title: Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.
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.
authors: 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. Electronic address: richard.squires@nih.gov.
authors: R Burke
authors: RB
authors: Squires
authors: Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA.
authors: Brett E
authors: BE
authors: Pickett
authors: Department of Computer Science, Missouri University of Science and Technology, Rolla, MO, USA.
authors: Sajal
authors: S
authors: Das
authors: Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA; Department of Pathology, University of California San Diego, San Diego, CA, USA.
authors: Richard H
authors: RH
authors: Scheuermann
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics; D007251:Influenza, Human / Q000453:epidemiology / Q000635:transmission / Q000821:virology; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral
keywords: Evolution; Influenza; Metadata; Pandemic; Swine flu; Virus