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首页> 外文期刊>Journal of Clinical Microbiology >Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing
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Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing

机译：通过使用非特异性下一代测序技术鉴定喀麦隆的丙型肝炎病毒重组

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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.
机译：目前尚不清楚重组在丙型肝炎病毒（HCV）的进化和遗传多样性中的重要性。迄今为止，仅鉴定了少数基因型间的重组体，每个重组体均具有归类为基因型2的核心和包膜基因。在这里，我们使用多种方法，包括标准的桑格，研究了喀麦隆南部的两个假定的基因型4/1重组体。测序，基因型特异性PCR扩增和非HCV特异性Illumina RNA测序（RNA-seq）。在两个样品中都证实了基因型1和4之间的重组，并且每个重组体的亲代都属于在喀麦隆高流行的HCV亚型。使用RNA-seq方法，我们获得了一个样品的完整基因组，该样品在E2 / P7基因连接处包含重组断点。我们开发并应用了一种名为Deep SimPlot的新方法，该方法可直接用于可视化和识别由下一代测序结合共有序列创建的短序列读取的病毒重组。

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