中国西南部分地区2020－2021年猪流行性腹泻病毒遗传变异分析

doi:10.16431/j.cnki.1671-7236.2022.06.028

摘要/Abstract

摘要： 【目的】了解中国西南部分地区流行的猪流行性腹泻病毒（PEDV）基因型及遗传变异规律。【方法】对2020－2021年四川和云南不同地区来源的200份腹泻猪肛门拭子进行RT-PCR检测，对PEDV S和ORF3基因进行克隆测序，利用MegAlign软件进行变异性分析，采用Mega 7.0软件进行系统进化分析，采用RDP4软件进行基因重组分析。【结果】在所有样本中PEDV总体阳性率为15.50%（31/200），群体阳性率为100%（8/8）。检出的8株PEDV S基因和ORF3基因序列与已登录毒株相似性分别为90.5%~99.4%和92.9%~100%。对S基因的进化分析显示，8个PEDV流行株分布于G2a、G2b和G2c 3个亚群中。其中，四川SCWJSWUN02株与福建CH/FJXM/1/2012株遗传距离较近，云南YNKMSWUN01株与越南毒株单独聚为一支，表明当前西南地区PEDV的流行呈现出区域间传播的特征。与本地区近年流行毒株和常用疫苗株相比，其S蛋白氨基酸序列均存在不同程度的变异，但ORF3蛋白相对保守。部分毒株S蛋白存在连续氨基酸的插入或缺失，如在SCMYSWUN03株S蛋白59－62位氨基酸处发现4个氨基酸的缺失；在YNKMSWUN01株78－82位氨基酸处和84－88位氨基酸处分别有5个氨基酸插入和缺失。部分氨基酸突变位点存在于已鉴定的PEDV S蛋白受体结合中。此外，基因重组分析结果显示，SCMYSWUN03株可能发生了基因重组事件，概率为98.2%（P<0.01）。【结论】本研究发现当前西南地区流行的PEDV毒株包括G2a、G2b和G2c 3个亚群，毒株基因型具有多样性，且不同毒株间的变异性较大，丰富了PEDV在四川和云南地区的分子流行病学调查资料，揭示了中国西南地区流行的8个PEDV毒株的分子遗传变异规律和进化特征，为本地区猪腹泻病防控措施的制定提供了理论依据。

关键词: 猪流行性腹泻病毒(PEDV); S基因; ORF3基因; 遗传进化分析

Abstract: 【Objective】 In order to investigate the genotypes and genetic variation of Porcine epidemic diarrhea virus (PEDV) strains spreading in parts of Southwest China.【Method】 200 anal swabs of diarrhea porcine which were collected in different regions of Sichuan and Yunnan from 2020 to 2021 were detected by RT-PCR methods.Then, the S and ORF3 genes of PEDV in positive samples were cloned and sequenced.MegAlign software was used for variability analysis, Mega 7.0 software was used for system evolution analysis, and RDP4 software was used for gene recombination analysis.【Result】 The positive rates of PEDV in all samples were 15.50%(31/200) and the positive rate of population was 100%(8/8).The PEDV S and ORF3 genes sequences of 8 isolates were 90.5%-99.4% and 92.9%-100%, respectively.Phylogenetic analysis based on the S gene showed that 8 PEDV strains were distributed in three subgroups, G2a, G2b, and G2c.Among them, the Sichuan SCWJSWUN02 strain was closed to Fujian CH/FJXM/1/2012 strain, Yunnan YNKMSWUN01 strain and Vietnamese strain were clustered in a separate group.It indicated that the current PEDV epidemic in Southwest China was characterized by inter-regional transmission.Compared with the previously circulating strains and vaccine strains, the amino acid of the S protein of 8 PEDV isolates were changed on different levels.However, ORF3 protein was relatively conserved.The continuous amino acid insertions and deletions were found in the S protein of parts of PEDV strains.Such as, 4 continuous amino acid deletions were found in 59-62 aimo acid of SCMYSWUN03 strain S protein.5 amino acid insertions and deletions were found in 78-82 and 84-88 aimo acid of YNKMSWUN01 strain, respectively.Some amino acid mutations were present in the identified receptor binding domains of the S protein.In addition, the recombination analysis showed that SCMYSWUN03 strain might have gene recombination events, with a probability of 98.2% (P<0.01).【Conclusion】 This study found that the current popular PEDV strains in Southwest China included three subgroups of G2a, G2b and G2c.The genotypes of the strains were diverse, and the variability among different strains was large, which enriched the molecular epidemiological investigation data of PEDV in Sichuan and Yunnan, and revealed the molecular genetic variation law and evolutionary characteristics of 8 PEDV strains prevalent in Southwest China, It provided a theoretical basis for the formulation of prevention and control measures of porcine diarrhea in this region.

Key words: Porcine epidemic diarrhea virus (PEDV); S gene; ORF3 gene; phylogenetic analysis

中图分类号:

S852.65

刘雨桐, 姚妍婷, 黎芮伶, 韩文琪, 石婷, 王一丹, 任玉鹏. 中国西南部分地区2020－2021年猪流行性腹泻病毒遗传变异分析[J]. 中国畜牧兽医, 2022, 49(6): 2279-2290.

LIU Yutong, YAO Yanting, LI Ruiling, HAN Wenqi, SHI Ting, WANG Yidan, REN Yupeng. Analysis of Genetic Variation of Porcine Epidemic Diarrhea Virus in Parts of Southwest China from 2020 to 2021[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2279-2290.

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