Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage

Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced 21 full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n=109) sampled in 19 countries from public databases (102...

重组是遗传多样性的重要驱动因素，尽管其在丙型肝炎病毒（hepatitis C virus, HCV）中相对罕见。近期针对HCV临床试验获得的序列数据开展的研究，共获得21株全基因组重组病毒，分属3种推定的亚型间重组型：2b/1a、2b/1b及2k/1b。其中2k/1b嵌合病毒是目前已知唯一的HCV流行重组型（circulating recombinant form, CRF），引发了学界对其遗传结构与起源的关注。该毒株相关病例于1999年在俄罗斯首次被发现，此后在前苏联全境、西欧及北美均有检出。尽管2k/1b的流行率在高加索山区（即亚美尼亚、阿塞拜疆与格鲁吉亚）最高，但由于可用序列资源匮乏，2k/1b型CRF的起源与传播模式至今仍不明确。本研究构建了一套覆盖HCV基因组全编码区的序列比对数据集，纳入了公共数据库中19个国家采集的所有符合要求的2k/1b序列（长度＞500核苷酸；样本量n=109）（102…）。