2020—2021年中国部分地区猪流行性腹泻病毒S1基因遗传变异分析

doi:10.16431/j.cnki.1671-7236.2023.06.031

摘要/Abstract

摘要： 【目的】了解2020―2021年猪流行性腹泻病毒（Porcine epidemic diarrhea virus，PEDV）的流行情况和遗传变异情况。【方法】本研究对中国部分地区73个猪场的525份样本进行RT-PCR检测，对检测为阳性的样本进行PEDV S1基因扩增与测序，并进行流行病学统计分析，使用DNAStar软件进行核苷酸相似性分析和氨基酸位点变异分析，利用Mega 6.06软件对PEDV S1基因进行遗传进化分析，对疑似重组的序列使用RDP4软件进行S1基因重组分析。【结果】在2020—2021年的525份临床样本中PEDV检出阳性率为26.29%（138/525）。流行病学统计分析显示，冬季属于PEDV高发季节，1日龄仔猪感染率最高，为42.75%（59/183），并在中国6个地区大范围流行。S1基因遗传进化分析显示，138株PEDV S1基因序列主要位于两个分支，131株毒株属于G2群，其中126株属于G2a亚群，与HBXY2、SNJ-P在同一亚群，5株属于G2b亚群，与AJ1102、LW/L、S14在同一亚群；其余7株毒株位于G1群和G2群之间，形成一个独立分支。经重组分析发现，该分支的7株毒株存在同一种重组事件，断点位于第59―695 bp处，可能为跨群重组毒株；138个S1基因序列之间核苷酸相似性为85.7%~100%，与经典毒株CV777的核苷酸相似性为85.2%~92.3%，其中131株G2群分离毒株与经典毒株CV777相比，在S1基因N端第56、59-62、138-139、159-160位，与G2群参考株氨基酸序列存在相同并具有特征性的缺失和插入。【结论】2020―2021年PEDV流行株呈变异趋势，其主要流行基因型为G2群，与2010年以后流行的变异株亲缘关系较近，与经典毒株亲缘关系较远，且存在跨群重组，对中国持续监测PEDV流行性和变异性具有重要意义。

关键词: 猪流行性腹泻病毒(PEDV); S1基因; 遗传变异; 重组

Abstract: 【Objective】 This study was aimed to understand the prevalence and genetic variation of Porcine epidemic diarrhea virus (PEDV) from 2020 to 2021.【Method】 In this study, 525 samples of 73 pig farms in some regions of China were tested by RT-PCR.The PEDV S1 gene of the positive samples were amplified and sequenced, and epidemiological statistical analysis was conducted.Nucleotide similarity and amino acid site variation were analyzed by DNAStar software.The genetic evolution of PEDV S1 gene was analyzed by Mega 6.06 software, and the suspected recombinant sequence of S1 gene was analyzed by RDP4 software.【Result】 The PEDV positive rate was 26.29%(138/525) in 525 clinical samples from 2020 to 2021.Epidemiological statistical analysis showed that winter was the high incidence season of PEDV, and the infection rate of 1-day-old piglets was the highest (42.75%, 59/183), which was widely prevalent in 6 regions of China.Genetic evolution analysis of S1 gene showed that 138 PEDV S1 gene sequences were mainly located in two branches, and 131 strains belonged to G2 group, of which 126 strains belonged to G2a subgroup with HBXY2 and SNJ-P, another 5 strains belonged to G2b subgroup with AJ1102, LW/L and S14, and the remaining 7 strains were located between G1 and G2 groups, forming an independent branch.The recombination analysis showed that 7 strains in this branch had the same recombination condition, and the breakpoint was at 59-695 bp, which might be cross-group recombination strains.The nucleotide similarity between 138 S1 gene sequences was 85.7%-100%, and the nucleotide similarity with classic strain CV777 was 85.2%-92.3%.Compared with the classical strain CV777, the nucleotides at 56, 59-62, 138-139 and 159-160 sites of S1 gene of 131 strains isolated from group G2 were similar.The amino acid sequence was the same as that of the reference strains in G2 group, with feature deletion and insertion.【Conclusion】 The PEDV epidemic strains showed a trend of variation from 2020 to 2021, and the main epidemic genotype was G2 group, which was closely related to the variation strains prevalent after 2010, but far related to the classical strains, and there was cross-group recombination, which was of great significance for the continuous monitoring of PEDV epidemic and variability in China.

Key words: Porcine epidemic diarrhea virus(PEDV); S1 gene; genetic variation; recombination

中图分类号:

S858.28

史秋颖, 段宝敏, 李颖, 牛登云, 耿晨阳, 周佳伟, 王蕊, 冯敬敬. 2020—2021年中国部分地区猪流行性腹泻病毒S1基因遗传变异分析[J]. 中国畜牧兽医, 2023, 50(6): 2468-2478.

SHI Qiuying, DUAN Baomin, LI Ying, NIU Dengyun, GENG Chenyang, ZHOU Jiawei, WANG Rui, FENG Jingjing. Analysis of Genetic Variation of S1 Gene of Porcine Epidemic Diarrhea Virus in Some Areas of China from 2020 to 2021[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2468-2478.

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