Swine influenza A viruses: quantifying genetic diversity with phylogenetics and the octoFLU pipeline

Authors: Anderson, Tavis; CHANG, JENNIFER - Orise Fellow; ARENDSEE, ZEBULUN - Orise Fellow; Baker, Amy

Submitted to: American Association of Swine Veterinarians Annual Meeting
Publication Type: Proceedings
Publication Acceptance Date: 1/6/2019
Publication Date: 3/8/2020
Citation: Anderson, T.K., Chang, J., Arendsee, Z.W., Vincent, A.L. 2020. Swine influenza A viruses: quantifying genetic diversity with phylogenetics and the octoFLU pipeline. Proceedings of American Association of Swine Veterinarians Annual Meeting. Seminar No. 9.

Interpretive Summary:

Technical Abstract: Influenza A virus (IAV) is one of the most important respiratory pathogens of swine. Infection causes mortality and morbidity, resulting in significant financial losses through decreased production and associated treatment costs. Although only three subtypes (H1N1, H1N2, and H3N2) are endemic in swine globally, considerable genetic diversity can be found in the genes encoding the major surface proteins, hemagglutinin (HA) and neuraminidase (NA), and the other six internal gene segments. This is the result of bidirectional transmission between swine and humans, the occasional transmission of an avian virus into swine, followed by periods of rapid genetic evolution through mutation or through exchange of the gene segments during coinfection, a process known as reassortment. Here, we describe the current diversity of swine IAV in the US, introduce general guidelines for quantifying genetic diversity using phylogenetic methods, and describe a bioinformatic tool that automatically classifies swine IAV genes to genetic clade or evolutionary lineage.