基孔肯雅病毒WJ0601株基因组全序列测定及分析

Complete genome sequencing and analysis of Chikungunya virus WJ0601 strain

目的对保存的基孔肯雅病毒WJ0601株基因组序列进行测定,并阐明该病毒与已报道毒株序列的关系。方法对基孔肯雅病毒基因组编码区分14段进行RT-PCR扩增,对非编码区采用RACE法进行扩增,将扩增产物直接进行测序,应用DNAStar软件将测序结果拼接得到基因组序列。结果与结论基孔肯雅病毒WJ0601株基因组核苷酸共11826nt,编码3722个氨基酸,其中5′端的2/3基因组编码4种非结构蛋白nsP1、nsP2、nsP3和nsP4;3′端的1/3基因组编码5种结构蛋白C、E3、E2、6K和E1蛋白。结构基因和非结构基因之间有68nt的连接区为非翻译区。病毒基因组5′端和3′端分别有76nt、526nt的非编码区。序列同源性分析结果表明,此株病毒与S27-African株的同源性最高,两者核苷酸序列同源性为99.9%,氨基酸序列同源性为99.8%,同属于(ESCA)基因型。

Objective To analyze the genome sequence of a Chikungunya virus strain WJ0601 and compare its genome differences with other reported Chikungunya virus strains.Methods The 14 different coding sequences of genome of Chikungunya virus were amplified by RT-PCR,and the noncoding region was amplified by RACE system and the sequenced cDNA fragments were analyzed by DNAStar software and spliced to a complete genome.Results and Conclusion The genome of WJ0601 strain was 11 826 nt in length and had the common genome of Chikungunya virus,which encoded 3722 amino acids.The two-thirds of RNA at 5＇ terminal encoded four nonstructural proteins,nsP1,nsP2,nsP3 and nsP4.The one-third of RNA at 3＇ terminal encoded five structural proteins,C,E3,E2,6K and E1.A 68 nt untranslated region connected the nonstructural with the structural coding sequences.The noncoding region of genome was constituted by 76 nt of 5＇ terminal and 526 nt of 3＇ terminal.Phylogenetic analysis showed that the WJ0601 strain has a nucleotide sequence identity of 99.9% and an amino acid sequence identity of 99.8% with S27-African strain.The WJ0601 strain has the highest homology with S27-African strain.Both of them belong to East/South/Central Africa（ESCA）genotype.