2008年柯萨奇病毒A组16型昆明分离株KMM08全基因组序列分析

目的 分析柯萨奇病毒A组16型(CA16)昆明分离株KMM08全基因序列,了解其遗传特性.方法 设计针对CA16引物,提取病毒RNA,RT-PCR扩增和产物直接测序获得序列.利用Mega 4.1,RDP3和SimPlot 3.5.1等软件分析全基因序列.结果 获得KMM08全基因组核苷酸序列长度为7409bp,编码含2193个氨基酸残基的多聚蛋白;与其他CA16参考株核苷酸和氨基酸同源性分别为79.0％～ 98.2％和94.5％ ～ 99.3％,其中SZ-HK08-3与国际标准株G10核苷酸和氨基酸同源性分别79.1％和94.8％;而与肠道病毒71型(EV71)标准株BrCr同源性分别为78.7％和89.0％.在各个区段上,KMM08与SZ-HK08-3的核苷酸和氨基酸同源性分别为97.0％～99.0％和98.0％～100.0％,同源性最高;与G10的核苷酸和氨基酸同源性分别为74.2％ ～ 86.9％和90.9％ ～97.0％;与EV71 BrCr核苷酸和氨基酸同源性分别在65.0％ ～ 84.9％和71.0％～95.2％.进化分析发现KMM08属于B基因型的一个分支.RDP3和SimPlot 3.5.1软件分析发现Tainan-5079-98序列发现重组信号,而KMM08未发现.结论 KMM08分离株为B基因型;CA16与EV71在非结构区发生重组.

Complete nucleotide sequence of a human coxsackievirus A16 strain KMM08 isolated in Kunming, China in 2008

Objective To describe the genetic characterization of complete genome from a human coxsackievirus A16(CA16) strain KMM08, isolated in Yunnan, China, in 2008, Methods By using RT-PCR, the seven fragments contained about 1000 nucleotides in the complete -genome were sequenced. The sequences were aligned with other enterovirus sequences downloaded from GenBank using Mega 4.1, RDP3 and SimPlot 3.5.1 software. Results As in other human enterovirus, its genome was 7409 nucleotides in length, encoding for 2193 amino acids. KMM08 strain was closely related to other reference strains of B genotype. In the complete genome, the homology of nucleotide and amino acid among the eleven CA16 isolated strains were 79.0%-98.2% and 94.5%-99.3%, respectively. The rates of homology were 79.1% and 94.8% when comparing with that of G10 strains and 78.7% and 89.0% comparing with that of BrCr strains, respectively. SZ-HK08-3 strain had high homology when compared to other strains. In different segment of genome, the rates of homology were 97.0%-99.0% and 98.0%-100.0% when compared with that of SZ-HK08-3 strains, respectively. The rates of homology were 74.2%-86.9% and 90.9%-97.0% when compared with that of G10 strains, respectively and were 65.0%-84.9% and 71.0%-95.2% when compared with that of BrCr strains. Data from Phylogenetic analysis showed that KMM08 belong to genotype B, The putative recombinant Tainan-5079-98 was detected positive with RDP3 and SimPlot 3.5.1. Conclusion KMM08 strains isolated in Yunnan in 2008 belonged to B genotype of coxsackivirus A16. The possible occurrence of inter-typic recombination would involve EV71 and CA16.