Lineages of varicella-zoster virus
Lineages of varicella-zoster virus
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DOI：
10.1099/vir.0.007658-0
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发表时间：
2009-04-01
影响因子：
3.8
通讯作者：
McGeoch, Duncan J.
中科院分区：
文献类型：
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作者：
McGeoch, Duncan J.
研究水痘-带状疱疹病毒(VZV；人类疱疹病毒3型)基因组序列之间的关系，以评估毒株的下降、谱系结构和重组事件的发生率。对18个已发表的完整基因组序列进行了比对，提取了494个单核苷酸多态(SNPs)，每个SNPs都是两个等位基因。在281个SNPs中，有一个序列与所有其他序列不同。其余213个SNPs的分布表明，这些序列分为5个组，这与以前认识的系统发育组相一致，分别为E1、E2、J、M1和M2。213个SNP可分为104个特定于单个群体的SNP和109个定义群体间关系的跨群体SNP。这最后一组是根据群体之间关系的连续性和这种模式中的中断来评估的，以识别交叉点并将它们归因于谱系。对于基因组长独特区的99个跨组SNP，可以看到E2组和M2组的SNP等位基因几乎完全不同，而EL组是由E2和M2的重组产生的。因此，可以构建4个E2株和2个M2株的有效系统发育树。在E2组或EL组(10株)内没有重组的实质性证据。J组和M1组各只包含一个毒株，两组都被解释为具有显著不同的历史加上来自E2和M2谱系的可能的重组元素。VZV重组和系统发育的观点代表了对VZV谱系之间深层关系的重大澄清。
Relationships among varicella-zoster virus (VZV; Human herpesvirus 3) genome sequences were examined to evaluate descent of strains, structures of lineages and incidence of recombination events. Eighteen complete, published genome sequences were aligned and 494 single nucleotide polymorphisms (SNPs) extracted, each as two alleles. At 281 SNPs, a single sequence differed from all the others. Distributions of the remaining 213 SNPs indicated that the sequences fell into five groups, which coincided with previously recognized phylogenetic groupings, termed E1, E2, J, M1 and M2. The 213-SNP set was divisible into 104 SNPs that were specific to a single group, and 109 cross-group SNPs that defined relationships among groups. This last set was evaluated by criteria of continuities in relationships between groups and breaks in such patterns, to identify crossover points and ascribe them to lineages. For the 99 cross-group SNPs in the genome's long unique region, it was seen that the E2 and M2 groups were almost completely distinct in their SNP alleles, and the El group was derived from a recombinant of E2 and M2. A valid phylogenetic tree could thus be constructed for the four E2 and two M2 strains. There was no substantive evidence for recombination within the E2 group or the El group (ten strains). The J and M1 groups each contained only one strain, and both were interpreted as having substantial distinct histories plus possible recombinant elements from the E2 and M2 lineages. The view of VZV recombination and phylogeny reached represents a major clarification of deep relationships among VZV lineages.