J Vet Sci.  2017 Sep;18(3):317-326. 10.4142/jvs.2017.18.3.317.

Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus in southern China from 2007 to 2014

• Wu Q
• Li Z
• Zhang G
• Niu J
• Zeng X
• Sun B
• Ma J

• KMID: 2412449
• DOI: http://doi.org/10.4142/jvs.2017.18.3.317

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) has a high degree of genetic variation. In this study, we characterized the genetic variation and evolutionary relationships among circulating PRRSV strains in southern China. We analyzed 29 NSP2 strains and 150 ORF5 strains from clinical samples collected in southern China during 2007-2014. The alignment results showed that the nucleotide identity similarities of the two genes among these strains were 80.5%-99.7% and 80.9%-100%, respectively. Phylogenetic analysis based on the NSP2 gene showed that highly pathogenic (HP)-PRRSV was still the dominant virus in southern China from 2013 to 2014. Compared with reference strains CH-1a and VR-2332, the field strain 131101-GD-SHC, which shared high homology with JXA1-P170, had a novel 12 amino acid deletion at position 499-510. Phylogenetic analysis based on the ORF5 gene showed that HP-PRRSV, VR2332-like strains, and QYYZ-like strains were simultaneously circulating in southern China from 2007 to 2014, suggesting that, in recent years, the type 2 PRRSV was more diverse in southern China. In conclusion, mutations in the decoy epitope and primary neutralizing epitope could be markers of viral evolution and used to study evolutionary relationships among PRRSV strains in China.

Keyword

GP5; NSP2; phylogenetic analysis; porcine reproductive and respiratory syndrome virus

MeSH Terms

Animals
China/epidemiology
Genetic Variation/*genetics
Phylogeny
Polymerase Chain Reaction/veterinary
Porcine Reproductive and Respiratory Syndrome/epidemiology/virology
Porcine respiratory and reproductive syndrome virus/*genetics
Sequence Alignment/veterinary
Sequence Analysis, DNA/veterinary
Sequence Analysis, Protein/veterinary
Swine

Figure

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  Fig. 1 Phylogenetic tree comparing PRRSV field strains and reference strains based on NSP2 gene sequences. Field PRRSV strains were collected between 2012 and 2014. The NSP2 gene (n = 29) was sequenced and compared to published reference strains in GenBank (n = 35; filled circles). The reliability of the tree was assessed by performing a bootstrap analysis with 1000 replications. The distinct subgroups are marked with different colors as indicated on the tree.

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  Fig. 2 The deduced amino acid sequence alignment of the NSP2 gene from PRRSV field strains and reference strains. (A) The deduced amino acid sequence alignment of the NSP2 at position 470–564 from PRRSV field strains and reference strains. (B) The deduced amino acid sequence alignment of the NSP2 at position 810–900 from PRRSV field strains and reference strains. The amino acid sequence of the complete NSP2 gene sequence from field strains (n = 29) collected between 2012 and 2014 was compared to published reference strains (n = 10). Solid dots indicate amino acids identical to the CH-1a sequence. Dashes indicate gaps. The red boxed residues indicate deletion regions. The blue boxed residues indicate insertion regions.

• 

  Fig. 3 Phylogenetic tree comparing PRRSV field strains and reference strains based on the ORF5 gene. Field PRRSV strains were collected between 2011 and 2014. The ORF5 gene (n = 150) was sequenced and compared to published reference strains in GenBank (n = 49; filled circles). The reliability of the tree was assessed by performing a bootstrap analysis with 1000 replications. The distinct subgroups are marked with different colors as indicated on the tree.

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