National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.
INSERM, U955, Créteil, France.
Sci Rep. 2018 Mar 8;8(1):4180. doi: 10.1038/s41598-018-22614-0.
Hepatitis C virus (HCV) genotype and subtype (1a/1b) identification is needed to tailor anti-HCV therapy. Currently available methods accurately identify the genotype and differentiate subtypes 1a from 1b. However, these assays have not been designed to identify other HCV subtypes, nor to recognize mixed genotype/subtype infections, emphasizing the need for a high-resolution system based on phylogenetic analysis of reads obtained by deep sequencing of a relevant genome region. The aim of this study was to evaluate the performance of the Sentosa SQ HCV Genotyping Assay, a novel deep sequencing-based assay targeting the HCV nonstructural 5B (NS5B) region, in clinical samples from patients with an indication for anti-HCV therapy. A high concordance rate with Sanger sequencing of the NS5B region, the reference method, was found for genotype 1 to 6 determination, 1a/1b subtype identification, and genotype 4, 5 and 6 subtyping. Discrepancies were seen essentially for HCV genotype 2 subtyping. Overall, the performance of the deep sequencing-based assay in generating the genotypes/subtype information needed to tailor anti-HCV treatment was adequate in this study. Further improvements, such as a longer NS5B fragment analyzed and enriching the database of reference prototype strains used for subtype assignment would make it a method of choice for HCV genotyping and subtyping for future clinical practice and research.
丙型肝炎病毒（HCV）基因型和亚型（1a/1b）的鉴定对于定制抗 HCV 治疗至关重要。目前可用的方法可以准确鉴定基因型，并区分 1a 型和 1b 型亚型。然而，这些检测方法并未设计用于鉴定其他 HCV 亚型，也无法识别混合基因型/亚型感染，这强调了需要一种基于相关基因组区域深度测序获得的读长进行系统发育分析的高分辨率系统。本研究旨在评估 Sentosa SQ HCV 基因分型检测（一种新型基于深度测序的检测方法，针对 HCV 非结构 5B（NS5B）区域）在有抗 HCV 治疗指征的患者临床样本中的性能。发现该检测方法与 Sanger 测序的 NS5B 区域（参考方法）在基因型 1 至 6 确定、1a/1b 亚型鉴定以及基因型 4、5 和 6 亚型鉴定方面具有很高的一致性。对于 HCV 基因型 2 亚型鉴定，基本上存在差异。总的来说，在本研究中，该基于深度测序的检测方法在生成用于定制抗 HCV 治疗的基因型/亚型信息方面的性能足够。进一步的改进，例如分析更长的 NS5B 片段并丰富用于亚型分配的参考原型株数据库，将使其成为未来临床实践和研究中 HCV 基因分型和亚型鉴定的首选方法。
