SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting
Identifieur interne : 001849 ( Pmc/Checkpoint ); précédent : 001848; suivant : 001850SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting
Auteurs : Joshua S. Rest ; David P. MindellSource :
- Infection, Genetics and Evolution [ 1567-1348 ] ; 2003.
Abstract
The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5′ fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3′ fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5′ tree could be rejected for the 3′ region, and the optimal 3′ tree could be rejected for the 5′ region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1–3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3′ RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.
Url:
DOI: 10.1016/j.meegid.2003.08.001
PubMed: 14522185
PubMed Central: 7129878
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting</title><author><name sortKey="Rest, Joshua S" sort="Rest, Joshua S" uniqKey="Rest J" first="Joshua S" last="Rest">Joshua S. Rest</name></author><author><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">14522185</idno><idno type="pmc">7129878</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129878</idno><idno type="RBID">PMC:7129878</idno><idno type="doi">10.1016/j.meegid.2003.08.001</idno><date when="2003">2003</date><idno type="wicri:Area/Pmc/Corpus">001054</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001054</idno><idno type="wicri:Area/Pmc/Curation">001054</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001054</idno><idno type="wicri:Area/Pmc/Checkpoint">001849</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001849</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting</title><author><name sortKey="Rest, Joshua S" sort="Rest, Joshua S" uniqKey="Rest J" first="Joshua S" last="Rest">Joshua S. Rest</name></author><author><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name></author></analytic><series><title level="j">Infection, Genetics and Evolution</title><idno type="ISSN">1567-1348</idno><idno type="eISSN">1567-7257</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5′ fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3′ fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5′ tree could be rejected for the 3′ region, and the optimal 3′ tree could be rejected for the 5′ region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1–3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3′ RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author><author><name sortKey="Cerruti, L" uniqKey="Cerruti L">L Cerruti</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author><author><name sortKey="Etwiller, L" uniqKey="Etwiller L">L Etwiller</name></author><author><name sortKey="Eddy, S R" uniqKey="Eddy S">S.R Eddy</name></author><author><name sortKey="Griffiths Jones, S" uniqKey="Griffiths Jones S">S Griffiths-Jones</name></author><author><name sortKey="Howe, K L" uniqKey="Howe K">K.L Howe</name></author><author><name sortKey="Marshall, M" uniqKey="Marshall 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Infect Genet Evol</journal-id><journal-id journal-id-type="iso-abbrev">Infect. Genet. Evol</journal-id><journal-title-group><journal-title>Infection, Genetics and Evolution</journal-title></journal-title-group><issn pub-type="ppub">1567-1348</issn><issn pub-type="epub">1567-7257</issn><publisher><publisher-name>Elsevier B.V.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">14522185</article-id><article-id pub-id-type="pmc">7129878</article-id><article-id pub-id-type="publisher-id">S1567-1348(03)00093-5</article-id><article-id pub-id-type="doi">10.1016/j.meegid.2003.08.001</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Rest</surname><given-names>Joshua S</given-names></name></contrib><contrib contrib-type="author"><name><surname>Mindell</surname><given-names>David P</given-names></name><email>mindell@umich.edu</email><xref rid="COR1" ref-type="corresp">∗</xref></contrib></contrib-group><aff>Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA</aff><author-notes><corresp id="COR1"><label>*</label>Corresponding author. Tel.: +1-734-647-2209; fax: +1-734-763-4080. <email>mindell@umich.edu</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>11</day><month>9</month><year>2003</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>9</month><year>2003</year></pub-date><pub-date pub-type="epub"><day>11</day><month>9</month><year>2003</year></pub-date><volume>3</volume><issue>3</issue><fpage>219</fpage><lpage>225</lpage><history><date date-type="received"><day>12</day><month>7</month><year>2003</year></date><date date-type="rev-recd"><day>21</day><month>7</month><year>2003</year></date><date date-type="accepted"><day>4</day><month>8</month><year>2003</year></date></history><permissions><copyright-statement>Copyright © 2003 Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2003</copyright-year><copyright-holder>Elsevier B.V.</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract><p>The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5′ fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3′ fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5′ tree could be rejected for the 3′ region, and the optimal 3′ tree could be rejected for the 5′ region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1–3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3′ RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.</p></abstract><kwd-group><title>Keywords</title><kwd>Severe acute respiratory syndrome</kwd><kwd>Coronavirus</kwd><kwd>SARS-CoV Nidovirales</kwd><kwd>Phylogeny</kwd><kwd>Recombination</kwd><kwd>Host-shift</kwd><kwd>RNA-dependent RNA polymerase</kwd></kwd-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name><name sortKey="Rest, Joshua S" sort="Rest, Joshua S" uniqKey="Rest J" first="Joshua S" last="Rest">Joshua S. Rest</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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