PRRSView: an analytical platform for the assessment of PRRSV ORF5 genetic sequences

Porcine reproductive and respiratory syndrome virus (PRRSV) is the most economically important swine pathogen in North America and is second globally only to African swine fever virus. PRRSV is a positive sense, single stranded RNA virus associated with reproductive disorder of sows and respiratory disease of pigs at all age. Diagnostic tests are commonly used to monitor the presence of PRRSV in swine populations including sequencing the open reading frame 5 (ORF5) gene to track the epidemiology of the virus and lateral introductions into a farm. PRRSView is a web portal created at the Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) to host analytical and phylogenetic tools related to PRRSV ORF5 sequences with the goal of assisting veterinarians and producers in evaluating the genetic diversity, spatial, and temporal aspects of ORF5 sequences maintained in the ISU VDL database. PRRSView works in conjunction with the broader Swine Disease Reporting System (SDRS) project to contextualize the ever changing patterns of PRRSV diversity, and supports interactive tools for veterinarians to analyze their sequence data compared to other sequences detected throughout the United States. The PRRSView homepage provides a phylogenetic overview of the sequences generated by the ISU VDL within the previous month, indicating the current strains detected in circulation. There are currently three ORF5 analytical tools available on PRRSView: a genetic sequence BLAST tool, a vaccine identity tool, and an RFLP tool. The ORF5 BLAST tool allows the users to submit their ORF5 gene sequences and returns up to 10 closely related sequences from the ISU VDL database, with metadata that includes the state, genetic lineage, RFLP, and identity to the query sequence. The vaccine identity tool allows users to quickly calculate the percent homology of their sequence(s) to five different PRRSV vaccines: Inglevac PRRS ATP, Inglevac PRRS MLV, Prime Pac PRRS, Fostera PRRS, and Prevacent PRRS, as well as the distance to the Lelystad strain. This tool also builds a neighbor joining tree with a set of curated strains to estimate the genetic lineage of the sequence, which is rendered in the web browser for viewing. Additionally, this tool will calculate the RFLP of the sequence, and the exact positions of the cut sites are shown when hovering over the RFLP value. The last analytical tool provided is the ORF5 RFLP tool, which quickly calculates the RFLP pattern of the input sequences. These analytical tools are designed to allow veterinarians and researchers to easily analyze their PRRSV ORF5 sequences against the expansive ISU VDL database to gain valuable epidemiologic information and comparative data regarding the genetic lineages and related metadata of the PRRSV circulating in a production system, while lowering the barrier of entry for use.