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Research Project: Intervention Strategies to Control Influenza A Virus Infection in Swine

Location: Virus and Prion Research

Title: OctoFlu: Automated classification of influenza A virus gene sequences detected in U.S. swine to evolutionary origin

Author
item CHANG, JENNIFER - Oak Ridge Institute For Science And Education (ORISE)
item Anderson, Tavis
item ZELLER, MICHAEL - Iowa State University
item GAUGER, PHILLIP - Iowa State University
item Vincent, Amy

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2019
Publication Date: 8/8/2019
Citation: Chang, J., Anderson, T.K., Zeller, M.A., Gauger, P.C., Vincent, A.L. 2019. OctoFlu: Automated classification of influenza A virus gene sequences detected in U.S. swine to evolutionary origin. Microbiology Resource Announcements. 8(32):e00673-19. https://doi.org/10.1128/MRA.00673-19.
DOI: https://doi.org/10.1128/MRA.00673-19

Interpretive Summary: Swine influenza A virus is a respiratory disease of swine caused by the influenza A virus (IAV) that can be divided into different subtypes based on the composition of genes contained within the virus. Although only H1N1, H1N2, and H3N2 subtypes of influenza A virus are found in swine around the world, much diversity can be detected in the genes coding for the major surface proteins, hemagglutinin (H) and neuraminidase (N), and in the other 6 internal gene segments. This diversity is the result of frequent bidirectional transmission between swine and humans, and the occasional transmission of an avian virus into swine followed by periods of virus mutation. Using a curated dataset of whole genome swine IAV sequences, we developed an adaptable bioinformatic pipeline that rapidly assigns evolutionary origin to swine IAV gene sequences. This tool will aid agricultural production and diagnostic capabilities through the identification of important changes in genetic diversity, and allow for the identification of novel viruses.

Technical Abstract: Influenza A viruses (IAV) in swine are classified as H1N1, H1N2, or H3N2 subtype, with diversity of the 8 genes reflecting introductions from non-swine hosts and subsequent antigenic drift and shift. Here, we curated a dataset and present a pipeline that assigns evolutionary lineage and genetic clade to query gene segments.