The Molecular Epidemiology And Genetic Diversity Of Porcine Reproductive And Respiratory Syndrome Virus In The Partial Regions Of China

Porcine reproductive and respiratory syndrome(PRRS) is widely popular and is an economically devastating viral disease threatening the healthy development of swine industry worldwide, which is characterized by reproductive failure in sows and respiratory disease in pigs of all ages. PRRSV is a single-strand positive-sense RNA virus. PRRSV is undergoing variation and has emerged new virus strains under the pressure from nature and immunity, posing a challenge to the prevention and control of PRRS.To investigate the epidemiology and genetic variation of pathogenic porcine reproductive and respiratory syndrome(PRRSV) in China from 2013 to 2014, 401 tissue samples collected from partial regions of China(mainly in the northeast of China) were tested by RT-PCR. The GP5 and partial NSP2 genes of 51 positive samples were amplified, sequenced, phylogenetic and alignment analyzed, respectively. The results showed that the PRRSV positive rate was 20.2%, The phylogenetic analysis of GP5 and NSP2 demonstrated that all strains belonged to North American genotype, which gave priority to HP-PRRSV, with coexistence of classic strains and mutant strains. The GP5 and NSP2 of JL580 are similar to NADC30, belonging to a new subtype and clearly differing from other prevalent strains in China. Amino acid analysis of GP5 revealed that most strains had mutations, especially in the hyper-variable regions, the primary neutralizing epitope and decoy epitope. Amino acid alignment of the NSP2 highly variable region of all PRRSV strains compared with those other strains showed that most virus strains had a 30-aa deletion, one strain had a 34-aa deletion and another strain had a 20-aa deletion. The phylogenetic and amino acid analysis of GP5 and NSP2 demonstrated that PRRSV is more complex and diverse in China.In consideration of the specificity of JL580 strain, the full-length genomic sequence of JL580 strains was amplified and analyzed. The results showed that JL580 strain was a recombination strain and clearly different from other prevalent strains in China, Which was a new genotype formed by a genetic exchange between a NADC30-like PRRSV strain in North America and the HP-PRRSV strains in China. JL580 strain shared 84.9% nucleotide similarity of complete sequence compared with CH-1a strain and 84.8%, 84.9%, 85% compared with JXA1, HuN4 and TJ strains. Amino acid mutations of GP5 in the signal peptide and transmembrane domain had huge variation compared to CH-1a, VR-2332 and HuN4. In addition, the full-length genomic sequence of the virus revealed three distinct deletions(131-aa) in NSP2 which was significantly differenct from the 30-aa of HP-PRRSV. The pathogenicity of JL580 is high comparatively. Our study described and characterized the importation of a NADC-30-like PRRSV strain from North America that has emerged in several provinces in China, which resulted in the difficulty to prevent and control with current measures. Therefore, we suggest that surveillance data and vaccine strategies be updated to prevent the disease from spreading further.This study aims to provide necessary experimental data for the epidemiological investigation of PRRS, which will lay a foundation for making effective prevention and treatment measures.