水痘-带状疱疹病毒VZV84-7株全基因序列测定及分析

目的分析我国自行分离的水痘-带状疱疹病毒疫苗株北京株(VZV84-7株)的全基因序列及特征。方法采用超速离心法获得纯化病毒颗粒,酚-氯仿法抽提病毒基因组DNA后超声破碎,回收1500～3000bp的片段,克隆至质粒pUC18中,构建病毒DNA文库,进行测序及序列分析,并与Dumas野毒株进行比较,绘制种系发育树,分析其与其他株VZV的同源性。结果VZV84-7株基因组全长125083bp,G+C含量为46.1%。基因组各区段长度及G+C含量分别为:UL:104746bp,G+C:44.3%;TRL和IRL:各89bp,G+C:69.7%;Us:5235bp,G+C:42.8%;TRS和IRS:各7462bp,G+C:59.3%。其R2可变区重复单位的拷贝数为7个,R4可变区为9个,R5可变区为1个。VZV84-7株共有71个ORFs,其中3个基因位于重复序列区,位于IRS的ORF69～71与位于TRS的ORF62～64序列完全一致。与Dumas株相比,共有248个核苷酸位置存在差异,大部分突变为单个核苷酸替换,另有部分插入或缺失性突变。其中碱基转换比碱基颠换更常见,发生率分别为66%和34%。种系发育分析结果显示,VZV84-7株与其他株VZV的同源性为95%以上。结论VZV84-7株具有其独特的基因特征,但与其他株VZV具有较高的同源性。

Sequencing of Whole Genome of Varicella-Zoster Virus 84-7 Strain

Objective To analyze the gene sequence and its character of varicella-zoster virus(VZV)84-7 strain isolated in China.Methods Purified virus particles of VZV were obtained by ultracentrifugation,from which viral genomic DNA was extracted with benzene-chloramine then ultrasonicated,and the gene fragments at lengths of 1 500 ～ 3 000 bp were recovered and cloned into vector pUC18 to construct viral DNA library.The genomic DNAs were sequenced,and the results were compared with those of wild Dumas strain,based on which a phylogenetic tree was generated to analyze the homologies of VZV84-7 strain to other strains.Results The whole genome of VZV84-7 strain consisted of 125 083 bp,with a G + C content of 46.1%.The lengths of regions UL,TRL,IRL,Us,TRS and IRS were 104 746,89,89,5 235,7 462 and 7 462 bp,while the G + C contents were 44.3%,69.7%,69.7%,42.8%,59.3% and 59.3%,respectively.The copy numbers of repeat regions R2,R4 and R5 in the genome were 7,9 and 1 respectively.A total of 71 ORFs were found in the genome of VZV84-7 strain,of which 3 genes were located within the repeat sequences,therefore the sequence of ORFs 69 ～ 71 in IRS region were completely identical to that of ORFs 62 ～ 64 in TRS region.A total of 248 nucleotide substitutions including a part of insertion and deletion mutations were observed as compared with Dumas strain,most of which were single nucleotide polymorphisms(SNPs).Transitions were more frequent than transversions(66% vs 34%).Phylogenetic tree showed that the homologies of VZV84-7 strain to other VZV strains were more than 95%.Conclusion Though VZV84-7 strain was unique genetically,it was highly homologous to other VZV strains.