ISU FLUture: using veterinary diagnostic laboratory data to monitor the temporal genetic patterns of influenza A virus in swine

Authors: ZELLER, MICHAEL - Iowa State University; Baker, Amy; ANDERSON, TRAVIS - Orise Fellow; MAIN, RODGER - Iowa State University; GAUGER, PHILLIP - Iowa State University

Submitted to: American Association of Swine Veterinarians Annual Meeting
Publication Type: Proceedings
Publication Acceptance Date: 2/1/2018
Publication Date: 3/3/2018
Citation: Zeller, M., Vincent, A.L., Anderson, T., Main, R., Gauger, P. 2018. ISU FLUture: using veterinary diagnostic laboratory data to monitor the temporal genetic patterns of influenza A virus in swine. In: Proceedings of the American Association of Swine Veterinarians Annual Meeting, March 3-6, 2018, San Diego, California. https://www.aasv.org/annmtg/.

Interpretive Summary:

Technical Abstract: Introduction Influenza A virus (IAV) is the cause of porcine respiratory disease and currently one of the top three health challenges in the swine industry. Producers are affected by the increased morbidity and mortality in their swine operations and the negative impact on production through increased costs associated with vaccination, treatment, and increased time to market (1). From 2009 to present, the United States Department of Agriculture (USDA) voluntary swine IAV surveillance system has improved the availability of IAV sequence data from swine (2,3). However, these data are derived from voluntary participation by producers and veterinarians and may not represent all IAV in the United States (US). Additionally, the lag in time between detection to release of IAV sequences in public databases may impact the ability of vaccine manufacturers to rapidly update vaccines or for veterinarians and producers to modify intervention strategies. To address these issues, ISU FLUture was designed for near real-time visualization of trends in IAV genetic diversity in swine with sequences derived from porcine respiratory samples submitted to the Iowa State University Veterinary Diagnostic Laboratory (ISU VDL). ISU FLUture provides an interactive web-based tool where epidemiological data linked to sequences can also be evaluated at near real-time. A unique strength of this platform is its integration into privately held diagnostic test data from the ISU VDL; consequently, ISU FLUture presents the most comprehensive data available of the activity of IAV in swine in the US. A suite of tools has been designed to analyze trends in the metadata and sequence data. The ISU FLUture platform complements other resources for IAV in swine such as the Influenza Research Database (4,5) by providing access to veterinary diagnostic results and metadata that may not be submitted to public databases due to client privacy or programmatic restrictions as well as a real-time perspective on swine IAV epidemiology and evolution. Materials and methods The Iowa State University Veterinary Diagnostic Laboratory The ISU VDL provided IAV diagnostic and sequencing services from 2003 to present, with significant increases in the previous two years. Since 2015, the ISU VDL processed over 1,000 IAV-related cases annually collected from 38 states in US. The IAV diagnostic results and related sequences are stored in the ISU VDL Laboratory Information Management System (LIMS), a private database of client records. Of the IAV diagnostic submissions, approximately 49% were eligible for the USDA IAV swine surveillance program beginning in 2009 (2) with the sequence data publicly released to NCBI GenBank (6). Consequently, the ISU VDL has accumulated over thirteen years of IAV diagnostic and sequence data in swine, of which a majority is not currently accessible by the public or stakeholders. These data include pig specific information such as age and location, as well as HA and NA nucleotide sequences. Data collection and curation The swine IAV cases from LIMS were extracted and curated in an independent SQL database for ISU FLUture. Diagnostic cases maintained privately at the ISU VDL were non-redundantly combined with ISU VDL cases submitted as part of the USDA swine IAV surveillance program. Updates to the ISU FLUture database occur at daily intervals. The data were reduced to received date, data source (USDA or ISU VDL diagnostic streams), specimen, pig age in days, pig weight in pounds, the geographic location (at US state resolution), the IAV subtype, the HA sequence, and the NA sequence (for cases included in the USDA IAV swine surveillance system). The case associated information was voluntarily provided by the clients, thus not all variables were available for every case. The description of the evolutionary dynamics of the sequenced samples was achieved by inferr