Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus isolates in East China

Porcine reproductive and respiratory syndrome virus (PRRSV) has been reported to have evolved at a high evolutionary rate and the extensive genetic variation. In this study, 44 PRRSV positive cases obtained from different provinces of China were sequenced and analyzed. Comparative analysis of partial isolates based on nsp2 sequences revealed that highly pathogenic PRRSV were the dominant viruses in China from 2008 to 2010 and some novel strains with an extra deletion of 19 aa. Phylogenetic analysis based on the GP5 genes showed that the PRRSV isolates from 1996 to 2010 had a great variation and the North American genotype was further divided into six subgenotypes. No apparent relationship between the heterogeneity and the geographic origin of isolates was observed. The 44 isolates and 29 representative strains were divided into six subgenotypes. Further analysis of the GP5 protein suggested that these strains of subgenotypes I, II and III exhibited variations in the primary neutralizing epitope and almost all isolates of subgenotypes II and III had more N-linked glycosylation sites. In addition, some mutations which could mirror the viral evolution and adaptation were also observed in this study. All these results might be useful to study the genetic variation and genetic relatedness among PRRSV strains in China.