College of Life Science and Technology, Southwest Minzu University, Chengdu 610041, China.
College of Life Science and Technology, Southwest Minzu University, Chengdu 610041, China; Institute of Animal Science of Ganzi Tibetan Autonomous Prefecture of Sichuan Province, Kangding 626000, China.
Virus Res. 2019 Sep;270:197652. doi: 10.1016/j.virusres.2019.197652. Epub 2019 Jul 10.
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.
本研究旨在调查 2018 年青藏高原藏猪流行腹泻病毒（PEDV）的流行情况和遗传变异。从 193 份藏猪粪便样本中，PCR 检测到 PEDV 的阳性检出率为 38.34%（95%CI=31.5-45.6%）。从藏猪中发现了新型 PEDV，获得并分析了七个完整的 S 基因。在藏猪 PEDV 的 S 基因中检测到独特的多个突变，其中一个导致中和表位的新氨基酸取代。系统进化分析显示，七个 S 基因与其他 PEDV 具有显著的遗传距离。特别地，两个 S 基因在 G2 分支上形成了一个新的亚群，其中不同株之间发生了相同的重组事件。其余五个 S 基因在 G1 分支上形成了一个新的亚群，其中 G1 和 G2 株之间发生了明显的重组事件。结果表明，藏猪 PEDV 的 S 基因中检测到新的重组事件，这些事件可能在青藏高原流行。值得注意的是，本研究获得的四个完整的 PEDV 基因组具有相同的 S2、ORF3 和 E 基因跨越的重组区域。这是 PEDV 基因组中交叉重组事件的首次报道。我们的研究结果不仅增强了对 PEDV 遗传进化的认识，还表明藏猪中出现了新型 PEDV 株。
