青岛市7株柯萨奇病毒A4型分离株全基因特征分析

Whole genome sequencing of 7 strains of coxsackievirus A4 isolated in Qingdao

目的 了解7株青岛市CVA4病毒株的全基因组特征,探讨CVA4毒株的基因变异进化特征。方法 对人恶性胚胎横纹肌瘤细胞(human malignant embryonal rhabdomyoma cell, RD cell)培养分离得到的7株来源于青岛市手足口病普通病例的CVA4毒株进行全基因组序列扩增,应用BioEdit7.09、DNASTAR6.0、MEGA5.2和SimPlot序列分析软件对扩增产物进行拼接比对测序,并与从GenBank中选取的5株中国CVA4毒株进行比对。结果 7株青岛CVA4毒株基因组核苷酸数目为7 344~7 395 bp,与原型株AY421762.1HIGH POINT比较,在编码区无碱基插入和缺失。对7株毒株进行两两同源比对,结果显示7株青岛CVA4毒株全基因组序列核苷酸一致性为87.44%~97.79%,氨基酸同源性为97.17%~99.09%。基因重组分析结果显示,15FG936株与A2/P373/2013/China株存在基因重组,15FG1059株与CV-A6/40428/TKM/2011株存在基因重组,其他5株CVA4毒株未发现明显的重组。结论 青岛市7株CVA4毒株中有2株发生了基因重组变异。

Objective To understand the whole genomic characteristics of 7 strains of coxsackievirus A4(CVA4) isolated in Qingdao, and to investigate the genetic evolution of CVA4. Methods The whole genomes of seven strains of CVA4 isolated from patients with hand, foot, mouth disease in Qingdao were sequenced.BioEdit7.09, DNASTAR 6.0, MEGA7.0 and SimPlot3.5.1 were used for genetic evolution, alignment and sequence analysis.The sequences were compared with 5 CVA4 strain sequences obtained from GenBank in China. Results The length of whole genome of 7 CVA4 strains ranged from 7 180-7 395 bp, and there was no nucleotide insertion or deletion in the coding region compared with the prototype strain AY421762.1 HIGH POINT.Phylogenetic analysis indicated that the nucleotide and amino acid homologies of 7 Qingdao CVA4 strains were 87.44%-97.79% and 97.17%-99.09%, respectively.Genetic recombination analysis revealed that gene recombination was identified between 15 FG936 strain and A2/p373/2013/China strain as well as between 15 FG1059 strain and CV-A6/40428/TKM/2011 strain. Conclusions Two of the seven CVA4 strains in Qingdao develop gene recombination mutations, this findings provide scientific basis for further study on the epidemic characteristics and evolution of CVA4 strain.