Sequence and Phylogenetic Analyses of the Nsp2 and ORF5 Genes of Porcine Reproductive and Respiratory Syndrome Virus in Boars from South China in 2015

Summary Porcine reproductive and respiratory syndrome virus (PRRSV) is highly genetically diverse; however, little is known about the molecular epidemiology of PRRSV in the boar farms of South China. In this study, 367 samples were collected from boar farms in South China in 2015. The Nsp2 hypervariable region and ORF5 gene were PCR amplified from 66 PRRSV‐positive samples, followed by sequencing and analysis. The percentage of PRRSV antigen‐positive samples was 17.98%; 8.72% were positive for highly pathogenic PRRSV (HP‐PRRSV), and 9.26% were positive for low pathogenic PRRSV (LP‐PRRSV). Sequence alignment and phylogenetic tree analyses revealed three novel patterns of deletion in the hypervariable region of Nsp2, which had not been identified previously. Furthermore, numerous amino acid substitutions were identified in the putative signal peptide and extravirion regions of GP5. These results demonstrate for the first time that the existence of multiple different strains on the same boar farm, and extensive genetic mutation and high infection rate of PRRSV in boars from South China. Our research contributes to the understanding of the epidemiology and genetic characteristics of PRRSV on boar farms.