Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China.
PLoS One. 2019 May 16;14(5):e0217010. doi: 10.1371/journal.pone.0217010. eCollection 2019.
HCV genotype 6 (HCV-6) typically circulates in Southeast Asia and exhibits the highest genetic diversity among the eight HCV genotypes. In our previous work, a group of HCV-6 sequences was not clearly classified. Here, we further characterized this HCV-6 variant and analyzed the evolutionary history of the enlarged HCV-6 family.
Blood samples from eight HCV seropositive samples collected from intravenous drug users (IDUs) in 2014 in Yunnan Province, China. The full-length HCV genome sequences were amplified by using reverse transcription PCR followed by DNA sequencing and phylogenetic analysis. Bayesian evolutionary analysis was performed with the complete coding region sequences of subtype 6a-6xh.
The eight genomes had the same coding region of 9051 nucleotides. The complete coding region sequences of the eight HCV isolates formed a distinct phylogenetic group from the previously assigned HCV-6 subtypes (6a-6xf), however which clustered with 6xg reference sequences that were found in Kachin State, Myanmar, and recently assigned and released. The p-distances of the eight isolates to subtype 6a-6xf and 6xh ranged from 0.143 to 0.283. Based on the HCV-6 complete coding region sequences, we constructed a timescaled phylogenetic tree to reveal the HCV-6 evolutionary history, in which there were four HCV-6 phylogenetic subsets, whose median tMRCAs were 294.8, 388.5, 348.5 and 197.0 years ago, respectively. Subtype 6xg clustered into Subset I, and had the most recent common ancestor with subtype 6n, which dated back to 101.2 (95% HPD: 78.7, 125.8) years ago. The genetic evolutionary analysis further confirmed that subtype 6xg originated from Myanmar, and transmitted to Dehong through cross-border IDUs.
The HCV-6 variant characterized in this study belonged to newly assigned subtype 6xg. Our finding further confirmed the assignment of 6xg. HCV-6 family was highly divers and had a complicated evolutionary history in Southeast Asia. It is necessary to further characterize HCV-6 genetics in this region.
HCV 基因型 6（HCV-6）通常在东南亚流行，其遗传多样性在八种 HCV 基因型中最高。在我们之前的工作中，一组 HCV-6 序列未被明确分类。在这里，我们进一步对该 HCV-6 变体进行了特征描述，并分析了扩大的 HCV-6 家族的进化历史。
采集 2014 年云南省静脉吸毒者（IDU）中 8 例 HCV 血清阳性样本的血液样本。采用逆转录 PCR 扩增全长 HCV 基因组序列，然后进行 DNA 测序和系统发育分析。采用贝叶斯进化分析对 6a-6xh 亚型的全长编码区序列进行分析。
这 8 个基因组具有相同的 9051 个核苷酸编码区。8 株 HCV 分离株的全长编码区序列与先前分配的 HCV-6 亚型（6a-6xf）形成了一个独特的进化群，但与在缅甸克钦邦发现的、最近分配并公布的 6xg 参考序列聚类。8 个分离株与 6a-6xf 和 6xh 亚型的 p-距离在 0.143 至 0.283 之间。基于 HCV-6 全长编码区序列，我们构建了一个时间尺度的系统发育树，以揭示 HCV-6 的进化历史，其中有四个 HCV-6 系统发育亚群，其中位数 tMRCAs 分别为 294.8、388.5、348.5 和 197.0 年前。6xg 亚型聚类到亚组 I，与 6n 亚型具有最近的共同祖先，可追溯到 101.2（95% HPD：78.7，125.8）年前。遗传进化分析进一步证实，6xg 亚型起源于缅甸，并通过跨境 IDU 传播到德宏。
本研究中鉴定的 HCV-6 变体属于新分配的 6xg 亚型。我们的发现进一步证实了 6xg 的分配。HCV-6 家族在东南亚高度多样化，进化历史复杂。有必要进一步对该地区的 HCV-6 遗传学进行特征描述。
