2017—2019年猪德尔塔冠状病毒广西流行毒株遗传多样性分析

Genetic diversity of porcine deltacoronavirus in Guangxi Province from 2017 to 2019

为了解广西壮族自治区猪德尔塔冠状病毒(PDCoV)流行毒株的遗传变异情况,采集2017—2019年广西各地病猪腹泻病料,采用RT-PCR方法检测PDCoV,并对阳性样品进行扩增、测序,共获得S、M、N基因序列各16株。同源性分析显示,S、M、N基因核苷酸序列同源性在广西流行毒株之间分别为95.8%~99.9%、95.9%~100%和97.9%~99.9%,在广西流行毒株与国内外参考毒株之间分别为95.1%~100%、95.0%~100%和96.3%~99.9%。序列比对显示,广西流行毒株S1蛋白区域存在氨基酸序列的突变及插入,不同流行毒株之间存在一定差异。基于S、M、N基因核苷酸序列绘制遗传进化树,获得相似的拓扑结构图,均可分为Ⅰ、Ⅱ、Ⅲ三个群,Ⅰ群毒株来自美国、日本、韩国等,Ⅱ群毒株来自中国,Ⅲ群毒株来自中国、越南、老挝、泰国等;广西流行毒株主要分布在Ⅱ群,个别毒株分布在Ⅲ群,部分毒株单独形成一个小分支。遗传进化速率计算显示,广西流行毒株及国内外参考毒株S、M、N基因的平均进化速率为2.57×10^-4、2.07×10^-4、1.70×10^-4substitutions/site/year,S基因进化速率最快。结果表明,PDCoV广西流行毒株间S、M、N基因序列存在遗传变异现象,具有遗传多样性。

To understand the genetic diversity of porcine deltacoronavirus(PDCo V) in Guangxi Province,clinical diarrhea samples were collected from suspected piglets in Guangxi Province from2017 to 2019,detected by RT-PCR for PDCoV,and the positive samples were used for amplification and sequence of S,M,N genes.Finally,16 S,M and N gene sequences of PDCoV were obtained.Homology analysis showed that the S,M,N gene nucleotide identity among Guangxi strains were 95.8% —99.9%,95.9% —100% and 97.9% —99.9%,respectively.The nucleotide identity of S,M and N genes among Guangxi strains and other reference strains were 95.1%—100%,95.0%—100%and 96.3%—99.9%,respectively.Sequence alignment showed that S1 protein existed amino acid mutations and insertions,and there were some variations among different epidemic strains.Phylogenetic trees based on S,M and N genes obtained similar topological diagram and all strains could be divided into GroupⅠ,GroupⅡ and GroupⅢ,of which Group Ⅰ came from USA,Japan and Korea,Group Ⅱ came from China,and Group Ⅲ came from China,Vietnam,Laos and Thailand.Most strains from Guangxi Province distributed in Group Ⅱ,individual strain distributed in GroupⅢ and some strains formed a single small branch.The evolutionary rates of S,M and N genes of Guangxi strains and other reference strains were 2.57×10^-4,2.07×10^-4,1.70×10^-4 substitutions/site/year,respectively,showing that the evolutionary rate of S gene was the fastest.The results indicated that the S,M,N genes of PDCo V strains from Guangxi Province had some variations and existed genetic diversity.