我国部分省份牛冠状病毒HE基因遗传变异分析

Genetic Variation Analysis of HE Gene of Bovine Coronavirus in Part Areas of China

2020-2023年收集我国14个省份78个临床发病牛群的肛拭子、粪便、组织等样品1819份,用实时荧光RT-PCR方法进行牛冠状病毒(BCoV)检测,并选取部分核酸阳性样品进行HE基因全长的扩增、测序与遗传变异分析。78个发病牛群中,BCoV阳性场占56.41%,共获得35条HE基因全长序列,与参考序列相比,核苷酸同源性为97.0%~100.0%,氨基酸同源性为97.0%~99.8%。系统进化分析表明,BCoV毒株HE基因在进化上呈现典型的地域性特点,亚洲毒株和美国毒株进化上较为接近,而欧洲毒株位于另一个分支,所测毒株与中国参考毒株处于亚-美型毒株分支中,位置相对较为集中。所测35个HE序列中,有34个没有发生插入或缺失突变,来自宁夏的BCoV/NX13/CHN/2023毒株其HE基因存在12个核苷酸的插入突变,证实了BCoV HE基因插入变异株在我国的存在。基因重组分析显示,该毒株与BCoV/HeB120/CHN/2021的HE基因可能发生了重组,预测重组值分别为0.797和0.759。说明了我国部分省份临床发病牛群BCoV感染及BCoV HE基因的遗传变异,为明晰我国BCoV流行毒株分子特征提供参考。

In order to understand the prevalence and genetic variation of bovine coronavirus(BCoV)in selected provinces of China,a total of 1819 samples including nasal swabs,feces and tissue specimens were collected from 78 clinical cases of affected cattle herds from 14 provinces during the period of 2020-2023.BCoV detection was performed using real-time reverse transcription-polymerase chain reaction(RT-PCR),and a subset of positive samples were subjected to full-length amplification,sequencing,and genetic variation analysis of the HE gene.Among the 78 affected herds,56.41%were tested positive for BCoV.A total of 35 complete HE gene sequences were obtained,with nucleotide homology ranging from 97.0%-100.0%compared to the reference sequences,and amino acid homology ranging from 97.0%-99.8%.Phylogenetic analysis revealed the typical geographical pattern of evolution in BCoV strains,with Asian and American strains showing closer evolutionary relationships,while European strains formed a distinct branch.The sequenced strains in this study were grouped within the Asia-America clade,closely related to Chinese reference strains.Among the 35 HE sequences,34 showed no insertions or deletions,except for the BCoV/NX13/CHN/2023 strain from Ningxia,which exhibited a 12-nucleotide insertion in the HE gene.This confirms the presence of BCoV strains with insertional variations in China and suggests the potential for further dissemination.Genetic recombination analysis indicated a possible recombination event between the BCoV/NX13/CHN/2023 strain and BCoV/HeB120/CHN/2021 strain,with predicted recombination values of 0.797 and 0.759,respectively.This study provides insights into the infection status and genetic variation of BCoV in clinical cases of cattle herds in selected provinces of China,serving as a reference for further characterization of circulating BCoV strains in China.