United States Swine Pathogen Database

Veterinarians have long needed a centralized database to compare and contrast the pathogen nucleotide sequences of their clinical samples to those seen concurrently in the field throughout the United States. In addition, meaningful molecular epidemiology studies require regular access to current nucleotide sequence data to provide criteria for updating vaccine composition and the identification of emerging viral threats. Presently, the majority of genetic sequence data derived from pathogens infecting US swine are not readily available to researchers outside of veterinary diagnostic laboratories. To overcome this problem, the National Pork Board granted the first year of funding (NPB #16-222) for a two-year project that would create a combined database for secure housing of all nucleotide sequences produced in the diagnostic laboratories of key universities. The funded NPB research has now established collaborations between the major swine diagnostic laboratories (South Dakota State University and Kansas State University initially, and then once the database is fully established, the University of Minnesota and Iowa State University) and the USDA-ARS National Animal Disease Center in order to generate a centralized sequence and related clinical information repository. Genetic sequences from diagnostic submissions [e.g., porcine reproductive and respiratory syndrome virus (PRRSV); Seneca virus A (SVA); porcine epidemic diarrhea virus (PEDV); others] are currently housed in a private centralized sequence database with an interactive public website that we have under development (United States Swine Pathogen Database). The submitting laboratories and other interested researchers will have access to all of the information stored on our database to view, query, and download genomic and other bibliographic information for molecular epidemiological analyses. The ultimate goal of this resource is to provide a resource for the swine health community to facilitate the development of vaccines, diagnostics and therapeutics to combat endemic (e.g., PRRSV) and emerging viruses (e.g., SVA).