Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan.
Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan.
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DOI：
10.3390/v14030464
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发表时间：
2022-02-24
期刊：
影响因子：
--
通讯作者：
Kukimoto I
中科院分区：
文献类型：
--
作者：
Tanaka K;Kogure G;Onuki M;Matsumoto K;Iwata T;Aoki D;Kukimoto I
人乳头瘤病毒（HPV）是一种性传播病毒，具有约8千碱基的DNA基因组，其在肛门生殖器组织中建立长期持续感染。高水平的遗传变异，包括病毒基因型和型内变异，已被描述为HPV基因组，以及基因型和变异分布的地理差异。在此，我们采用最大似然法对GenBank中的HPV16、HPV18和HPV58的全基因组序列（分别为n = 627、146和157）进行了系统发育分析。我们发现了几个只包含来自日本的HPV基因组的特征性簇：两个HPV16（亚系A4和A5），一个HPV18（亚系A1）和两个HPV58（亚系A1和A2）。串联病毒基因序列的贝叶斯系统发育分析显示，这些日本特有分支的最近共同祖先的分歧估计发生在距今约98，000年（YBP）的HPV 16 A4，HPV 16 A5约39，000 YBP，HPV 18 A1约38，000 YBP，HPV 58 A1约26，000和HPV 25，000 YBP用于HPV 58 A2。日本特定分支的分歧的估计时间框架表明，这些HPV变体引入日本群岛可以追溯到至少约25，000 YBP，并提供了旧石器时代晚期期间来自亚洲大陆的祖先日本人群的病毒共迁移场景。
Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (n = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period.
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