Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens
Identifieur interne : 000F31 ( Pmc/Checkpoint ); précédent : 000F30; suivant : 000F32Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens
Auteurs : Wendy Mok [Canada] ; Kelly Seto [Canada] ; Jon Stone [Canada]Source :
- Evolutionary Bioinformatics Online [ 1176-9343 ] ; 2007.
Abstract
Researchers routinely adopt molecular clock assumptions in conducting sequence analyses to estimate dates for viral origins in humans. We used computational methods to examine the extent to which this practice can result in inaccurate ‘retrodiction.’ Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance.
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PubMed: 19461973
PubMed Central: 2684125
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wicri:level="4"><nlm:aff id="af2-ebo-03-263">Department of Molecular and Medical Genetics, University of Toronto, 1 King’s College Circle, Toronto ON M5S 1A8, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Department of Molecular and Medical Genetics, University of Toronto, 1 King’s College Circle, Toronto ON M5S 1A8</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Stone, Jon" sort="Stone, Jon" uniqKey="Stone J" first="Jon" last="Stone">Jon Stone</name><affiliation wicri:level="4"><nlm:aff id="af3-ebo-03-263">Department of Biology and Origins Institute, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Department of Biology and Origins Institute, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1</wicri:regionArea><orgName type="university">Université McMaster</orgName><placeName><settlement type="city">Hamilton (Ontario)</settlement><region type="state">Ontario</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19461973</idno><idno type="pmc">2684125</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684125</idno><idno type="RBID">PMC:2684125</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">001960</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001960</idno><idno type="wicri:Area/Pmc/Curation">001960</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001960</idno><idno type="wicri:Area/Pmc/Checkpoint">000F31</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000F31</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Non-Molecular-Clock-Like Evolution following Viral Origins in <italic>Homo sapiens</italic></title><author><name sortKey="Mok, Wendy" sort="Mok, Wendy" uniqKey="Mok W" first="Wendy" last="Mok">Wendy Mok</name><affiliation wicri:level="4"><nlm:aff id="af1-ebo-03-263">Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1</wicri:regionArea><orgName type="university">Université McMaster</orgName><placeName><settlement type="city">Hamilton (Ontario)</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Seto, Kelly" sort="Seto, Kelly" uniqKey="Seto K" first="Kelly" last="Seto">Kelly Seto</name><affiliation wicri:level="4"><nlm:aff id="af2-ebo-03-263">Department of Molecular and Medical Genetics, University of Toronto, 1 King’s College Circle, Toronto ON M5S 1A8, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Department of Molecular and Medical Genetics, University of Toronto, 1 King’s College Circle, Toronto ON M5S 1A8</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Stone, Jon" sort="Stone, Jon" uniqKey="Stone J" first="Jon" last="Stone">Jon Stone</name><affiliation wicri:level="4"><nlm:aff id="af3-ebo-03-263">Department of Biology and Origins Institute, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Department of Biology and Origins Institute, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1</wicri:regionArea><orgName type="university">Université McMaster</orgName><placeName><settlement type="city">Hamilton (Ontario)</settlement><region type="state">Ontario</region></placeName></affiliation></author></analytic><series><title level="j">Evolutionary Bioinformatics Online</title><idno type="eISSN">1176-9343</idno><imprint><date when="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Researchers routinely adopt molecular clock assumptions in conducting sequence analyses to estimate dates for viral origins in humans. We used computational methods to examine the extent to which this practice can result in inaccurate ‘retrodiction.’ Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc xml:lang="EN" article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Evol Bioinform Online</journal-id><journal-id journal-id-type="publisher-id">101256319</journal-id><journal-title>Evolutionary Bioinformatics Online</journal-title><issn pub-type="epub">1176-9343</issn><publisher><publisher-name>Libertas Academica</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19461973</article-id><article-id pub-id-type="pmc">2684125</article-id><article-id pub-id-type="publisher-id">ebo-03-263</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Research</subject></subj-group></article-categories><title-group><article-title>Non-Molecular-Clock-Like Evolution following Viral Origins in <italic>Homo sapiens</italic></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Mok</surname><given-names>Wendy</given-names></name><xref ref-type="aff" rid="af1-ebo-03-263">1</xref></contrib><contrib contrib-type="author"><name><surname>Seto</surname><given-names>Kelly</given-names></name><xref ref-type="aff" rid="af2-ebo-03-263">2</xref></contrib><contrib contrib-type="author"><name><surname>Stone</surname><given-names>Jon</given-names></name><xref ref-type="aff" rid="af3-ebo-03-263">3</xref><xref ref-type="corresp" rid="c1-ebo-03-263"></xref></contrib></contrib-group><aff id="af1-ebo-03-263"><label>1</label>Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1, Canada.</aff><aff id="af2-ebo-03-263"><label>2</label>Department of Molecular and Medical Genetics, University of Toronto, 1 King’s College Circle, Toronto ON M5S 1A8, Canada.</aff><aff id="af3-ebo-03-263"><label>3</label>Department of Biology and Origins Institute, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1, Canada.</aff><author-notes><corresp id="c1-ebo-03-263">Correspondence: Jon Stone, Department of Biology, McMaster University, 1280 Main Street West, Hamilton ON L8S 4K1, Canada. Tel: 001-905-525-9140 (+26136); Email:
<email>jstoner@mcmaster.ca</email></corresp></author-notes><pub-date pub-type="collection"><year>2007</year></pub-date><pub-date pub-type="epub"><day>26</day><month>9</month><year>2007</year></pub-date><volume>3</volume><fpage>263</fpage><lpage>266</lpage><permissions><copyright-statement>Copyright © 2007 The authors.</copyright-statement><copyright-year>2007</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0"><p><pmc-comment>CREATIVE COMMONS</pmc-comment>This article is published under the Creative Commons Attribution By licence. For further information go to: <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0">http://creativecommons.org/licenses/by/3.0.</ext-link></p></license></permissions><abstract><p>Researchers routinely adopt molecular clock assumptions in conducting sequence analyses to estimate dates for viral origins in humans. We used computational methods to examine the extent to which this practice can result in inaccurate ‘retrodiction.’ Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance.</p></abstract><kwd-group><kwd>computational biology</kwd><kwd>epidemic</kwd><kwd>mutation</kwd><kwd>virus</kwd><kwd>SARS-CoV</kwd></kwd-group></article-meta></front><floats-wrap><fig id="f1-ebo-03-263" position="float"><label>Figure 1.</label><caption><p>Quantifying Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) sequence modification over time. The points represent nucleotide substitution rates r among 51 SARS-CoV sequences obtained between November 2002 and March 2003, inferred on the basis of a recently published phylogenetic tree (<xref ref-type="bibr" rid="b4-ebo-03-263">He et al. 2004</xref>). The upper and lower points at t = 0 represent r (civet sequence SZ16, human sequence GZ02) and r (human sequence GZ02, human sequence GD01), respectively. The curve is a gamma distribution function that is similar to the gamma distribution function that was used in computer simulations. t = time (days since estimated initial transmission from civets to humans); r = sequence divergence rate (substitutions per site per evolutionary step).</p></caption><graphic xlink:href="EBO-03-263-g001"></graphic></fig><fig id="f2-ebo-03-263" position="float"><label>Figure 2.</label><caption><p>Estimated origin times for Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in humans. The distribution was obtained using a computer simulation program that evolved virtually on the basis of a recently published phylogenetic tree (<xref ref-type="bibr" rid="b4-ebo-03-263">He et al. 2004</xref>) 51 SARS-CoV sequences (1000 replicates); performed a linear regression involving divergence times and genetic distances from a hypothetical ancestor; and extrapolated backward to 0 divergence to obtain estimated origin times t.</p></caption><graphic xlink:href="EBO-03-263-g002"></graphic></fig></floats-wrap></pmc><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Hamilton (Ontario)</li><li>Toronto</li></settlement><orgName><li>Université McMaster</li><li>Université de Toronto</li></orgName></list><tree><country name="Canada"><region name="Ontario"><name sortKey="Mok, Wendy" sort="Mok, Wendy" uniqKey="Mok W" first="Wendy" last="Mok">Wendy Mok</name></region><name sortKey="Seto, Kelly" sort="Seto, Kelly" uniqKey="Seto K" first="Kelly" last="Seto">Kelly Seto</name><name sortKey="Stone, Jon" sort="Stone, Jon" uniqKey="Stone J" first="Jon" last="Stone">Jon Stone</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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