tetano
Editor, Senior Moderator
Infect Genet Evol. 2014 Jul 24. pii: S1567-1348(14)00244-5. doi: 10.1016/j.meegid.2014.07.015. [Epub ahead of print]
Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.
Squires RB1, Pickett BE2, Das S3, Scheuermann RH4.
Author information
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.
Copyright ? 2014. Published by Elsevier B.V.
KEYWORDS:
Evolution; Influenza; Metadata; Pandemic; Swine flu; Virus
PMID:
25064525
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/25064525
Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.
Squires RB1, Pickett BE2, Das S3, Scheuermann RH4.
Author information
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.
Copyright ? 2014. Published by Elsevier B.V.
KEYWORDS:
Evolution; Influenza; Metadata; Pandemic; Swine flu; Virus
PMID:
25064525
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/25064525