Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing.
Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing.
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DOI：
10.1128/jcm.00483-15
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发表时间：
2015-10
影响因子：
9.4
通讯作者：
Pybus OG
中科院分区：
文献类型：
--
作者：
Iles JC;Njouom R;Foupouapouognigni Y;Bonsall D;Bowden R;Trebes A;Piazza P;Barnes E;Pépin J;Klenerman P;Pybus OG
重组在丙型肝炎病毒的进化和遗传多样性中的重要性目前尚不确定。到目前为止，只有一小部分基因间型重组子被鉴定出来，每个重组子的核心和包膜基因都被归类为基因2。在这里，我们使用多种方法对来自喀麦隆南部的两个假定的4/1基因重组体进行了研究，包括标准Sanger测序、基因特异性PCR扩增和非丙型肝炎病毒特异性Illumina RNA测序(RNA-seq)。在两个样本中都证实了基因1和4之间的重组，每个重组的父母谱系属于在喀麦隆高流行的丙型肝炎病毒亚型。使用RNA-seq方法，我们获得了一个样本的完整基因组，该基因组在E2/P7基因连接处包含一个重组断裂点。我们开发并应用了一种名为Deep Simplot的新方法，该方法可以直接从下一代测序结合共识序列创建的短序列读数中可视化和识别病毒重组。
The importance of recombination in the evolution and genetic diversity of the hepatitis C virus (HCV) is currently uncertain. Only a small number of intergenotypic recombinants have been identified so far, and each has core and envelope genes classified as belonging to genotype 2. Here, we investigated two putative genotype 4/1 recombinants from southern Cameroon using a number of approaches, including standard Sanger sequencing, genotype-specific PCR amplification, and non-HCV-specific Illumina RNA sequencing (RNA-seq). Recombination between genotypes 1 and 4 was confirmed in both samples, and the parental lineages of each recombinant belong to HCV subtypes that are cocirculating at a high prevalence in Cameroon. Using the RNA-seq approach, we obtained a complete genome for one sample, which contained a recombination breakpoint at the E2/P7 gene junction. We developed and applied a new method, called Deep SimPlot, which can be used to visualize and identify viral recombination directly from the short sequence reads created by next-generation sequencing in conjunction with a consensus sequence.