Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus
Identifieur interne : 000649 ( Main/Exploration ); précédent : 000648; suivant : 000650Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus
Auteurs : R. Burke Squires [États-Unis] ; Brett E. Pickett [États-Unis] ; Sajal Das [États-Unis] ; Richard H. Scheuermann [États-Unis]Source :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [ 1567-1348 ] ; 2014.
Abstract
In 2009 a novel pandemic H1N1 influenza virus (H1N1pdm09) emerged as the first official influenza pandemic of the 21st century. Early genomic sequence analysis pointed to the swine origin of the virus. Here we report a novel computational approach to determine the evolutionary trajectory of viral sequences that uses data-driven estimations of nucleotide substitution rates to track the gradual accumulation of observed sequence alterations over time. Phylogenetic analysis and multiple sequence alignments show that sequences belonging to the resulting evolutionary trajectory of the H1N1pdm09 lineage exhibit a gradual accumulation of sequence variations and tight temporal correlations in the topological structure of the phylogenetic trees. These results suggest that our evolutionary trajectory analysis (ETA) can more effectively pinpoint the evolutionary history of viruses, including the host and geographical location traversed by each segment, when compared against either BLAST or traditional phylogenetic analysis alone.
Url:
DOI: 10.1016/j.meegid.2014.07.015
PubMed: 25064525
PubMed Central: 4257861
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000809
- to stream Pmc, to step Curation: 000809
- to stream Pmc, to step Checkpoint: 000438
- to stream Ncbi, to step Merge: 000A65
- to stream Ncbi, to step Curation: 000A65
- to stream Ncbi, to step Checkpoint: 000A65
- to stream Main, to step Merge: 000650
- to stream Main, to step Curation: 000649
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus</title>
<author><name sortKey="Squires, R Burke" sort="Squires, R Burke" uniqKey="Squires R" first="R. Burke" last="Squires">R. Burke Squires</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pickett, Brett E" sort="Pickett, Brett E" uniqKey="Pickett B" first="Brett E." last="Pickett">Brett E. Pickett</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Das, Sajal" sort="Das, Sajal" uniqKey="Das S" first="Sajal" last="Das">Sajal Das</name>
<affiliation wicri:level="2"><nlm:aff id="A3">Department of Computer Science, Missouri University of Science and Technology, Rolla, MO, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science, Missouri University of Science and Technology, Rolla, MO</wicri:regionArea>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="A4">Department of Pathology, University of California San Diego, San Diego, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Pathology, University of California San Diego, San Diego, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25064525</idno>
<idno type="pmc">4257861</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257861</idno>
<idno type="RBID">PMC:4257861</idno>
<idno type="doi">10.1016/j.meegid.2014.07.015</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000809</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000809</idno>
<idno type="wicri:Area/Pmc/Curation">000809</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000809</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000438</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000438</idno>
<idno type="wicri:Area/Ncbi/Merge">000A65</idno>
<idno type="wicri:Area/Ncbi/Curation">000A65</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000A65</idno>
<idno type="wicri:doubleKey">1567-1348:2014:Squires R:toward:a:method</idno>
<idno type="wicri:Area/Main/Merge">000650</idno>
<idno type="wicri:Area/Main/Curation">000649</idno>
<idno type="wicri:Area/Main/Exploration">000649</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus</title>
<author><name sortKey="Squires, R Burke" sort="Squires, R Burke" uniqKey="Squires R" first="R. Burke" last="Squires">R. Burke Squires</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pickett, Brett E" sort="Pickett, Brett E" uniqKey="Pickett B" first="Brett E." last="Pickett">Brett E. Pickett</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Das, Sajal" sort="Das, Sajal" uniqKey="Das S" first="Sajal" last="Das">Sajal Das</name>
<affiliation wicri:level="2"><nlm:aff id="A3">Department of Computer Science, Missouri University of Science and Technology, Rolla, MO, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science, Missouri University of Science and Technology, Rolla, MO</wicri:regionArea>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="A4">Department of Pathology, University of California San Diego, San Diego, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Pathology, University of California San Diego, San Diego, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</title>
<idno type="ISSN">1567-1348</idno>
<idno type="eISSN">1567-7257</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P1">In 2009 a novel pandemic H1N1 influenza virus (H1N1pdm09) emerged as the first official influenza pandemic of the 21st century. Early genomic sequence analysis pointed to the swine origin of the virus. Here we report a novel computational approach to determine the evolutionary trajectory of viral sequences that uses data-driven estimations of nucleotide substitution rates to track the gradual accumulation of observed sequence alterations over time. Phylogenetic analysis and multiple sequence alignments show that sequences belonging to the resulting evolutionary trajectory of the H1N1pdm09 lineage exhibit a gradual accumulation of sequence variations and tight temporal correlations in the topological structure of the phylogenetic trees. These results suggest that our evolutionary trajectory analysis (ETA) can more effectively pinpoint the evolutionary history of viruses, including the host and geographical location traversed by each segment, when compared against either BLAST or traditional phylogenetic analysis alone.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Maryland</li>
<li>Missouri (État)</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Maryland"><name sortKey="Squires, R Burke" sort="Squires, R Burke" uniqKey="Squires R" first="R. Burke" last="Squires">R. Burke Squires</name>
</region>
<name sortKey="Das, Sajal" sort="Das, Sajal" uniqKey="Das S" first="Sajal" last="Das">Sajal Das</name>
<name sortKey="Pickett, Brett E" sort="Pickett, Brett E" uniqKey="Pickett B" first="Brett E." last="Pickett">Brett E. Pickett</name>
<name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name>
<name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/H2N2V1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000649 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000649 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= H2N2V1 |flux= Main |étape= Exploration |type= RBID |clé= PMC:4257861 |texte= Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25064525" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a H2N2V1
This area was generated with Dilib version V0.6.33. |