Genetic characterization of a novel recombined porcine reproductive and respiratory syndrome virus 2 among Nadc30-like, Jxa1-like and TJ-like strains

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating viral diseases in the global pig industry, including China. Recently, we successfully isolated a porcine reproductive and respiratory syndrome virus (PRRSV) from lung tissue and peripheral blood of piglets at a farm from Dujiangyan in Sichuan, China, and named it the DJY-19 strain. The full-length genome sequence of DJY-19 shared 86.8%-94.1% nucleotide similarity with NADC30-like and NADC30 PRRSV strains. We compared the open reading frame (ORF) 5 gene of DJY-19 with 34 PRRSV strains from Genbank. Phylogenetic analysis showed that DJY-19 clustered with NADC30 strains, characterized by a predicted 131-amino-acid deletion in the nonstructural protein (NSP) 2. The results of homology analysis showed that the homology between DJY-19 and NADC30 (JN654459.1) strains was the highest (95.9%), whereas homology with other domestic strains was lower (80.9%-92.6%). Furthermore, we identified four recombination breakpoints in the DJY-19 genome; they separated the DJY-19 genome into four regions. The 8106-9128 nucleotide (nt) region of DIY-19 was highly similar to the TJ strain, and the 12106-12580 nt region of DIY-19 was highly similar to the JXA1-R strain. Our findings demonstrate that DJY-19 arose from the recombination of North America NADC30 strain and TJ strain and JXA1-R in China. The application of multiple attenuated vaccine strains has led to complex recombination of PRRSV strains in China. This study provides a theoretical basis for making a more reasonable PRRS virus control and prevention strategy.