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首页> 外文期刊>Journal of Clinical Microbiology >High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods
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High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

机译：使用NS5B深度测序和系统发育技术（目前方法的替代方法）进行高分辨率C型肝炎病毒亚型分析

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Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.
机译：丙型肝炎病毒（HCV）分为7种主要基因型和67种亚型。最近的研究表明，在感染了HCV基因型1的患者中，对包含直接作用抗病毒药物（DAA）的治疗方案的反应率是亚型依赖的。当前可用的基因分型方法具有有限的分型准确性。我们评估了针对454 / GS-Junior平台开发的基于深度测序的HCV亚型分析的性能，并与两种商业分析（Versant HCV基因型2.0和Abbott Real-time HCV基因型II）进行了比较，并使用直接用NS5B测序作为金标准（直接测序），用于先前通过第一代杂交测定法检测的114个临床样本中（82个基因型1和32个基因型，结果无法解释）。深度测序的系统发生分析读取了81个标本中通过群体Sanger测序（69％1b，31％1a）匹配的匹配的亚型1，并在一个样品中鉴定出混合亚型感染（1b / 3a / 1a）。同样，在32个先前不确定的标本中，通过直接和深度测序在四个感染双重感染的样本中获得了相同的基因型和亚型结果。相反，Versant HCV基因型2.0和Abbott Real-time HCV基因型II均失败了亚型1，分别调用了13个样本（16％），并且无法识别超过一半非基因型1中的HCV基因型和/或亚型。样品。我们得出的结论是，深层测序比目前可用的方法更有效地进行HCV亚型分型，并且可以对混合感染进行定性鉴定，并且在告知所有HCV亚型新的含DAA方案的治疗策略方面可能更有帮助。

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