河北省一株猪流行性腹泻病毒S1基因的遗传变异与重组分析
Genetic variation and recombination analysis of S1 gene of a strain of porcine epidemic diarrhea virus in Hebei Province
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摘要: 为了解近年来河北地区猪流行性腹泻病毒(Porcine epidemic diarrhea virus, PEDV)的流行性和遗传变异性,试验采集河北省某发病猪场仔猪的小肠组织,提取RNA,对S1基因进行RT-PCR,对扩增的阳性产物进行克隆与测序,对测序结果进行同源性分析,对S1蛋白进行亲水性、表面可触性、抗原指标及T细胞基序分析,利用MEGA X 10.0.5软件对PEDV S1基因进行最大似然法(maximum likelihood, ML)遗传进化分析,利用RDP4软件进行PEDV S1基因的重组分析。结果表明:成功克隆出pMD18-T-PEDV-S1,将该毒株命名为HB/HS/2019株,其包含N末端域和C末端域的S1基因近全长序列,长度为2 163 bp,编码721个氨基酸;成功预测S1潜在的B细胞表位和T细胞基序。经同源性分析,HB/HS/2019与四川株CH/SCJY/2018 S1基因的相似性最高,为99.8%;与比利时CV777毒株的基因相似性为91.4%,存在插入和缺失现象。经进化分析,40株PEDV分为GⅠ群和GⅡ群,HB/HS/2019属于GⅡ群。在GⅡ群内,我国流行株均为2010年后出现,HB/HS/2019与市售疫苗株AJ1102和LW/L亲缘关系较近,与CV777和attenuated CV777株亲缘关系较远。经重组分析,未发现HB/HS/2019 S1序列含有潜在的重组事件,发现GⅠ群和GⅡ群的毒株之间S1基因存在3个重组事件。说明HB/HS/2019 S1基因与2010年以后我国报道的变异毒株亲缘关系较近,虽然该基因存在一些核酸位点变异,但是尚未发生基因重组事件。Abstract: In order to understand the prevalence and genetic variability of Porcine epidemic diarrhea virus(PEDV) in Hebei region in recent years, this experiment was conducted to collect small intestinal tissues of piglets from a pig farm in Hebei Province, for extracting RNA,performing RT-PCR based on S1 gene, cloning and sequencing of amplified positive products, homology analysis of sequencing results, and the analysis of hydrophilicity, surface palpability, antigenic indicators and T cell motifs of S1 protein. MEGA X 10.0.5 software was used to perform genetic evolution analysis of PEDV S1 gene using maximum likelihood(ML). RDP4 software was used to carry out the recombination analysis of PEDV S1 gene. The results showed that pMD18-T-PEDV-S1 was successfully cloned, and the strain was named HB/HS/2019 strain, which contained the nearly full-length sequence of the S1 gene with the N-terminal domain and the C-terminal domain, and the length was 2 163 bp, encoding 721 amino acids; potential B cell epitopes and T cell motifs of S1 were successfully predicted. After homology analysis, HB/HS/2019 had the highest gentic similarity with Sichuan strain CH/SCJY/2018 S1 gene, which was 99.8%,and 91.4% gentic similarity with Belgium CV777 strain, with insertions and deletions. According to evolutionary analysis, 40 PEDV strains were divided into G Ⅰ group and G Ⅱ group; HB/HS/2019 belonged to G Ⅱ group, and in G Ⅱ group, all epidemic strains appeared in China after 2010;HB/HS/2019 was closely related to the commercially available vaccine strains AJ1102 and LW/L,and relatively distant to the CV777 and attenuated CV777 strains. After recombination analysis, no potential recombination events were found in the HB/HS/2019 S1 sequence, and there were 3 recombination events in the S1 gene between the strains of G Ⅰ group and G Ⅱ group. The results suggested that the HB/HS/2019 S1 gene was closely related to the mutant strains reported in China after 2010;although there were some nucleic acid site mutations in this gene, no genetic recombination event had occurred yet.