猪流行性腹泻病毒CH/JSXZ/2015株的全基因组、重组及系统发育分析
Whole-Genome, Recombinant, and Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus Strain CH/JSXZ/2015.
作者信息
Huan Changchao, Guo Xinyue, Cheng Jinlong, Chen Pengxiang, Ni Bo, Zhang Wei, Yao Jingting, Jiang Luyao, Gao Song
机构信息
Institutes of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China.
Yangzhou University and Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China.
出版信息
Transbound Emerg Dis. 2023 Nov 8;2023:2991270. doi: 10.1155/2023/2991270. eCollection 2023.
BACKGROUND
Porcine epidemic diarrhea virus (PEDV) is an important pathogen causing highly contact infectious intestinal infections in pigs belonging to the family , genus , which can cause porcine epidemic diarrhea (PED). Since 2010, outbreaks of PEDV variants have caused great economic losses to the swine industry worldwide. Our study will provide the basis for discovering the key points of PEDV variation and help in understanding the trend of popularity and evolution of PEDV in China.
METHODS
We amplify the complete PEDV CH/JSXZ/2015 genome sequence from naturally infected piglets in Xuzhou, Jiangsu Province, China, by RT-PCR. The comparative genome circle graph, characterization and phylogenetic analysis, and recombination in the PEDV CH/JSXZ/2015 and other PEDVs are analyzed by bioinformatics analysis software.
RESULTS
At the whole-genome level, CH/JSXZ/2015 showed the highest nucleotide identity (99.5%) with CH/GDZHDM/1401 strain (KR153326.1 and KX016034.1) and the lowest similarity (93.5%) to 85-7-mutant1 strain. CH/JSXZ/2015 S amino acid identity was 90.8%-99.8% compared with other strains. CH/JSXZ/2015 ORF3 amino acid identity was 91.2%-100.0% compared with other PEDV strains. Phylogenetic analysis based on the whole genome, S, and ORF3 revealed that CH/JSXZ /2015 is most genetically close to the CH/GDZHDM/1401 strain (KR153326.1 and KX016034.1) isolated in China in 2014. In addition, we revealed that the CH/GDZHDM/1401 (KX016034.1) strain, PEDV 1842/2016 ITA, and CH/JSXZ /2015 had recombination, and the position of recombination was 1-5530 and 28185-28544 bp. 5531-28184 bp of JSXZ are highly homologous to CH/GDZHDM/1401 (KX016034.1), while 1-5530 and 28185-28544 bp of JSXZ are highly homologous to 1842/2016 ITA. These results helped discover PEDV variation rules and provided a basis for preventing and controlling PEDV.
CONCLUSIONS
Our study revealed that PEDV CH/JSXZ/2015 was a variant strain, the current epidemic strain in China. The CH/GDZHDM/1401 (KX016034.1) strain, PEDV 1842/2016 ITA (KY111278) and CH/JSXZ /2015 had recombination.
背景
猪流行性腹泻病毒（PEDV）是引起猪高度接触性传染性肠道感染的重要病原体，属于 科 属，可引发猪流行性腹泻（PED）。自2010年以来，PEDV变异株的爆发给全球养猪业造成了巨大经济损失。我们的研究将为发现PEDV变异的关键点提供依据，并有助于了解PEDV在中国的流行和进化趋势。
方法
我们通过逆转录聚合酶链反应（RT-PCR）从中国江苏省徐州市自然感染的仔猪中扩增出完整的PEDV CH/JSXZ/2015基因组序列。利用生物信息学分析软件对PEDV CH/JSXZ/2015与其他PEDV的比较基因组环形图、特征及系统发育分析以及重组情况进行分析。
结果
在全基因组水平上，CH/JSXZ/2015与CH/GDZHDM/1401株（KR153326.1和KX016034.1）的核苷酸同一性最高（99.5%），与85-7-mutant1株的相似性最低（93.5%）。CH/JSXZ/2015的S氨基酸同一性与其他毒株相比为90.8%-99.8%。CH/JSXZ/2015的ORF3氨基酸同一性与其他PEDV毒株相比为91.2%-100.0%。基于全基因组、S和ORF3的系统发育分析表明，CH/JSXZ /2015在遗传上与2014年在中国分离的CH/GDZHDM/1401株（KR153326.1和KX016034.1）最为接近。此外，我们发现CH/GDZHDM/1401（KX016034.1）株、PEDV 1842/2016 ITA和CH/JSXZ /2015发生了重组，重组位置为1-5530和28185-28544 bp。JSXZ的5531-28184 bp与CH/GDZHDM/1401（KX016034.1）高度同源，而JSXZ的1-5530和28185-28544 bp与1842/2016 ITA高度同源。这些结果有助于发现PEDV变异规律，为PEDV的防控提供依据。
结论
我们的研究表明，PEDV CH/JSXZ/2015是一个变异株，是中国目前的流行毒株。CH/GDZHDM/1401（KX016034.1）株、PEDV 1842/2016 ITA（KY111278）和CH/JSXZ /2015发生了重组。
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