Differential stepwise evolution of SARS coronavirus functional proteins in different host species
Identifieur interne : 002B38 ( Main/Exploration ); précédent : 002B37; suivant : 002B39Differential 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.
Descripteurs français
- KwdFr :
- ARN viral (génétique), Alignement de séquences, Analyse de séquence d'ARN, Animaux, Chiroptera (virologie), Glycoprotéine de spicule des coronavirus, Glycoprotéines membranaires (génétique), Humains, Modèles génétiques, Phylogénie, Protéines de l'enveloppe virale (génétique), RNA replicase (génétique), Spécificité d'espèce, Syndrome respiratoire aigu sévère (virologie), Sélection génétique, Virus du SRAS (génétique), Évolution moléculaire.
- MESH :
- génétique : ARN viral, Glycoprotéines membranaires, Protéines de l'enveloppe virale, RNA replicase, Virus du SRAS.
- virologie : Chiroptera, Syndrome respiratoire aigu sévère.
- Alignement de séquences, Analyse de séquence d'ARN, Animaux, Glycoprotéine de spicule des coronavirus, Humains, Modèles génétiques, Phylogénie, Spécificité d'espèce, Sélection génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- Animals, Chiroptera (virology), Evolution, Molecular, Humans, Membrane Glycoproteins (genetics), Models, Genetic, Phylogeny, RNA Replicase (genetics), RNA, Viral (genetics), SARS Virus (genetics), Selection, Genetic, Sequence Alignment, Sequence Analysis, RNA, Severe Acute Respiratory Syndrome (virology), Species Specificity, Spike Glycoprotein, Coronavirus, Viral Envelope Proteins (genetics).
- MESH :
- chemical , genetics : Membrane Glycoproteins, RNA Replicase, RNA, Viral, Viral Envelope Proteins.
- genetics : SARS Virus.
- virology : Chiroptera, Severe Acute Respiratory Syndrome.
- Animals, Evolution, Molecular, Humans, Models, Genetic, Phylogeny, Selection, Genetic, Sequence Alignment, Sequence Analysis, RNA, Species Specificity, Spike Glycoprotein, Coronavirus.
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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id="Aff5"><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</nlm:aff><wicri:noCountry code="subfield">Victoria 3220 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Zhang, Shuyi" sort="Zhang, Shuyi" uniqKey="Zhang S" first="Shuyi" last="Zhang">Shuyi Zhang</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></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><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chiroptera (virology)</term><term>Evolution, Molecular</term><term>Humans</term><term>Membrane Glycoproteins (genetics)</term><term>Models, Genetic</term><term>Phylogeny</term><term>RNA Replicase (genetics)</term><term>RNA, Viral (genetics)</term><term>SARS Virus (genetics)</term><term>Selection, Genetic</term><term>Sequence Alignment</term><term>Sequence Analysis, RNA</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Species Specificity</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Envelope Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Alignement de séquences</term><term>Analyse de séquence d'ARN</term><term>Animaux</term><term>Chiroptera (virologie)</term><term>Glycoprotéine de spicule des coronavirus</term><term>Glycoprotéines membranaires (génétique)</term><term>Humains</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Protéines de l'enveloppe virale (génétique)</term><term>RNA replicase (génétique)</term><term>Spécificité d'espèce</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Sélection génétique</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Glycoproteins</term><term>RNA Replicase</term><term>RNA, Viral</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Glycoprotéines membranaires</term><term>Protéines de l'enveloppe virale</term><term>RNA replicase</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Chiroptera</term><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Selection, Genetic</term><term>Sequence Alignment</term><term>Sequence Analysis, RNA</term><term>Species Specificity</term><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ARN</term><term>Animaux</term><term>Glycoprotéine de spicule des coronavirus</term><term>Humains</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Spécificité d'espèce</term><term>Sélection génétique</term><term>Évolution moléculaire</term></keywords></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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uniqKey="Dong B">B Dong</name></author><author><name sortKey="Chen, B" uniqKey="Chen B">B Chen</name></author><author><name sortKey="Zhao, Z" uniqKey="Zhao Z">Z Zhao</name></author><author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Cong, Y" uniqKey="Cong Y">Y Cong</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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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