Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus
Identifieur interne : 000D71 ( Main/Exploration ); précédent : 000D70; suivant : 000D72Toward 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.
Descripteurs français
- KwdFr :
- ARN viral (analyse), ARN viral (génétique), Alignement de séquences, Analyse de séquence d'ARN, Bases de données génétiques, Biologie informatique (), Données de séquences moléculaires, Grippe humaine (transmission), Grippe humaine (virologie), Grippe humaine (épidémiologie), Humains, Pandémies, Phylogénie, Sous-type H1N1 du virus de la grippe A (), Sous-type H1N1 du virus de la grippe A (génétique), Séquence nucléotidique, Évolution moléculaire.
- MESH :
- analyse : ARN viral.
- génétique : ARN viral, Sous-type H1N1 du virus de la grippe A.
- virologie : Grippe humaine.
- épidémiologie : Grippe humaine.
- Alignement de séquences, Analyse de séquence d'ARN, Bases de données génétiques, Biologie informatique, Données de séquences moléculaires, Humains, Pandémies, Phylogénie, Sous-type H1N1 du virus de la grippe A, Séquence nucléotidique, Évolution moléculaire.
English descriptors
- KwdEn :
- Base Sequence, Computational Biology (methods), Databases, Genetic, Evolution, Molecular, Humans, Influenza A Virus, H1N1 Subtype (classification), Influenza A Virus, H1N1 Subtype (genetics), Influenza, Human (epidemiology), Influenza, Human (transmission), Influenza, Human (virology), Molecular Sequence Data, Pandemics, Phylogeny, RNA, Viral (analysis), RNA, Viral (genetics), Sequence Alignment, Sequence Analysis, RNA.
- MESH :
- chemical , analysis : RNA, Viral.
- classification : Influenza A Virus, H1N1 Subtype.
- epidemiology : Influenza, Human.
- genetics : Influenza A Virus, H1N1 Subtype, RNA, Viral.
- methods : Computational Biology.
- transmission : Influenza, Human.
- virology : Influenza, Human.
- Base Sequence, Databases, Genetic, Evolution, Molecular, Humans, Molecular Sequence Data, Pandemics, Phylogeny, Sequence Alignment, Sequence Analysis, RNA.
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:
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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. 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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)
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