The prevalent status and genetic diversity of porcine reproductive and respiratory syndrome virus in China: a molecular epidemiological perspective

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) has been epidemic more than 30 years in America and 20 years in China. It is still one of the most important causative agents to the worldwide swine industry. Here, we systematically analyzed the prevalence status of PRRSV in China by a molecular epidemiological perspective. Now both PRRSV-1 and PRRSV-2 are circulating and approximately more than 80% of pig farms are seropositive for PRRSV. For PRRSV-2, there are four lineages (lineage 1, lineage 3, lineage 5, lineage 8) circulating in the fields. Lineage 8 (CH-1a-like) and lineage 5 (BJ-4-like) appeared almost at the same time during 1995-1996. Notably, BJ-4 shares 99.6% and 99.8% identity with VR2332 and RespPRRS MLV, respectively. It means that lineage 5 is likely to be imported from America. Now highly pathogenic PRRSV (HP-PRRSV) which was considered to be evolved from local diversity of lineage 8 strains is predominant with different variants. Lineage 3 appeared in 2010 which is mainly sporadic in south of China. Lineage 1, also known as NADC30-like strains in China, has been prevalent since 2013 and leads to PRRS pandemic again. For PRRSV-1, although sporadic at present, more than 9 provinces/regions have been reported. All the circulating strains belong to subtype I. It should be paid more attention since there are no vaccines available. Our analysis would help to deeply understand the prevalent status of PRRSV in China and provide useful information for prevention and control of porcine reproductive and respiratory syndrome (PRRS).

Keywords: Control strategies; Molecular epidemiology; PRRSV-1; PRRSV-2; Porcine reproductive and respiratory syndrome virus (PRRSV).

Fig. 1

The phylogenetic analysis based on ORF5 genes from 127 reference virus strains of PRRSV-2. The unrooted phylogenetic tree was constructed using the distanced-based neighbor-joining method in MEGA6.0 with bootstrap values (1000 replicates). The PRRSV-2 circulating in China were clustered into four lineages. Lineage 8 is predominant in 1996-2016 in China and could be further subdivided into five subgroups. Lineage 1 spreads rapidly since 2013 in China. The lineages are according to previous report. The circles (●) indicate the representative virus strains of each lineage in China. The triangles (▲) mean the attenuated live vaccine strains or vaccine derivatives. The squares (■) represent two transition virus strains

Fig. 2

The phylogenetic assay based on ORF5 gene sequences of PRRSV-1. All the Chinese isolated strains belong to subtype 1 (pan-European) and can be classified into 4 subgroups according to the phylogenetic relationships. The Chinese PRRSV strains are marked with black circles (●)

Fig. 3

The amino acid alignment of ORF5 for PRRSV-1. The amino acid sequences were aligned by Clustal W method in MEGA 6.0. The signal sequence(1-32aa) and hypervariable domains (33-67aa, 89-110aa) were indicated by solid boxes. Potential N-glycosylation sites were shown in the red boxes. The hypervariable mutation sites were marked with dark spot (●) and the highly conserved mutation sites were indicated by asterisk (*)

Fig. 4

The alignment assay based on amino acid sequence of N protein for PRRSV-1. The sequence alignment was performed using Clustal W method. A2-12, B25-30, C40-46, D51-67 and D80-90 represent known epitopes in N protein; E50-58, E64-72, E105-113 and E113-121 indicate four porcine T –cell epitopes. The insertion site of amino acid was indicated by triangle (△). The highly conserved mutation sites in Chinese PRRSV-1 strains were marked with asterisk (*)