ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of influenza A virus in swine

Authors: ZELLER, MICHAEL - Iowa State University; Anderson, Tavis; WALIA, RASNA - Orise Fellow; Baker, Amy; GAUGER, PHILLIP - Iowa State University

Submitted to: BMC Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2018
Publication Date: 11/1/2018
Citation: Zeller, M.A., Anderson, T.K., Walia, R.W., Vincent, A.L., Gauger, P.C. 2018. ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of influenza A virus in swine. BMC Bioinformatics. 19:397. https://doi.org/10.1186/s12859-018-2408-7.
DOI: https://doi.org/10.1186/s12859-018-2408-7

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 state veterinary diagnostic laboratories (VDL) for testing to determine the cause which includes genetic sequencing of disease agents like IAV. The genetic sequence of the swine IAV isolates can be used to inform vaccine selection. Iowa State University (ISU) VDL possessed a database of influenza diagnostic test results and sequences accumulated since 2003, but these data were not publically available. Therefore, we created FLUture, a web portal to summarize and graphically visualize IAV case and genetic sequence information derived from swine farms across the United States of America. The data are held in a secure database to protect the privacy of submitting clients, while providing public access to monitor changes in the diversity of IAV and the expedited identification of abundant or newly identified viruses. This rapid access information about IAV in swine provides rational criteria to inform vaccine design and current control efforts.

Technical Abstract: Background: Influenza A Virus (IAV) causes respiratory disease in swine and is a zoonotic pathogen. Uncontrolled IAV in swine herds not only affects animal health, it also impacts production through increased costs associated with treatment and prevention efforts. The Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) diagnoses influenza respiratory disease in swine and provides epidemiological analyses on samples submitted by veterinarians. Description: To assess the incidence of IAV in swine and inform stakeholders, the ISU FLUture website was developed as an interactive visualization tool that allows the exploration of the ISU VDL swine IAV data in the clinical diagnostic database. The information associated with diagnostic cases has varying levels of completeness and is anonymous, but minimally contains: sample collection date, specimen type, and IAV subtype. Many IAV positive samples are sequenced, and in these cases, the hemagglutinin (HA) sequence and genetic classification are collected. These data are collected and presented on ISU FLUture in near real-time, and more than 6,000 IAV positive diagnostic cases and their epidemiological and evolutionary information since 2003 are presented to date. The database and web interface provides rapid and unique insight into the trends of IAV derived from both large- and small-scale swine farms across the United States of America. Conclusion: ISU FLUture provides a suite of tools to allow stakeholders to search for trends and correlations in IAV case metadata in swine. Since the database infrastructure is updated in near real-time and is integrated within a high-volume veterinary diagnostic laboratory, earlier detection is now possible for emerging IAV in swine that subsequently cause vaccination and control challenges. The access to real-time swine IAV data provides a link with the national USDA swine IAV surveillance system and allows veterinarians to make objective decisions regarding the management and control of IAV in swine. The website is publicly accessible at http://influenza.cvm.iastate.edu.