一株高度变异的中国SV40分离株的全基因组序列分析

对SV40中国云南分离株YNQD38进行了全基因组核苷酸序列测定。覆盖了整个基因组的9个重叠的基因片段被扩增和测序,与其它SV40株进行了序列比对并基于全基因序列建立了遗传进化树。结果显示:基因组全长5125bp,基因组构成与其它SV40毒株相似,均有6个开放读码框架和1个调控区。YNQD38与已被证实高度保守的其它SV40比,全基因组核苷酸同源性仅为91.0%。在SV40的保守区VP1、VP2、VP3、小t抗原(t-ag)和部分大T抗原(不包括大T抗原C末端)区,YNQD38与其它SV40之间核苷酸同源性分别为90.7%~91.1%、91.7%~92.0%、90.2%~90.8%、92.8%~93.3%、88.5%~89.7%。在SV40的可变区大T抗原C末端(T-ag-C)编码区,YNQD38同源性更低,仅为65.7%~74.3%。YNQD38发生在保守区的核苷酸变异多为无义突变,而发生在变异区的核苷酸变异多为有义突变。YNQD38的调控区缺少一个完整的72bp增强子,这种特别的调控区的结构以前未见报道。基于整个基因组构建的进化树显示该株病毒形成了一个独特的组。以上结果表明YNQD38是目前报道的SV40中变异最大的一株,而且也是第一株被完整测序的SV40中国株。这个报道不仅为SV40中国株的基础研究提供了一个完整清楚的分子生物学资料,还对这样一株高度变异的SV40能否成为人类致病因子进行了初步探讨。

Analysis of the Complete Genome Sequence of a Highly Divergent SV40 Chinese Isolate

We reported here the complete genome sequence of a Chinese SV40 isolate called YNQD38.Nine overlapping fragments covering the entire viral genome were amplified by PCR and sequenced.The complete genome sequence of YNQD38 was compared with the other reported SV40 isolates and the phylogenetic tree was established based on the complete genome sequence.The whole genome of YNQD38 was 5125bp in length and the genomie organization was similar to that of the other SV40 isolates.Compared with sequences of other SV40 isolates published up to date,which had already been demonstrated to be highly conserved,the complete genome of YNQD38 showed 91.0% identity.Comparison of the VP1,VP2,VP3,small t antigen(t-ag) and part of large T antigen(excluding the C terminus of large T antigen) genes of YNQD38 with that of the other SV40 isolates,which are usually highly conserved within the SV40 family,showed 90.7%-91.1%,91.7%-92.0%,90.2%-90.8%,92.8%-93.3%,88.5%-89.7% identity respectively.Whereas for the variable region such as T-ag-C,smaller nucleotide identity of 65.7%-74.3% was found.Most of the nucleotide diversity in the conserved region of YNQD38 did not result in amino acid alterations,but most of the nucleotide diversity in the variable region of YNQD38 resulted in amino acid alterations.The regulatory region of YNQD38 was unique because of lacking an intact 72bp enhancer element which did exist in the other SV40 isolates.Phylogenetic tree based on the whole genome showed that YNQD38 formed a distinct group.These findings suggest that YNQD38 is the most divergent strain among all the SV40 isolates discovered.This is also the first,and until now the only Chinese SV40 isolate being completely sequenced.This report provides not only a molecular biological data for study of SV40 Chinese isolates but also new insights into possible pathogenesis of YNQD38 infection in humans.