Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus
Identifieur interne : 000418 ( Ncbi/Merge ); précédent : 000417; suivant : 000419Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus
Auteurs : Mario Dos Reis ; Alan J. Hay ; Richard A. GoldsteinSource :
- Journal of Molecular Evolution [ 0022-2844 ] ; 2009.
Abstract
Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens evolving in different hosts. It has been noticed that influenza viruses show marked differences in nucleotide composition in human and avian hosts. We take advantage of this fact to identify the host shift event that led to the 1918 ‘Spanish’ influenza. This disease killed over 50 million people worldwide, ranking it as the deadliest pandemic in recorded history. Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882–1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913–1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.
Url:
DOI: 10.1007/s00239-009-9282-x
PubMed: 19787384
PubMed Central: 2772961
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<front><journal-meta><journal-id journal-id-type="nlm-ta">J Mol Evol</journal-id><journal-title>Journal of Molecular Evolution</journal-title><issn pub-type="ppub">0022-2844</issn><issn pub-type="epub">1432-1432</issn><publisher><publisher-name>Springer-Verlag</publisher-name><publisher-loc>New York</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19787384</article-id><article-id pub-id-type="pmc">2772961</article-id><article-id pub-id-type="publisher-id">9282</article-id><article-id pub-id-type="doi">10.1007/s00239-009-9282-x</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name name-style="western"><surname>dos Reis</surname><given-names>Mario</given-names></name><address><phone>+44-20-8816-2300</phone><fax>+44-20-8816-2460</fax><email>m.reis@mail.cryst.bbk.ac.uk</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name name-style="western"><surname>Hay</surname><given-names>Alan J.</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name name-style="western"><surname>Goldstein</surname><given-names>Richard A.</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><aff id="Aff1">The MRC National Institute for Medical Research, London, NW7 1AA UK</aff></contrib-group><pub-date pub-type="epub"><day>29</day><month>9</month><year>2009</year></pub-date><pub-date pub-type="ppub"><month>10</month><year>2009</year></pub-date><volume>69</volume><issue>4</issue><fpage>333</fpage><lpage>345</lpage><history><date date-type="received"><day>5</day><month>6</month><year>2009</year></date><date date-type="accepted"><day>15</day><month>9</month><year>2009</year></date></history><permissions><copyright-statement>© The Author(s) 2009</copyright-statement></permissions><abstract xml:lang="EN"><p>Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens evolving in different hosts. It has been noticed that influenza viruses show marked differences in nucleotide composition in human and avian hosts. We take advantage of this fact to identify the host shift event that led to the 1918 ‘Spanish’ influenza. This disease killed over 50 million people worldwide, ranking it as the deadliest pandemic in recorded history. Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882–1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913–1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.</p></abstract><kwd-group><title>Keywords</title><kwd>Influenza</kwd><kwd>Spanish flu</kwd><kwd>Swine flu</kwd><kwd>H1N1</kwd><kwd>Non-homogeneous model</kwd><kwd>CG content</kwd><kwd>Molecular dating</kwd></kwd-group><custom-meta-wrap><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© Springer Science+Business Media, LLC 2009</meta-value></custom-meta></custom-meta-wrap></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Dos Reis, Mario" sort="Dos Reis, Mario" uniqKey="Dos Reis M" first="Mario" last="Dos Reis">Mario Dos Reis</name><name sortKey="Goldstein, Richard A" sort="Goldstein, Richard A" uniqKey="Goldstein R" first="Richard A." last="Goldstein">Richard A. Goldstein</name><name sortKey="Hay, Alan J" sort="Hay, Alan J" uniqKey="Hay A" first="Alan J." last="Hay">Alan J. Hay</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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