Dirani G, Paesini E, Mascetra E, Farabegoli P, Dalmo B, Bartolini B, Garbuglia A R, Capobianchi M R, Sambri V
Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy.
Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy.
J Virol Methods. 2018 Jan;251:88-91. doi: 10.1016/j.jviromet.2017.10.005. Epub 2017 Oct 16.
Chronic HCV infection is one of the leading causes of liver-related death and in many countries it is a primary reason for having a liver transplant. HCV genotype identification has long been used in the clinical practice, since different genotypes have different response rates and required different doses and durations of IFN/RBV treatment; moreover both the frequency and the pattern of resistance to different Direct-Acting Antivirals (DAAs) classes are subtype specific. Hence the necessity to make an accurate HCV subtyping becomes a fundamental tool to optimize current and future clinical management of HCV infected subjects. In the present study the performance of a next generation sequencing (NGS: based on the Ion Torrent Platform-Vela Sentosa SQ 301 sequencer) HCV genotyping assay has been evaluated. The current method targets a region of the NS5B gene and it is the unique NGS based market CE-IVD assay. As a comparative method a commercial method based on the detection via reverse hybridization of 5'UTR and core regions (Versant HCV Genotype 2.0 Assay, LiPA, Siemens) was selected. A total 207 plasma samples from HCV infected individuals were used. No selection was made for these samples that were submitted for routine HCV genotyping. The results show Vela NGS assay assigns major number of HCV subtypes with respect LiPA. Concerning genotype 1 and 3, the discrepancy of assigned subtypes for LiPA with respect to Vela NGS assay is not relevant (1.8% and 2%, respectively); in contrast, the difference of assigned subtypes for genotypes 2 and 4 is very high (96.6% and 100%, respectively). The resistance mutations data, except for 1a and 1b subtypes, remain scarce; the future relevant challenge will be to identify subtypes-specific drug resistance mutations, which are essential to create highly personalized therapeutic pathways.
慢性丙型肝炎病毒（HCV）感染是肝脏相关死亡的主要原因之一，在许多国家，它是进行肝移植的主要原因。HCV基因型鉴定长期以来一直用于临床实践，因为不同的基因型有不同的应答率，并且需要不同剂量和疗程的干扰素/利巴韦林治疗；此外，对不同类直接作用抗病毒药物（DAA）的耐药频率和模式都是亚型特异性的。因此，准确进行HCV基因分型的必要性成为优化当前和未来HCV感染患者临床管理的基本工具。在本研究中，评估了一种基于新一代测序（NGS：基于Ion Torrent平台-Vela Sentosa SQ 301测序仪）的HCV基因分型检测方法。当前方法针对NS5B基因的一个区域，它是唯一基于NGS的市场CE-IVD检测方法。作为比较方法，选择了一种基于5'UTR和核心区域反向杂交检测的商业方法（Versant HCV Genotype 2.0 Assay，LiPA，西门子公司）。总共使用了207份来自HCV感染个体的血浆样本。对这些用于常规HCV基因分型的样本未进行选择。结果显示，与LiPA相比，Vela NGS检测方法能够鉴定出更多的HCV亚型。关于基因型1和3，LiPA与Vela NGS检测方法在亚型鉴定上的差异不显著（分别为1.8%和2%）；相比之下，基因型2和4在亚型鉴定上的差异非常大（分别为96.6%和100%）。除了1a和1b亚型外，耐药突变数据仍然很少；未来的相关挑战将是识别亚型特异性的耐药突变，这对于创建高度个性化的治疗方案至关重要。
