Epidemiology and evolutionary characteristics of the porcine reproductive and respiratory syndrome virus in China between 2006 and 2010

Abstract

In 2006, an emerging highly pathogenic strain of porcine reproductive and respiratory syndrome virus (PRRSV), which causes continuous high fever and a high proportion of deaths in vaccinated pigs of all ages, broke out in mainland China and spread rapidly to neighboring countries. To examine the epidemiology and evolutionary characteristics of Chinese PRRSV after the 2006 outbreak, we tested 2,981 clinical samples collected from 2006 to 2010 in China, determined 153 Nsp2 sequences and 249 ORF5 sequences, and analyzed the epidemiology and genetic diversity of Chinese PRRSV. Our results showed that the percentage of PRRSV-positive specimens collected from sick pigs averaged 60.85% in the past 5 years and that the highly pathogenic PRRSV has become the dominant strain in China. Furthermore, a reemerging strain which apparently evolved from the highly pathogenic PRRSV strain in 2006 appeared to be widely prevalent in China from 2009 onwards. Sequence analyses revealed that the hypervariable region of Nsp2 in most of the isolates contained a discontinuous deletion equivalent to 30 amino acids, along with other types of deletions. Extensive amino acid substitutions in the GP5 sequence translated from ORF5 were found, particularly in the potential neutralization epitope and the N-glycosylation sites. Our results suggest that Chinese PRRSV has undergone rapid evolution and can circumvent immune responses induced by currently used vaccines. Information from this study will help in understanding the evolutionary characteristics of Chinese PRRSV and assist ongoing efforts to develop and use PRRSV vaccines in the future.

Fig. 1.

Alignment of the deduced partial Nsp2 amino acid sequences of 23 representative clinical PRRSV isolates. The sequences of VR-2332 (U87392), RespPRRS_MLV(AF066183), CH-1a (AY032626), HB-1(sh)/2002 (AY150312), JXA1(EF112445), HUN4 (EF635006), JXwn06 (EF641008), and SY0608 (EU144079) were also used for comparison. Dashes indicate positions where the amino acid exactly matches the reference sequence of VR-2332. The deletion regions are highlighted by gray.

Fig. 2.

Phylogenetic tree of the clinical PRRSV isolates based on their translated partial Nsp2 amino acid sequences. The phylogenetic tree was generated by the distance-based neighbor-joining method using MEGA4 software. Bootstrap values were calculated from 1,000 replicates of the alignment. The different subgroups are marked.

Fig. 3.

Phylogenetic analysis of the translated PRRSV GP5 amino acid sequences of representative PRRSV strains by the distance-based neighbor-joining method using MEGA4 software. The robustness of the tree was assessed by bootstrap analysis with 1,000 replications. The four Chinese subgroups are marked.

Fig. 4.

Alignment of the deduced amino acid sequences of GP5s from representative clinical PRRSV isolates. The sequences of VR-2332 (U87392), RespPRRS_MLV(AF066183), CH-1a (AY032626), HB-1(sh)/2002 (AY150312), JXA1(EF112445), HUN4 (EF635006), JXwn06 (EF641008), and SY0608 (EU144079) were also used for comparison. The dashed box indicates the putative signal sequence. The solid box indicates the hypervariable domains. The main amino acid mutations within different subgroups are highlighted by gray. A novel substitution is marked with a star. Dashes indicate positions where the amino acid exactly matches the consensus sequence.