云南省1株基孔肯雅毒株全基因组序列测定及特征分析

目的 对1例缅甸输入基孔肯雅热病例血清标本进行病毒分离及全基因组测序,分析其基因特征。方法 采用real-time RT-PCR方法对标本进行检测,分离培养后获得毒株,对病毒核酸扩增后的产物进行全基因组测序,使用DNAStar 7.1软件对测序结果进行拼接,Mega5.0软件对序列进行比对和系统发生树构建。结果 病例血清标本核酸检测显示CHIKV阳性,经分离培养获得CHIKV毒株(YN0627株),全基因组测序得到其序列,YN0627全长为11 586 nt,其基因结构符合CHIKV的基因特征。系统进化分析显示,YN0627与东中南非洲遗传谱系(East, Central and South African Lineage, ECSA)的其他流行株聚集在一起,属于ECSA谱系。YN0627的编码区与参考序列相比,核苷酸同源性为85.24%~99.96%,氨基酸同源性为95.34%~99.97%,结构蛋白编码区域有28个氨基酸变异位点。结论 云南省输入性CHIKV-YN0627属于ECSA谱系,且观察到多个氨基酸位点突变,提示云南省应当加强对CHIKV的监测和研究。

Sequencing and characterization analysis of a chikungunya virus imported into Yunnan Province

We performed viral isolation and whole genome sequencing of a serum sample from an imported chikungunya case from Myanmar,and analyzed its genetic characteristics.Real-time RT-PCR was used to detect Chikungunya virus(CHIKV),and the CHIKV strain was obtained after isolation and culture.The amplified products of the CHIKV nucleic acid were whole genome sequenced,and DNAStar 7.1 and Mega5.0 software were used for sequence assembly and phylogenetic tree construction.The real-time RT-PCR results indicated CHIKV positivity in the serum specimen,and we obtained the CHIKV strain(YN0627)and whole genome sequence.The full length of YN0627 was 11586 nt,and its genetic structure was consistent with the genetic characteristics of CHIKV.Phylogenetic analysis showed that YN0627 clustered with other endemic strains of the East,Central and South African(ECSA)lineage,and belonged to the ECSA lineage.Compared with the reference sequences,the nucleotide similarity of YN0627 was 85.24%~99.96%,and the amino acid sequence similarity was 95.34%~99.97%.There were 28 amino acid mutation sites in the structural protein coding region.These results suggest that CHIKV monitoring and research should be strengthened in Yunnan province.