore the presence of recombination in SARS-CoV genome. Finally, we conducted phylogenetic analyses to further explore whether recombination has indeed occurred in the course of coronaviruses history predating the emergence of SARS-CoV. Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). Thus, our analyses substantiate the presence of recombination events in history that led to the SARS-CoV genome. Like the other coronaviruses used in the analysis, SARS-CoV is also a mosaic structure.</p>
</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000048 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 000048 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Sante |area= CovidV2 |flux= Ncbi |étape= Curation |type= RBID |clé= PMC:7087341 |texte= Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:15480857" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \ | NlmPubMed2Wicri -a CovidV2
This area was generated with Dilib version V0.6.33. |