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

Abstract

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

CLC Number:

S858.28

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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Analysis of Genetic Variation of S1 Gene of Porcine Epidemic Diarrhea Virus in Some Areas of China from 2020 to 2021

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