Chen Jinlong, Tian Lulu, Liu Yucheng, Sun Yaoqiang, Li Zhiyuan, Cai Xuepeng, Meng Qingling, Qiao Jun
College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
Xinjiang Agricultural Vocational and Technical College, Changji, 831100, Xinjiang, China.
Arch Virol. 2024 Apr 15;169(5):96. doi: 10.1007/s00705-024-06029-z.
In recent years, the pig industry in Xinjiang, China, has been severely impacted by outbreaks of porcine epidemic diarrhea (PED), despite vaccination efforts. In this study, we investigated the genetic characteristics of currently prevalent porcine epidemic diarrhea virus (PEDV) strains in the region. We collected 548 samples from animals with suspected PED on large-scale pig farms in Xinjiang. Of these, 258 tested positive for PEDV by RT-PCR, yielding an overall positivity rate of 47.08%. S1 gene sequencing and phylogenetic analysis were conducted on 23 randomly selected RT-PCR-positive samples. Three endemic strains of PEDV (PEDV/CH/XU/2020, PEDV/CH/XK/2020, and PEDV/CH/XA/2020) were isolated, and their complete genome sequences were analyzed for evidence of genetic recombination. Sequence comparison of the S gene indicated significant variations in the S1 gene of the Xinjiang strains compared to the vaccine strains CV777, AJ1102, and LWL, with 90.2%-98.5% nucleotide sequence identity. Notably, both the N-terminal and C-terminal domains of the S protein showed significant variation. Genetic evolutionary analysis identified the GIIa subtype as the dominant genotype among the epidemic strains in Xinjiang. Recombination analysis revealed inter-subtype recombination events in the PEDV/CH/XK/2020 and XJ1904-34 strains. These findings highlight the extensive genetic variation in the predominant GIIa genotype of PEDV in Xinjiang, which does not match the genotype of the currently used vaccine strains. These data may guide further efforts toward the development of effective vaccines for the control of PED.
近年来，尽管采取了疫苗接种措施，但中国新疆的养猪业仍受到猪流行性腹泻（PED）疫情的严重冲击。在本研究中，我们调查了该地区当前流行的猪流行性腹泻病毒（PEDV）毒株的遗传特征。我们从新疆大型养猪场疑似患有PED的动物中收集了548份样本。其中，258份样本经逆转录聚合酶链反应（RT-PCR）检测PEDV呈阳性，总体阳性率为47.08%。对23份随机选择的RT-PCR阳性样本进行了S1基因测序和系统发育分析。分离出三株PEDV地方流行毒株（PEDV/CH/XU/2020、PEDV/CH/XK/2020和PEDV/CH/XA/2020），并对其完整基因组序列进行分析以寻找基因重组证据。S基因序列比较表明，与疫苗毒株CV777、AJ1102和LWL相比，新疆毒株的S1基因存在显著变异，核苷酸序列同一性为90.2%-98.5%。值得注意的是，S蛋白的N端和C端结构域均显示出显著变异。遗传进化分析确定GIIa亚型是新疆流行毒株中的优势基因型。重组分析揭示了PEDV/CH/XK/2020和XJ1904-34毒株中存在亚型间重组事件。这些发现突出了新疆PEDV优势GIIa基因型中广泛的遗传变异，这与目前使用的疫苗毒株基因型不匹配。这些数据可能为进一步开发控制PED的有效疫苗提供指导。
