A new recombined porcine reproductive and respiratory syndrome virus virulent strain in China

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important swine diseases worldwide. In the present study, a new virulent strain of PRRS virus (PRRSV), GDsg, was isolated in Guangdong province, China, and caused high fever, high morbidity, and high mortality in sows and piglets. The genome of this new strain was 15,413 nucleotides (nt) long, and comparative analysis revealed that GDsg shared 82.4% to 94% identity with type 2 PRRSV strains, but only 61.5% identity with type 1 PRRSV Lelystad virus strain. Phylogenetic analysis indicated that type 2 PRRSV isolates include five subgenotypes (I, II, III, IV, and V), which are represented by NADC30, VR-2332, GM2, CH-1a, and HuN4, respectively. Moreover, GDsg belongs to a newly emerging type 2 PRRSV subgenotype III. More interestingly, the newly isolated GDsg strain has multiple discontinuous nt deletions, 131 (19 + 18 + 94) at position 1404-1540 and a 107 nt insertion in the NSP2 region. Most importantly, the GDsg strain was identified as a virus recombined between low pathogenic field strain QYYZ and vaccine strain JXA1-P80. In conclusion, a new independent subgenotype and recombinant PRRSV strain has emerged in China and could be a new threat to the swine industry of China.

Keywords: new subgenotype; phylogenetic analysis; porcine reproductive and respiratory syndrome virus; recombinant strain.

Fig. 1. Phylogenetic trees based on the complete genome, NSP2, and ORF5 of PRRSV. (A) Complete genome-based tree. (B) NSP2 nucleotide-based tree. (C) ORF5-based tree. The isolate identified in this study is indicated by a black dot. NSP, nonstructural protein; ORF, open reading frame; PRRSV, porcine reproductive and respiratory syndrome virus; NA type, North American type; EU type, European type.

Fig. 2. Alignment of the partial NSP2 nucleotide sequence and the ORF5 translated amino acid sequence of GDsg with representative PRRSV strains. (A) Alignment of the partial NSP2 nucleotide sequence. The deleted regions are indicated by a red square and the inserted regions are indicated by an orange square. (B) Alignment of the ORF5 translated amino acid sequence. The signal peptide, transmembrane regions 1, 2, and 3 (TM1, TM2, and TM3) are indicated by a red square. NSP, nonstructural protein; ORF, open reading frame; PRRSV, porcine reproductive and respiratory syndrome virus.

Fig. 3. Recombination analyses of the GDsg strain. (A) Similarity plot analysis using GDsg as the query sequence against those of JXA1-P80 (red) and QYYZ (green). Recombination breakpoints are shown as blue dotted lines. The minor parental regions are identified as region A, whereas that the major parental regions are identified as region B. (B) Phylogenies of parental regions A. (C) Phylogenies of parental regions B. The minor parental group (i.e., HP-PRRSV and related vaccine virus) is marked by asterisks; the major parental group (i.e., a new subgenotype in China) is marked by daggers. HP-PRRSV, highly pathogenic porcine reproductive and respiratory syndrome virus.