1株辛德毕斯病毒基因组编码区序列测定及分析

Determination and analysis of the coding sequence of one Sindbis virus strain

目的:对保存的一株辛德毕斯病毒基因组编码区序列进行测定,阐明其与已报道毒株序列的差异。方法:对辛德毕斯病毒基因组编码区进行分段RT-PCR扩增,将扩增产物直接进行测序,采用DNA Star软件将分段测序结果拼接得到全长编码区序列。结果与结论:此株辛德毕斯病毒基因组编码区全长11 322 nt,编码3 774个氨基酸,其中非结构基因长7 539 nt,编码4种非结构蛋白NSp1,NSp2,NSp3,NSp4;结构基因全长3 735 nt,编码5种结构蛋白E1,E2,E3,6K和C蛋白。非结构基因和结构基因之间有48 nt的不翻译连接区。序列同源性分析结果表明,此株病毒与HRsp株的同源性最高,两者核苷酸序列同源性为99.7%,氨基酸序列同源性为99.6%。此株病毒与HRsp株病毒亲缘性最高,同属于南非-欧洲组。

Objective： To analyze the sequence of a Sindbis virus strain MEI and compare its genome differences with other reported Sindbis virus strains. Methods： The coding sequences were amplified by 12 different RT-PCR, and the sequenced cDNA fragments were analyzed by DNA Star software and spliced to form a complete genome. Results and Conclusion： This MEI strain has a coding genome of 11 322 nt, the common genome of Sindbis virus, which encodes 3 774 amino acids. The 5＇ terminal 7 539 nt encode four nonstructural proteins, NSpl, NSp2, NSp3 and NSp4. The 3＇ terminal 3 735 nt encode five structural proteins, E1, E2, E3, 6K and C. A 48 nt non-translated region connected the non- structural and the structural coding sequences. Phylogenetic analysis showed that the MEI strain has a nucleotide sequence identity of 99.7% and an amino acid sequence identity of 99.6% with HRsp strain. The MEI strain has the highest homology with HRsp strain. They all belong to group SA-EU.