Újgenerációs szekvenálás alkalmazása a hazai PRRSV fertőzések genomi epidemiológiájában

Abstract

The two viral pathogens of the porcine reproductive and respiratory syndrome (PRRSV-1 and PRRSV-2) are disseminated worldwide. The PRRSVs belong to the subfamily Variarterivirinae within the family Arteriviridae of the order Nidovirales. Our main objective was to expand the available sequencing methods in order to support the molecular genetic studies of PRRSV. In this study, we successfully evaluated a PRRSV-specific amplicon library preparation method compatible with Illumina short-read sequencing based on a two-step PCR assay. Two different library preparation protocols have been developed. One of the approaches targets the ORF7 region of both PRRSV species, while the other is specific to the whole genome of certain PRRSV-1 vaccine strains (Porcilis® and Unistrain® PRRS) and their descendants. The ORF7 targeted amplicon deep sequencing provided insights into the heterogeneous composition of the PRRSV-1 viral population circulating in Hungary and the microevolutionary mechanisms acting on this region. In addition, we have demonstrated that this method is suitable to discriminate between vaccine- and wild-type strains, as well as to detect multiple strains simultaneously and promote the genetic characterization of PRRSVs.