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.

Department(s)

Computer Science

Comments

National Institute of Allergy and Infectious Diseases, Grant N01AI40041

Keywords and Phrases

Evolution; Influenza; Metadata; Pandemic; Swine flu; Virus

International Standard Serial Number (ISSN)

1567-7257; 1567-1348

Document Type

Article - Journal

Document Version

Final Version

File Type

text

Language(s)

English

Rights

© 2024 Elsevier, All rights reserved.

Creative Commons Licensing

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.

Publication Date

01 Dec 2014

PubMed ID

25064525

Link to Full Text

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