Complete Genomic Characterization of Porcine Reproductive and Respiratory Syndrome Virus Strain HB-XL

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causal agent of a serious disease of swine. Here, we report the genome sequence of PRRSV strain HB-XL isolated from a pig farm with a clinical outbreak of porcine reproductive and respiratory syndrome. The genome is 15,323 bp long and has nine open reading frames (GenBank: KP162169). Comparative and phylogenetic analysis showed that HB-XL belongs to the highly pathogenic PRRSV (HP-PRRSV) subfamily in the family PRRSV. The viral nonstructural protein 2 (Nsp2) of the HB-XL strain contained 30 discontinuous amino acid (AA) deletions relative to that of the Nsp2 of the VR2332 strain. The AA substitutions R13 and R151 suggested high virulence of the HB-XL strain. The unique mutations in glycoprotein 5 (GP5) and Nsp2 revealed that HB-XL might be a novel variant PRRSV strain recombined with vaccine strains. However, the low morbidity and mortality in the pig herd from which HB-XL was isolated indicate that the virulence of the virus was weak, so it has potential as a future vaccine strain.

Keywords: GP5; Nsp2; porcine reproductive and respiratory syndrome virus; variation analysis.

Figure 1

PCR amplification on the complete gene of HB-XL strain M, DL2000Maker; 1–12, complete gene of the HB-XL strain.

Figure 2

Phylogenetic trees based on the complete genome, ORF5, and Nsp2 of PRRSV. (A) Complete genome; (B) Open reading frame (ORF); (C) Nsp2 nucleotide. The multiple sequence alignment was obtained using the MEGA5 program, and the phylogenetic tree was constructed by the neighbor-joining method using 1000 bootstrap replicates of the sequence data. Bootstrap confidence limits are shown at each node. The isolate identified in this study is indicated by black dots.

Figure 2

Phylogenetic trees based on the complete genome, ORF5, and Nsp2 of PRRSV. (A) Complete genome; (B) Open reading frame (ORF); (C) Nsp2 nucleotide. The multiple sequence alignment was obtained using the MEGA5 program, and the phylogenetic tree was constructed by the neighbor-joining method using 1000 bootstrap replicates of the sequence data. Bootstrap confidence limits are shown at each node. The isolate identified in this study is indicated by black dots.

Figure 3

Alignment of the partial Nsp2 amino acid sequence of HB-XL and several representative PRRSV strains with VR2332. The amino acid deletions are shown with lines. The isolate identified in this study is indicated by a black dot.