Whole-Genome, Recombinant, and Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus Strain CH/JSXZ/2015

Abstract

Background. Porcine epidemic diarrhea virus (PEDV) is an important pathogen causing highly contact infectious intestinal infections in pigs belonging to the family Coronaviridae, genus Coronavirus, 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.