Emergence of porcine epidemic diarrhea viruses with the novel S genes in Tibetan pigs in the Qinghai-Tibetan plateau in China.

The purpose of present study was to investigate the prevalence and genetic variation of porcine epidemic diarrhea virus (PEDV) in Tibetan pigs on the Qinghai-Tibetan Plateau in 2018. The PCR yielded a significantly high detection rate (38.34%, 95%CI=31.5-45.6%) for PEDV from 193 fecal samples from Tibetan pigs. The novel PEDVs were discovered in Tibetan pigs and seven complete S genes were obtained and analyzed. The unique multiple mutations were detected in S genes of PEDV from Tibetan pigs, one of which led to a new amino acid substitution of a neutralizing epitope. Phylogenetic analysis showed that seven S genes had significant genetic distance to other PEDV. Specially, two S genes formed a novel subgroup on the genogroup 2 (G2) branch, of which same recombination event occurred between different strains from genotype G2. The remaining five S genes formed a new subgroup on the G1 branch, among which distinct recombination events occurred between genotypes G1 and G2 strains. The result indicated that the new recombination events were detected in the S genes of PEDV from Tibetan pigs, which could be circulating in the Qinghai-Tibetan Plateau. Notably, the four complete PEDV genomes obtained in this study had an identical recombination region spanning S2, ORF3 and E genes. This is the first report of the crossover regional recombination event in PEDV genome. Our findings not only augmented current understanding of the genetic evolution of PEDV, but also indicated that new variants of PEDV strains have been emerging in Tibetan pigs.