Genetic diversity analysis of genotype 2 porcine reproductive and respiratory syndrome viruses emerging in recent years in China

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by its extensive genetic diversity. Here we analyzed 101 sequences of NSP2 hypervariable region, 123 ORF3 sequences, and 118 ORF5 sequences from 128 PRRSV-positive clinical samples collected in different areas of China during 2008-early 2012. The results indicated that the amino acid identities of the three genes among these sequences were 87.6%-100%, 92.5%-100%, and 77%-100%, respectively. Meanwhile, 4 novel patterns of deletion and insertion in NSP2 region or GP5 were first found. The phylogenetic analysis on these 3 genes revealed that the Chinese PRRSV strains could be divided into three subgroups; majority of genes analyzed here were clustered in subgroup 3 with multiple branches; the strains with 30-aa deletion in NSP2-coding region were still the dominant virus in the field. Further phylogenetic analysis on four obtained complete genomic sequences showed that they were clustered into different branches with the Chinese corresponding representative strains. Our analyses suggest that the genetic diversity of genotype 2 PRRSV in the field displays a tendency of increasing in recent years in China, and the 30-aa deletion in NSP2-coding region should be no longer defined as the molecular marker of the Chinese HP-PRRSV.

Figure 1

Phylogenetic tree based on the deduced amino acid sequence of NSP2 HV region. The bootstrap consensus tree is shown. The sequence downloaded from GenBank had a suffix “NSP2”. The representative strains were labeled with “black triangle” and the vaccine strains were labeled with “black diamond.” The bootstrap values were shown close to the branches.

Figure 2

Phylogenetic tree based on the deduced amino acid sequence of ORF3. The bootstrap consensus tree is shown. The sequence downloaded from GenBank had a suffix “ORF3.” The representative strains were labeled with “black triangle” and the vaccine strains were labeled with “black diamond.” The bootstrap values were shown close to the branches.

Figure 3

Phylogenetic tree based on the deduced amino acid sequence of ORF5.The bootstrap consensus tree is shown. The sequence downloaded from GenBank had a suffix “ORF5.” The representative strains were labeled with “black triangle” and the vaccine strains were labeled with “black diamond.” The bootstrap values were shown close to the branches.

Figure 4

The alignment of NSP2 amino acid sequence of PRRSV. A multiple alignment of PRRSV NSP2 amino acid sequences was performed by ClustalW. The sequence of VR-2332 is shown on the top; the residues conserved with it are hidden. The deleted or inserted residues are labeled with box.

Figure 5

The alignment of PRRSV ORF5 amino acid sequence. Multiple alignments of PRRSV ORF5 amino acid sequences were performed by ClustalW. The sequence of VR-2332 is shown on the top; the residues conserved with it are hidden. The deleted residues are labeled with box.

Figure 6

Phylogenetic tree based on full-length genomic sequence of PRRSV. The strains isolated in this study were labeled with “black triangle.” The bootstrap values were shown close to the branches. The numbers below the scale bar indicate amino acid substitution (100x).