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 : 001149 ( Main/Curation ); précédent : 001148; suivant : 001150Using 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 [Royaume-Uni] ; Alan J. Hay [Royaume-Uni] ; Richard A. Goldstein [Royaume-Uni]Source :
- Journal of Molecular Evolution [ 0022-2844 ] ; 2009-10-01.
English descriptors
- KwdEn :
Abstract
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:
- https://api.istex.fr/ark:/67375/VQC-F6M5VN34-3/fulltext.pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2772961
DOI: 10.1007/s00239-009-9282-x
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000D06
- to stream Istex, to step Curation: Pour aller vers cette notice dans l'étape Curation :000D06
- to stream Istex, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000267
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000472
- to stream Pmc, to step Curation: Pour aller vers cette notice dans l'étape Curation :000472
- to stream Pmc, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000978
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000418
- to stream Ncbi, to step Curation: Pour aller vers cette notice dans l'étape Curation :000418
- to stream Ncbi, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000418
- to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :001159
Links to Exploration step
ISTEX:7771935EE3E1DD5C2B9678AD5E154D7BAC3A29A4Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus</title>
<author><name sortKey="Dos Reis, Mario" sort="Dos Reis, Mario" uniqKey="Dos Reis M" first="Mario" last="Dos Reis">Mario Dos Reis</name>
</author>
<author><name sortKey="Hay, Alan J" sort="Hay, Alan J" uniqKey="Hay A" first="Alan J." last="Hay">Alan J. Hay</name>
</author>
<author><name sortKey="Goldstein, Richard A" sort="Goldstein, Richard A" uniqKey="Goldstein R" first="Richard A." last="Goldstein">Richard A. Goldstein</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:7771935EE3E1DD5C2B9678AD5E154D7BAC3A29A4</idno>
<date when="2009" year="2009">2009</date>
<idno type="doi">10.1007/s00239-009-9282-x</idno>
<idno type="url">https://api.istex.fr/ark:/67375/VQC-F6M5VN34-3/fulltext.pdf</idno>
<idno type="wicri:Area/Istex/Corpus">000D06</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000D06</idno>
<idno type="wicri:Area/Istex/Curation">000D06</idno>
<idno type="wicri:Area/Istex/Checkpoint">000267</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000267</idno>
<idno type="wicri:doubleKey">0022-2844:2009:Dos Reis M:using:non:homogeneous</idno>
<idno type="wicri:source">PMC</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2772961</idno>
<idno type="RBID">PMC:2772961</idno>
<idno type="wicri:Area/Pmc/Corpus">000472</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000472</idno>
<idno type="wicri:Area/Pmc/Curation">000472</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000472</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000978</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000978</idno>
<idno type="wicri:Area/Ncbi/Merge">000418</idno>
<idno type="wicri:Area/Ncbi/Curation">000418</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000418</idno>
<idno type="wicri:doubleKey">0022-2844:2009:Dos Reis M:using:non:homogeneous</idno>
<idno type="wicri:Area/Main/Merge">001159</idno>
<idno type="wicri:Area/Main/Curation">001149</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus</title>
<author><name sortKey="Dos Reis, Mario" sort="Dos Reis, Mario" uniqKey="Dos Reis M" first="Mario" last="Dos Reis">Mario Dos Reis</name>
<affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The MRC National Institute for Medical Research, NW7 1AA, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><country wicri:rule="url">Royaume-Uni</country>
</affiliation>
</author>
<author><name sortKey="Hay, Alan J" sort="Hay, Alan J" uniqKey="Hay A" first="Alan J." last="Hay">Alan J. Hay</name>
<affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The MRC National Institute for Medical Research, NW7 1AA, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Goldstein, Richard A" sort="Goldstein, Richard A" uniqKey="Goldstein R" first="Richard A." last="Goldstein">Richard A. Goldstein</name>
<affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>The MRC National Institute for Medical Research, NW7 1AA, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Journal of Molecular Evolution</title>
<title level="j" type="abbrev">J Mol Evol</title>
<idno type="ISSN">0022-2844</idno>
<idno type="eISSN">1432-1432</idno>
<imprint><publisher>Springer-Verlag</publisher>
<pubPlace>New York</pubPlace>
<date type="published" when="2009-10-01">2009-10-01</date>
<biblScope unit="volume">69</biblScope>
<biblScope unit="issue">4</biblScope>
<biblScope unit="page" from="333">333</biblScope>
<biblScope unit="page" to="345">345</biblScope>
</imprint>
<idno type="ISSN">0022-2844</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">0022-2844</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>CG content</term>
<term>H1N1</term>
<term>Influenza</term>
<term>Molecular dating</term>
<term>Non-homogeneous model</term>
<term>Spanish flu</term>
<term>Swine flu</term>
</keywords>
</textClass>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/H2N2V1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001149 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 001149 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= H2N2V1 |flux= Main |étape= Curation |type= RBID |clé= ISTEX:7771935EE3E1DD5C2B9678AD5E154D7BAC3A29A4 |texte= Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus }}
![]() | This area was generated with Dilib version V0.6.33. | ![]() |