Differential stepwise evolution of SARS coronavirus functional proteins in different host species
Identifieur interne : 000D31 ( Pmc/Checkpoint ); précédent : 000D30; suivant : 000D32Differential stepwise evolution of SARS coronavirus functional proteins in different host species
Auteurs : Xianchun Tang [République populaire de Chine, États-Unis] ; Gang Li [République populaire de Chine] ; Nikos Vasilakis [États-Unis] ; Yuan Zhang [République populaire de Chine] ; Zhengli Shi [République populaire de Chine] ; Yang Zhong [République populaire de Chine] ; Lin-Fa Wang [République populaire de Chine] ; Shuyi Zhang [République populaire de Chine]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2009.
Abstract
SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known.
We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified.
This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events.
The online version of this article (doi:10.1186/1471-2148-9-52) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2148-9-52
PubMed: 19261195
PubMed Central: 2676248
Affiliations:
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wicri:step="Checkpoint">000D31</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Differential stepwise evolution of SARS coronavirus functional proteins in different host species</title><author><name sortKey="Tang, Xianchun" sort="Tang, Xianchun" uniqKey="Tang X" first="Xianchun" last="Tang">Xianchun Tang</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.22069.3f</institution-id><institution-id institution-id-type="ISNI">0000000403696365</institution-id><institution>School of Life Science,</institution><institution>East China Normal University,</institution></institution-wrap>Shanghai, 200062 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.21925.3d</institution-id><institution-id institution-id-type="ISNI">0000000419369000</institution-id><institution>Present Address: Center for Vaccine Research,</institution><institution>University of Pittsburgh,</institution></institution-wrap>Pennsylvania, 15261 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Pennsylvania</wicri:regionArea></affiliation></author><author><name sortKey="Li, Gang" sort="Li, Gang" uniqKey="Li G" first="Gang" last="Li">Gang Li</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.22069.3f</institution-id><institution-id institution-id-type="ISNI">0000000403696365</institution-id><institution>School of Life Science,</institution><institution>East China Normal University,</institution></institution-wrap>Shanghai, 200062 PR China</nlm:aff><country xml:lang="fr">République populaire de 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institution-id-type="ISNI">0000000101252443</institution-id><institution>School of Life Sciences,</institution><institution>Fudan University,</institution></institution-wrap>Shanghai, 200433 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai</wicri:regionArea></affiliation></author><author><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><affiliation wicri:level="1"><nlm:aff id="Aff4"><institution-wrap><institution-id institution-id-type="GRID">grid.9227.e</institution-id><institution-id institution-id-type="ISNI">0000000119573309</institution-id><institution>Institute of Virology,</institution><institution>Chinese Academy of Sciences,</institution></institution-wrap>Wuhan, 430071 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Wuhan</wicri:regionArea></affiliation></author><author><name sortKey="Zhong, Yang" sort="Zhong, 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institution-id-type="GRID">grid.22069.3f</institution-id><institution-id institution-id-type="ISNI">0000000403696365</institution-id><institution>School of Life Science,</institution><institution>East China Normal University,</institution></institution-wrap>Shanghai, 200062 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known.</p></sec><sec><title>Results</title><p>We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified.</p></sec><sec><title>Conclusion</title><p>This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2148-9-52) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Peiris, Js" uniqKey="Peiris J">JS Peiris</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y Guan</name></author><author><name sortKey="Yuen, Ky" uniqKey="Yuen K">KY Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ksiazek, Tg" uniqKey="Ksiazek T">TG Ksiazek</name></author><author><name sortKey="Erdman, D" uniqKey="Erdman D">D Erdman</name></author><author><name sortKey="Goldsmith, Cs" uniqKey="Goldsmith C">CS Goldsmith</name></author><author><name sortKey="Zaki, Sr" uniqKey="Zaki 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Evol Biol</journal-id><journal-id journal-id-type="iso-abbrev">BMC Evol. Biol</journal-id><journal-title-group><journal-title>BMC Evolutionary Biology</journal-title></journal-title-group><issn pub-type="epub">1471-2148</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19261195</article-id><article-id pub-id-type="pmc">2676248</article-id><article-id pub-id-type="publisher-id">966</article-id><article-id pub-id-type="doi">10.1186/1471-2148-9-52</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Differential stepwise evolution of SARS coronavirus functional proteins in different host species</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tang</surname><given-names>Xianchun</given-names></name><address><email>xtang@pitt.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Gang</given-names></name><address><email>li_gang1978@yahoo.com.cn</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Vasilakis</surname><given-names>Nikos</given-names></name><address><email>vasilan@pitt.edu</email></address><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Yuan</given-names></name><address><email>yuanzhang5@fudan.edu.cn</email></address><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Shi</surname><given-names>Zhengli</given-names></name><address><email>zlshi@wh.iov.cn</email></address><xref ref-type="aff" rid="Aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Zhong</surname><given-names>Yang</given-names></name><address><email>yangzhong@fudan.edu.cn</email></address><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Lin-Fa</given-names></name><address><email>linfa.wang@csiro.au</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff5">5</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Zhang</surname><given-names>Shuyi</given-names></name><address><email>syzhang@bio.ecnu.edu.cn</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="GRID">grid.22069.3f</institution-id><institution-id institution-id-type="ISNI">0000000403696365</institution-id><institution>School of Life Science,</institution><institution>East China Normal University,</institution></institution-wrap>Shanghai, 200062 PR China</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="GRID">grid.21925.3d</institution-id><institution-id institution-id-type="ISNI">0000000419369000</institution-id><institution>Present Address: Center for Vaccine Research,</institution><institution>University of Pittsburgh,</institution></institution-wrap>Pennsylvania, 15261 USA</aff><aff id="Aff3"><label>3</label><institution-wrap><institution-id institution-id-type="GRID">grid.8547.e</institution-id><institution-id institution-id-type="ISNI">0000000101252443</institution-id><institution>School of Life Sciences,</institution><institution>Fudan University,</institution></institution-wrap>Shanghai, 200433 PR China</aff><aff id="Aff4"><label>4</label><institution-wrap><institution-id institution-id-type="GRID">grid.9227.e</institution-id><institution-id institution-id-type="ISNI">0000000119573309</institution-id><institution>Institute of Virology,</institution><institution>Chinese Academy of Sciences,</institution></institution-wrap>Wuhan, 430071 PR China</aff><aff id="Aff5"><label>5</label><institution-wrap><institution-id institution-id-type="GRID">grid.413322.5</institution-id><institution-id institution-id-type="ISNI">0000000121888254</institution-id><institution>CSIRO Livestock Industries,</institution><institution>Australian Animal Health Laboratory and Australian Biosecurity Cooperative Research Centre,</institution></institution-wrap>Geelong, Victoria 3220 Australia</aff></contrib-group><pub-date pub-type="epub"><day>05</day><month>03</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>05</day><month>03</month><year>2009</year></pub-date><pub-date pub-type="collection"><year>2009</year></pub-date><volume>9</volume><elocation-id>52</elocation-id><history><date date-type="received"><day>23</day><month>09</month><year>2008</year></date><date date-type="accepted"><day>05</day><month>03</month><year>2009</year></date></history><permissions><copyright-statement>© Tang et al; licensee BioMed Central Ltd. 2009</copyright-statement><license><license-p>This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known.</p></sec><sec><title>Results</title><p>We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified.</p></sec><sec><title>Conclusion</title><p>This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2148-9-52) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Severe Acute Respiratory Syndrome</kwd><kwd>Severe Acute Respiratory Syndrome</kwd><kwd>Receptor Binding Domain</kwd><kwd>Strong Positive Selection</kwd><kwd>Severe Acute Respiratory Syndrome Coronavirus</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2009</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Tang, Xianchun" sort="Tang, Xianchun" uniqKey="Tang X" first="Xianchun" last="Tang">Xianchun Tang</name></noRegion><name sortKey="Li, Gang" sort="Li, Gang" uniqKey="Li G" first="Gang" last="Li">Gang Li</name><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><name sortKey="Wang, Lin Fa" sort="Wang, Lin Fa" uniqKey="Wang L" first="Lin-Fa" last="Wang">Lin-Fa Wang</name><name sortKey="Zhang, Shuyi" sort="Zhang, Shuyi" uniqKey="Zhang S" first="Shuyi" last="Zhang">Shuyi Zhang</name><name sortKey="Zhang, Yuan" sort="Zhang, Yuan" uniqKey="Zhang Y" first="Yuan" last="Zhang">Yuan Zhang</name><name sortKey="Zhong, Yang" sort="Zhong, Yang" uniqKey="Zhong Y" first="Yang" last="Zhong">Yang Zhong</name></country><country name="États-Unis"><noRegion><name sortKey="Tang, Xianchun" sort="Tang, Xianchun" uniqKey="Tang X" first="Xianchun" last="Tang">Xianchun Tang</name></noRegion><name sortKey="Vasilakis, Nikos" sort="Vasilakis, Nikos" uniqKey="Vasilakis N" first="Nikos" last="Vasilakis">Nikos Vasilakis</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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