The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China.
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China.
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作者：
丙型肝炎病毒是一种高度多样化的病原体，经常导致慢性长期感染，但人类人群中丙型肝炎病毒多样性的起源和驱动因素尚不清楚。中国，最近在海南岛白沙县黎族慢性感染者中发现了未知的丙型肝炎病毒6型(GT6)毒株。黎族是海南岛上的早期定居者，与岛上其他民族和大陆中国相比，他们具有独特的宿主遗传背景和文化认同。在这份报告中，我们生成了33个完整的病毒基因组序列，以东南亚存在的GT6分离株为背景，对这些新的GT6毒株进行了全面的分子流行病学分析。除了1个gt6a分离株外，LI GT6序列从两个谱系中形成了三个新的分支，构成了3个新的GT6亚型和30个未指定的菌株。使用贝叶斯推断方法，我们确定了所有可用的GT6全病毒基因组序列的最新共同祖先约为2767 公元前(95 %最高后验密度区间，3670-1397 公元前)，这远远早于先前的估计。代换率为1.2 0 × 10−4 置换/位/年(S/S/y)，在基因组5‘非翻译区为1.0 2 × 10−5 S/S/y，在E2区为3.0 7 × 10−4 S/S/y。因此，我们对海南岛一个孤立的少数民族群体的研究大大增加了已知的丙型肝炎病毒GT6的多样性，GT6已经被认为是最多样化的丙型肝炎病毒基因。这项研究中现存的丙型肝炎病毒GT6序列可能是通过至少三个独立的事件传递给李氏人的，这些事件可能可以追溯到大约4,000 年前。这一分析描述了对丙型肝炎病毒GT6分子进化的基本方面的更深层次的洞察，包括在孤立的黎族中GT6序列的广泛多样性。
Hepatitis C virus (HCV) is a highly diverse pathogen that frequently establishes a chronic long-term infection, but the origins and drivers of HCV diversity in the human population remain unclear. Previously unidentified strains of HCV genotype 6 (gt6) were recently discovered in chronically infected individuals of the Li ethnic group living in Baisha County, Hainan Island, China. The Li community, who were early settlers on Hainan Island, has a distinct host genetic background and cultural identity compared to other ethnic groups on the island and mainland China. In this report, we generated 33 whole virus genome sequences to conduct a comprehensive molecular epidemiological analysis of these novel gt6 strains in the context of gt6 isolates present in Southeast Asia. With the exception of one gt6a isolate, the Li gt6 sequences formed three novel clades from two lineages which constituted 3 newly assigned gt6 subtypes and 30 unassigned strains. Using Bayesian inference methods, we dated the most recent common ancestor for all available gt6 whole virus genome sequences to approximately 2767 bce (95 per cent highest posterior density (HPD) intervals, 3670–1397 bce), which is far earlier than previous estimates. The substitution rate was 1.20 × 10−4 substitutions/site/year (s/s/y), and this rate varied across the genome regions, from 1.02 × 10−5 s/s/y in the 5’untranslated region (UTR) region to 3.07 × 10−4 s/s/y in E2. Thus, our study on an isolated ethnic minority group within a small geographical area of Hainan Island has substantially increased the known diversity of HCV gt6, already acknowledged as the most diverse HCV genotype. The extant HCV gt6 sequences from this study were probably transmitted to the Li through at least three independent events dating perhaps from around 4,000 years ago. This analysis describes deeper insight into basic aspects of HCV gt6 molecular evolution including the extensive diversity of gt6 sequences in the isolated Li ethnic group.
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影响因子：
30.8
作者：
Ansari MA;Pedergnana V;L C Ip C;Magri A;Von Delft A;Bonsall D;Chaturvedi N;Bartha I;Smith D;Nicholson G;McVean G;Trebes A;Piazza P;Fellay J;Cooke G;Foster GR;STOP-HCV Consortium;Hudson E;McLauchlan J;Simmonds P;Bowden R;Klenerman P;Barnes E;Spencer CCA
通讯作者：
Spencer CCA
DOI：
10.1099/jgv.0.001495
发表时间：
2021-03
期刊：
The Journal of general virology
影响因子：
--
作者：
Bamford CGG;McLauchlan J
通讯作者：
McLauchlan J
影响因子：
5.8
作者：
Pond, Sergei L. Kosakovsky;Posada, David;Frost, Simon D. W.
通讯作者：
Frost, Simon D. W.
影响因子：
3.8
作者：
Lu, L;Nakano, T;Hagedorn, CH
通讯作者：
Hagedorn, CH
影响因子：
5.3
作者：
Martin DP;Murrell B;Golden M;Khoosal A;Muhire B
通讯作者：
Muhire B