一株柯萨奇病毒B组5型分离株V1641/YN/CHN/2016的全基因序列分析

Full-length-genome Analyses of A Coxsackievirus B5 Strain V1641/YN/CHN/2016 Isolated from Yunnan Province,China,in 2016

对2016年云南省昆明市手足口病相关的柯萨奇病毒B组5型分离株V1641/YN/CHN/2016(简称V1641)全基因组进行测序,并分析其分子变异和进化特点。设计针对V1641的引物,提取病毒RNA,RT-PCR扩增和测序,拼接获得的全基因组序列。利用MEGA7.0.26、Geneious9.1.4和SimPlot3.5.1软件分析全基因序列。V1641毒株基因组全长7 392nt,5’-UTR和3’-UTR分别长744nt和90nt,编码区长6 558nt,与其他CVB5相比未见核苷酸的插入和缺失,编码一个2 185aa的多聚蛋白。CVB5流行株大体上分为两个基因组,中国大陆流行株同原型株Faulkner一起分布于GenogroupⅠ分支,外国流行株大多分布于GenogroupⅡ分支。在GenBank中,V1641与KY303900-417/JS-CHN-2013最为同源,相似性为97.86%。V1641与其他中国大陆流行株的全基因组序列的核苷酸和氨基酸相似性分别为85.1%~97.8%和97.1%~99.6%。V1641在P1、P2和P3区段均与EV-B不同血清型的原型株聚类,经SimPlot3.5.1软件验证,提示有重组事件发生。云南CVB5分离株V1641同中国大陆流行株一样属于GenogroupⅠ基因群,在进化过程中可能发生了重组。中国大陆可能存在多条CVB5传播链。

To analyze the whole-genome sequence of coxsackievirus B5(CVB5)V1641/YN/CHN/2016 strain(V1641)and its molecular variation and evolutionary characteristics. Primers for V1641 were designed,viral RNA was extracted,and amplification and sequencing using reverse transcription-polymerase chain reaction were undertaken to obtain the whole genome sequence. Mega 7.0.26,Geneious9.1.4 and Simplot 3.5.1 were used to analyze the complete gene sequence. The length of the V1641-strain genome was 7392 nt,and the length of the 5’-untranslated region(UTR)and 3’-UTR was 744 nt and 90 nt,respectively. The coding region was 6558 nt. Nucleotide insertions/deletions were not found in the coding sequence of the V1641 strain,which encoded a polyprotein containing 2185 amino acids. The CVB5 strains were,in general,divided into two genomes. The isolated strains from the Chinese mainland and the prototype strain(Faulkner)were distributed in the Genogroup-I branch,whereas the foreign strains were distributed mostly in the Genogroup-II branch. In GenBank,V1641 was the most homologous,with 97.86% homology to KY303900-417/JS-CHN-2013. The homology of nucleotides and amino acids of V1641 was 85.1% – 97.8% and 97.1% – 99.6%,respectively,with the whole genome sequence of other endemic strains in China's Mainland. The V1641 strain was clustered with prototype strains with different serotypes of enterovirus(EV)-B in P1,P2,and P3 regions,and verified by Simplot 3.5.1,suggesting that there was a recombination event. The isolate V1641 along with strains from China's Mainland belong to the same epidemic strain:genogroup gene cluster(Genogroup I). The V1641 strain may have recombined during evolution. There may be multiple CVB5 transmission chains in China's Mainland.