Date Full Report Received09/23/2015
Date Abstract Report Received09/23/2015
InvestigationInstitution: Kansas State University
Primary Investigator: Ben Hause
Co-Investigators: Richard Hesse, Jianfa Bai
Funded ByNational Pork Board
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most significant swine diseases with near worldwide distribution. In the U.S., open reading frame 5 (ORF5) is commonly sequenced to investigate viral epidemiology. While glycoprotein 5 (GP5) is the major protein on the surface of the virion, the minor glycoproteins GP2a, GP3 and GP4 exhibit similar genetic diversity and are responsible for receptor binding and are important antigens for the immune response. Additionally, the non-structural protein 2 (nsp2) plays key role in viral pathogenicity and deletions in nsp2 have been associated with strains with increased virulence.
The goal of this project was to develop next generation (metagenomic) sequencing methodology to enable full PRRSV genome sequencing directly from clinical samples. The current standard GP5 sequencing for epidemiological investigations takes into account only <5% of the genome and advances in sequencing technology now make it cost-effective to determine a comprehensive picture of PRRSV genetics. Metagenomic sequencing of PRRSV-positive nasal swabs and oral fluids were able to detect PRRSV however read coverage was insufficient to determine complete genomes. In contrast, metagenomic sequencing of PRRSV-positive sera was successful in determining complete PRRSV genomes. Metagenomic sequencing was performed on a collection of 182 PRRSV-positive sera submitted to veterinary diagnostic laboratories. Complete PRRSV genomes were determined from 66 of these samples. Analysis of the viral structural proteins found 4-7 lineages currently circulating in the U.S. This study identified more diversity in the PRRSV structural proteins than previously recognized, possibly due to direct sequencing of clinical samples as opposed to sequencing viruses isolated in cell culture.