四川地区藏猪戊型肝炎病毒的检测和遗传演化分析

旨在调查四川地区藏猪戊型肝炎病毒（hepatitis E virus，HEV）的流行情况和遗传演化，作者用RT-PCR法对2018—2020年采集自四川省甘孜藏族自治州和阿坝藏族自治州的22个藏猪场332份藏猪粪便样本进行HEV检测，并对阳性样本进行基因分型。RT-PCR检测结果表明HEV核酸阳性率为20.48%（68/332，95% CI=16.3%~25.2%），22个规模藏猪场中HEV猪场阳性率为77.27%（17/22，95% CI=54.6%~92.2%），健康样本阳性率为2.86%（3/105，95% CI=0.6%~8.1%），腹泻样本阳性率为28.63%（65/227，95% CI=22.8%~35.0%），系统进化分析显示所有阳性株均为G4型。为了进一步研究该地区流行毒株的演化过程，以贝叶斯进化分析软件进行分歧时间估算，结果表明，藏猪流行毒株的分歧时间最早为1999年，最晚为2016年。并分别从每年的样本中挑选1份阳性样本得到全基因组序列，核酸序列相似性为89.5%~93.1%。通过对3条全基因组重组分析发现SWU/301/2019存在重组现象，SWU/301/2019重组区域位于ORF1的3 746—4 655 bp。本研究首次对四川地区藏猪源HEV进行调查，结果表明四川藏猪中存在一定程度的HEV感染，为四川地区对藏猪感染HEV的防治以及深入研究四川藏猪源HEV遗传变异及生物学特性提供了参考依据。

Detection and Genetic Evolution of Hepatitis E Virus in Tibetan Pigs in Sichuan

The present study aimed to investigate the prevalence and genetic evolution of hepatitis E virus (HEV) in Tibetan pigs in Sichuan. Three hundred and thirty-two Tibetan pig fecal samples collected from 22 Tibetan pig farms in Ganzi Tibetan Autonomous Prefecture and Aba Tibetan Autonomous Prefecture of Sichuan Province from 2018 to 2020 were tested for HEV by RT-PCR, and the positive samples were genotyped. The results of RT-PCR showed that the positive rate of HEV nucleic acid was 20.48% (68/332, 95% CI=16.3%-25.2%), the positive rate of HEV pig farms was 77.27% (17/22, 95% CI=54.6%-92.2%), the positive rate of healthy samples was 2.86% (3/105, 95% CI=0.6%-8.1%), and the positive rate of diarrhea samples was 28.63% (65/227, 95% CI=22.8%-35.0%) in 22 large-scale Tibetan pig farms. Phylogenetic analysis showed that all positive strains were G4 type. In order to further study the evolution process of epidemic strains in this area, Bayesian evolutionary analysis software was used to estimate the divergence time, and the results showed that the divergence time of epidemic strains in Tibetan pigs was as early as 1999 and as late as 2016. The complete genome sequences were obtained from one positive sample each year, and the nucleic acid sequence identities were 89.5%-93.1%. Recombination was found in SWU/301/2019 by analysis of three genome-wide recombinations, and the SWU/301/2019 recombination region was located at 3 746-4 655 bp of ORF1. This study is the first to investigate HEV in Tibetan pigs in Sichuan. The results show that there is a certain degree of HEV infection in Tibetan pigs in Sichuan, which provides a reference for the prevention and control of HEV infection in Tibetan pigs in Sichuan and for the in-depth study of genetic variation and biological characteristics of HEV in Tibetan pigs in Sichuan.