Genetic signatures of the immune-escaping type 2 porcine reproductive and respiratory syndrome virus in farms with a robust vaccination program.

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important porcine viruses worldwide. Recently, severe PRRS outbreaks had occurred in two farms located in eastern and southern Thailand where stringent vaccination had been routinely practiced. Genetic analysis of GP5 identified two highly virulent PRRSVs designated as NA/TH/S001/2015 and NA/TH/E001/2016 from the southern and eastern farms, respectively. Both incidences were the first outbreaks of severe PRRSV since the implementation of the modified live virus (MLV) vaccine, indicating the concurrent emergence of immune-escape viruses. The genetics of the two PRRSV variants, the previous studied sequences from Thailand, and the reference strains were characterized with a focus on the GP5 and NSP2 genes. The results indicated that NA/TH/S001/2015 and NA/TH/E001/2016 shared less than 87% nucleotide similarity to the MLV and PRRSV type 2, lineages 1 and 8.7 (NA), respectively. A comparative analysis of the retrospective GP5 sequences categorized the PRRSVs into five groups based on the clinical outcomes, and both of the novel PRRSV strains were in the same group. Epitope A, T cell epitope, and N-linked glycosylation patterns within GP5 of both PRRSV variants were highly variable and significantly differed from those of MLV. As observed in highly virulent type 2 strains, NA/TH/S001/2015 contained a single amino acid deletion at position 33 in the hypervariable region 1 (HV-1) of GP5. Amino acid analysis of the hypervariable region of NSP2 revealed that NA/TH/E001/2016 had a unique deletion pattern that included two discontinuous deletions: a 127-amino acid deletion from residues 301 to 427 and a single amino acid deletion at position 470. These results indicate the emergence of two novel PRRSV strains and highlight the common genetic characteristics of the immune-escaping PRRSV variants.