藏猪源捷申病毒的检测和遗传演化分析

Detection and Genetic Evolution of Teschovirus of Tibetan Pig Origin in Sichuan

旨在调查四川地区藏猪捷申病毒(porcine teschovirus, PTV)的流行及分子特征和遗传演化。用RT-PCR法对2017—2018年采自四川省甘孜藏族自治州康定市14个藏猪场96份粪便样品进行检测,并对全基因组进行序列分析和基因分型。PCR检测结果表明,PTV核酸阳性率为20.8%(20/96,95%CI=13.2%~30.3%),14个规模藏猪场中PTV猪场阳性率为57.1%(8/14,95%CI=28.9%~82.3%),并从2份阳性样本中获得了2条近似全长的PTV全基因组序列,分别命名为SWU-E5-2018和SWU-ZG2-2018,核苷酸序列相似性为83.1%。通过VP1序列分析发现2条序列的血清型分别为3型和6型。通过基因重组分析发现SWU-E5-2018存在重组现象,重组区域位于衣壳蛋白基因P1的552—3 082 nt处。为了进一步研究2条PTV序列的演化过程,以贝叶斯进化分析软件进行分歧时间估算,结果表明,SWU-E5-2018的分歧时间约为2010年,SWU-ZG2-2018的分歧时间约为2011年。本研究首次对藏猪源PTV进行了初步调查,结果表明藏猪中存在一定程度的PTV感染,为深入研究藏猪源PTV遗传变异及其生物学特性提供了参考依据。

In this study, we investigated the prevalence, molecular characteristics, and genetic evolution of porcine teschovirus (PTV) in Tibetan pigs in Sichuan. Ninety-six fecal samples of Tibetan pigs were collected from 14 farms in Kangding region of Ganzi Tibetan Autonomous Prefecture, Sichuan Province from 2017 to 2018. The samples were detected by the RT-PCR method, and the viral genome was sequenced and genotyped. The overall positive rate of PTV was 20.8% (20/96, 95% CI = 13.2% - 30.3%), and the positive rate of PTV was 57.1% (8/14, 95% CI = 28.9% - 82.3%) in 14 pig farms. Two nearly full-length PTV complete genome sequences were obtained from 2 different clinical samples. The two genomes were of 83.1% nucleotide identity and were named as SWU-E5-2018 and SWU-ZG2-2018. The serotypes of the two sequences were found to be type 3 and type 6 by VP 1 sequence analysis. Furthermore, the SWU-E5-2018 was found to be a recombinant strain by recombination analysis, and the recombinant region was located at 552-3 082 nt of capsid protein P1. To have a further understanding of the evolution process of the two PTV sequences, the divergence time estimation was performed using the Bayesian evolutionary analysis software. The result showed that the divergence timepoints of SWU-E5-2018 and SWU-ZG2-2018 was about 2010 and 2011, respectively. It was the first time to investigate the PTV from Tibetan pigs and to confirm the existence and prevalence of PTV in Tibetan pigs, which provided a reference for further study of viral genetic variation and biological characteristics.