Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China.
Transbound Emerg Dis. 2021 Nov;68(6):3482-3497. doi: 10.1111/tbed.13953. Epub 2021 Feb 7.
Porcine epidemic diarrhea virus (PEDV), which re-emerged in China since 2010, has swept across the whole country leading to tremendous economic losses. In this study, a total of 645 diarrhea samples collected from 156 pig farms in Sichuan and Guizhou province during 2014-2018 were tested for PEDV. We found that samples from 47.66% (84/156) of the farms were positive for PEDV with an overall detection rate of 35.81% (231/645). Fifty-two strains were selected for full-length S gene analyses, and these strains were classified into three subgroups, an S-INDEL subgroup (G1c), and two non-S-INDEL subgroups (G2b, AJ1102-like and G2c), accounting for 15.38% (8/52), 23.08% (12/52) and 59.62% (31/52) of the total analysed strains, respectively. We found these three subgroups of PEDV coexisted in Sichuan province, and the S-INDEL strain was detected in Guizhou. Further antigenic variation analysis of the neutralizing epitopes (S10, COE, SS2, SS6 and 2C10) on the spike protein revealed that the S-INDEL and non-S-INDEL strains shared similar variation features in COE and SS6, but exhibited distinct variation patterns in the S10 domain. Unique variation patterns on N-glycosylation sites in the S protein were also observed for the S-INDEL and non-S-INDEL strains. Moreover, nine strains (three from each subgroup) were subjected to full-genome characterization. Complete genome phylogeny showed an inconsistent tree topology for genotyping, with two G2c strains grouped into the GII-b (AH2012-like) genogroup and the remaining seven strains including three S-INDEL strains grouped into the GII-c genogroup. Further recombination analyses indicated that six of the GII-c strains probably originated from intra-genogroup recombinations. Notably, three newly emerged S-INDEL strains with novel recombination patterns were first identified. Together, our data revealed a new status of PEDV in southwest China, which can increase understanding of the prevalence, genetic characteristics and evolutionary profiles of circulating PEDV strains in China.
猪流行性腹泻病毒（PEDV）自 2010 年在中国再次出现以来，已席卷全国，造成了巨大的经济损失。本研究共检测了 2014-2018 年来自四川和贵州 156 个猪场的 645 份腹泻样本，发现 47.66%（84/156）的猪场样本 PEDV 检测呈阳性，总检出率为 35.81%（231/645）。选择 52 株进行全长 S 基因分析，这些毒株分为三个亚群，一个 S-INDEL 亚群（G1c）和两个非 S-INDEL 亚群（G2b、AJ1102 样和 G2c），分别占总分析株的 15.38%（8/52）、23.08%（12/52）和 59.62%（31/52）。我们发现 PEDV 的这三个亚群在四川省共存，并且在贵州省检测到 S-INDEL 株。进一步对刺突蛋白上中和表位（S10、COE、SS2、SS6 和 2C10）的抗原变异分析表明，S-INDEL 和非 S-INDEL 株在 COE 和 SS6 上具有相似的变异特征，但在 S10 结构域上表现出不同的变异模式。S 蛋白上 N-糖基化位点也观察到 S-INDEL 和非 S-INDEL 株的独特变异模式。此外，对 9 株（每个亚群 3 株）进行了全基因组特征分析。完整基因组系统进化树显示，基因分型的树拓扑不一致，2 株 G2c 株分为 GII-b（AH2012 样）基因群，其余 7 株包括 3 株 S-INDEL 株分为 GII-c 基因群。进一步的重组分析表明，6 株 GII-c 株可能来源于种内重组。值得注意的是，首次鉴定了三种新出现的具有新型重组模式的 S-INDEL 株。总之，我们的数据揭示了中国西南地区 PEDV 的新现状，这可以提高对中国流行的 PEDV 株的流行情况、遗传特征和进化特征的认识。
