Use of the ISU FLUture multisequence identity tool for rapid interpretation of swine influenza A virus sequences in the United States

Authors: ZELLER, MICHAEL - Iowa State University; SAXENA, ANUGRAH - Iowa State University; Anderson, Tavis; Baker, Amy; GAUGER, PHILLIP - Iowa State University

Submitted to: Journal of Veterinary Diagnostic Investigation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/11/2022
Publication Date: 7/25/2022
Citation: Zeller, M.A., Saxena, A., Anderson, T.K., Baker, A.L., Gauger, P.C. 2022. Use of the ISU FLUture multisequence identity tool for rapid interpretation of swine influenza A virus sequences in the United States. Journal of Veterinary Diagnostic Investigation. 34(5):874-878. https://doi.org/10.1177/10406387221111128.
DOI: https://doi.org/10.1177/10406387221111128

Interpretive Summary: Influenza A Virus (IAV) causes respiratory disease in swine impacting health and production. Although IAV vaccines are commonly used in swine, they may not work well if the vaccine strain does not match the strain or strains on a farm. Cases of respiratory disease in swine are routinely submitted to the Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) for testing to determine the cause which includes genetic sequencing of the major surface protein of IAV, hemagglutinin (HA). The genetic sequence the HA swine IAV gene can be used to inform vaccine design, but there are no simple computational interfaces that allow practitioners to determine what should be included in a vaccine based on genomic surveillance data. We created a multisequence identity tool deployed on a web portal to summarize and graphically visualize IAV genetic sequence similarity. The tool identifies the genetic similarity and geographic distribution of sequences to user submitted query sequences, and presents a tabulation of the most similar IAV sequence and associated epidemiological information. This tool allows veterinarians and researchers the ability to rapidly classify and identify similar sequences to their diagnostic submissions to aid vaccine design to improve animal health.

Technical Abstract: Rapid and reliable identification of the hemagglutinin (HA) and neuraminidase (NA) genetic clades of an influenza A virus (IAV) sequence from swine can inform control measures and multivalent vaccine composition. Current approaches to genetically characterize HA or NA sequences are often based on nucleotide similarity or phylogenetic analyses. Existing databases have facilitated the acquisition of IAV genetic sequences for comparison, but it remains difficult for individuals at the diagnostic or production level to adequately update and maintain relevant IAV in swine sequence databases. Further, phylogenetic analyses are time intensive, and inference drawn from these methods is impacted by input sequence data and associated metadata. This report describes the development and utility of an IAV multisequence identity tool as an integrated public webpage located on the ISU FLUture website: https://influenza.cvm.iastate.edu/. The multisequence identity tool makes use of diagnostic sequence data collected at the Iowa State University Veterinary Diagnostic Laboratory, employs a BLAST algorithm that identifies genetically similar sequences to submitted query sequences, and presents a tabulation of the most similar IAV sequence and associated metadata from the FLUture database. This tool removes bioinformatic barriers and allows clients, veterinarians, and researchers the ability to rapidly classify and identify similar sequences to their diagnostic submissions.