High genetic diversity of Chinese porcine reproductive and respiratory syndrome viruses from 2016 to 2019

High genetic diversity and limited cross-protection are two major reasons for ineffective control of porcine reproductive and respiratory syndrome virus (PRRSV) infection. Therefore, it's important to dynamically monitor the prevalence of PRRSV for adopting appropriate control strategy. In this study, we analyzed PRRSV infection by detecting 712 clinical samples collected from 2016 to 2019 in China. Totally 100 samples were detected as PRRSV positive, including 2 and 98 samples were infected with PRRSV1 and PRRSV2, respectively. In addition, two out of the 98 PRRSV2 positive samples were co-infected with two distinct viruses. ORF5-based phylogenetic analysis showed that JXA1-like HP-PRRSV2 (lineage 8) and NADC30-like PRRSV2 (lineage 1) isolates are currently predominant, but QYYZ-like PRRSV2, CH-1a-like PRRSV2 and PRRSV1 isolates also co-exist in Chinese swine herds. In addition, two commercial MLV-derived viruses (TJM-F92-like and JXA1-R-like) were frequently detected. GP5 alignment also detected insertion and deletion in the extravirion domain. Our study presents the up-to-date PRRSV infection status and highlights the high genetic diversity of PRRSV currently circulating in China.