2020—2021年我国部分地区猪流行性腹泻病毒S1、M和ORF3基因遗传进化分析

Genetic evolution analysis of Porcine epidemic diarrhea virus S1,M and ORF3 genes in some areas of China from 2020 to 2021

为了解2020—2021年我国部分地区猪流行性腹泻病毒(Porcine epidemic diarrhea virus,PEDV)毒株变异及遗传进化情况,试验从多个地区的51家猪场采集340份疑似感染PEDV的猪小肠组织、粪便和肛拭子,提取病毒核酸后采用RT-PCR方法扩增S1、M和ORF3基因并测序,与GenBank中PEDV参考毒株进行比对分析,利用生物信息学软件构建遗传进化树,分析核苷酸序列同源性及氨基酸序列。结果表明:共获得57份PEDV阳性样品,来源于14家猪场,猪场阳性率为27.5%,并对从阳性猪场获得的14株毒株进行命名。与经典毒株CV777相比,14株PEDV毒株的S1、M和ORF3基因均出现不同程度的氨基酸突变。在14株毒株的S1基因中,Heyuan2021-7毒株位于G1-2分支,其余13株位于G2分支,14株毒株与参考毒株GD-A核苷酸序列的相似性较高,为89.3%~99.9%,存在多处氨基酸的缺失和插入。在M基因中,14株毒株位于G2分支且与参考毒株FR-001核苷酸序列的相似性为98.1%~99.7%,只存在氨基酸突变。在ORF3基因中,FC2021-1、GDzq2020-12、GDmm^(2)021-1和GDjm-DG-2021-12毒株位于G1-2分支,其余10株位于G2分支,14株毒株与参考毒株VN-JFP1013核苷酸序列的相似性为95.4%~99.3%,同源性较高,只存在氨基酸突变。说明2020—2021年我国部分地区流行的PEDV毒株有G1型和G2型毒株,其S1基因较M和ORF3基因突变程度更大,PEDV的流行情况相对复杂。

In order to understand the variation and genetic evolution of the strains of Porcine epidemic diarrhea virus(PEDV)in some areas of China from 2020 to 2021,in this experiment,340 small intestinal tissue,feces and anus swabs suspected of being infected with PEDV were collected from 51 pig farms in multiple areas.After extracting viral nucleic acids,S1,M and ORF3 genes were amplified by RT-PCR and sequenced,and compared with the PEDV reference strains in GenBank.Bioinformatics softwares were used to construct an evolutionary tree and analyze nucleotide sequence homology and amino acid sequences.The results showed that a total of 57 PEDV-positive samples were obtained from 14 pigfarmswith a positive rate of 27.5%,and 14 strains obtained from positive pig farms were named.Compared with the classical strain CV777,the S1,M and ORF3 genes of the 14 PEDV strains all had different degrees of amino acid mutations.Among the S1 gene of 14 strains,the Heyuan2021-7 strain was located in the G1-2 branch,and the remaining 13 strains were located in the C2 branch;the similarity of nucleotide sequences of 14 strains and the reference strain CD-A was high,which were 89.3%-99.9%,and there were multiple amino acid deletions and insertions.Among the M gene,14 strains were located in the G2 branch,and the nucleotide sequence similarity with the reference strain FR-001 was 98.1%-99.7%,and only amino acid mutations existed.Among the ORF3 gene,FC2021-1,GDzq2020-12,GDmm^(2)021-1 and CDjm-DG-2021-12 strains were located in the G1-2 branch,and the remaining 10 strains were located in the G2 branch.The similarity of nucleotide sequences of the 14 strains and the reference strain VN-JFP1013 was 95.4%-99.3%,and the homology was high,and only amino acid mutations existed.The results suggested that the PEDV strains broke out in some areas of China from 2020 to 2021 included G1 type and G2 type,and their S1 gene had a greater mutation degree than M and ORF3 genes,and the prevalence of PEDV wasrelativelycomplicated.