Location: Virus and Prion ResearchTitle: octoFLUshow: an interactive tool describing spatial and temporal trends in the genetic diversity of influenza A virus in U.S. swine
|ARENDSEE, ZEBULUN - Orise Fellow|
|CHANG, JENNIFER - Orise Fellow|
|HUFNAGEL, DAVID - Orise Fellow|
|MARKIN, ALEXEY - Iowa State University|
Submitted to: Microbiology Resource Announcements
Publication Type: Rapid Release Publication
Publication Acceptance Date: 11/27/2021
Publication Date: 12/16/2021
Citation: Arendsee, Z.W., Chang, J., Hufnagel, D.E., Markin, A., Baker, A.L., Anderson, T.K. 2021. octoFLUshow: an interactive tool describing spatial and temporal trends in the genetic diversity of influenza A virus in U.S. swine. Microbiology Resource Announcements. 10(50). Article e01081-21. https://doi.org/10.1128/MRA.01081-21.
Interpretive Summary: In the United States, influenza A virus (IAV) in swine is passively monitored through a U.S. Department of Agriculture (USDA) IAV in swine surveillance system. The system was established in 2009, and has since tested over 178,000 samples from more than 55,000 swine diagnostic submissions, resulting in more than 9,000 publicly available virus isolates and genetic sequences. A consistent and continued assessment of the genetic diversity of IAV collected as part of the surveillance system can identify spatial and temporal trends in diversity and novel viruses that require additional characterization. We generated a tool for publicly reporting the USDA IAV surveillance sequencing efforts on single gene and whole virus genome levels. The tool, called octoFLUshow, is an interactive visualization platform. It offers a searchable overview of all IAV in swine strains collected in the surveillance system from 2009 to present. These data may be refined by collection date, collection location, subtype, genetic clade, and whole genome constellation. This tool provides objective measures of genetic diversity, and allows stakeholders to make informed decisions on vaccine design or use, or in the selection of relevant viruses circulating in U.S. swine herds for further characterization.
Technical Abstract: Influenza A virus (IAV) is passively surveilled in swine in the United States through a U.S. Department of Agriculture administered surveillance system. We present an interactive web tool to visualize and explore trends in the genetic and geographic diversity of IAV derived from the surveillance system.