猪丁型冠状病毒的分离鉴定与基因分析

Isolation, Identification and Genetic Analysis of Porcine Deltacoronavirus

关键词:  猪丁型冠状病毒  分离鉴定  腹泻  基因分析

Key words:  porcine deltaconoravirus  identification  isolation  diarrhea  genetic analysis

摘要:

对山东省某养殖场的腹泻病料进行检测，确认为猪丁型冠状病毒（PDCoV）阳性。使用ST细胞分离到一株PDCoV，命名为SD株。全基因序列测定以及与GenBank中其他68株PDCoV全基因序列比对分析以及遗传进化分析结果表明：PDCoV SD株的全基因组（不包括3""poly（A）尾）序列长度为25414个核苷酸（nt），与参考株HKU15-155、CH/Sichuan/S27/2012和CH-HB-2014的核苷酸同源性分别为98.97%、99.06%和99.13%；此外，在nsp2区的1739~1744位（对应于HKU15-44序列）中的6 nt（TTTGAA）缺失和nsp3区的2810~2818位的9 nt（TCGGCAATG）缺失为特征性基因突变；69株PDCoV呈现出明显的地域特征，其中美国与韩国的PDCoV毒株为一个大分支，越南与泰国PDCoV毒株为另一个小分支，中国的23株PDCoV则呈现出4个小分支，充分展现了该病毒的基因多样性。试验可为中国PDCoV的流行病学和诊断研究以及进一步的疫苗开发提供参考。

Abstract:

Diarrheal samples collected from a farm in Shandong Province, were detected and verified as PDCoV positive. Afterwards, a PDCoV strain was isolated by using the ST cell line and denominated as strain SD. Complete genome sequencing and alignment with other 68 strains of PDCoV in GenBank were performed, and the results showed that the complete genome sequence length of PDCoV SD strain was 25414 nucleotides (nt), excluding the 3""poly(A) tail. The nucleotide homology of SD strains with reference strains HKU15-155, CH/Sichuan/S27/2012, and CH-HB-2014 were 98.97%, 99.06%, and 99.13%, respectively, and there were several characteristic genetic mutations, such as 1739 to 1744 in the nsp2 region (corresponding to 6nt (TTTGAA) deletion in the HKU 15-44 sequence) and 9nt (TCGGCAATG) deletion in 2810 to 2818 in the nsp3 region. Phylogenetic analysis revealed that 69 PDCoV strains showed obvious regional characteristics. Among them, PDCoV strains in the United States and South Korea formed one large branch, and PDCoV strains in Vietnam and Thailand formed another small branch. Besides that, a number of 23 PDCoV in China shows four smaller branches, fully demonstrates the genetic diversity of PDCoV. These data will faciliate epidemiological and diagnostic studies of PDCoV in China, as well as further vaccine development.