National Reference Laboratory of HIV and Hepatitis B and C, Department of Infectious Diseases, National Institute of Health, Avenue Padre Cruz, Lisbon, Portugal.
J Med Virol. 2013 May;85(5):815-22. doi: 10.1002/jmv.23545.
Hepatitis C virus (HCV) genotype determination is required in clinical practice to establish the dose and duration of antiviral treatment. Although subtype identification does not impact on current therapy this is changing with new specific inhibitors of HCV enzymes and functions which are becoming available worldwide. These new drugs may yield different antiviral responses and resistance profiles. Accurate classification of HCV genotype and subtype is therefore crucial. An "in-house" method was developed for improving HCV subtyping and the results were compared with a second-generation line probe assay (LiPA) used extensively in Portugal. Phylogenetic analysis was undertaken of the C/E1 and NS5B genomic regions of HCV isolated from 72 prisoners with chronic HCV infection and from reference samples. Although LiPA is considered to be a good method for genotyping, HCV was subtyped in only 47.2% of cases compared with 95.8% of cases by the "in-house" method. Molecular data for both C/E1 and NS5B regions were obtained in 88.9% of the samples. Two out of 23 cases of subtype 1a were misclassified as subtype 1b by LiPA. A putative recombinant like RF1_2k/1b, two potential inter-genotypic recombinants 1b/4a and 3a/4a, and also a potential intra-genotypic recombinant 2q/2k in C/E1 and 2k/2a in NS5B were also identified. The "in-house" method enabled HCV to be subtyped accurately with the detection, in some cases, of recombinant viruses or dual HCV infections. Near full-length genomic analysis to characterize these potential recombinant viruses is planned.
丙型肝炎病毒 (HCV) 基因型的确定在临床实践中是必要的，以确定抗病毒治疗的剂量和持续时间。虽然亚型鉴定对目前的治疗没有影响，但随着新的 HCV 酶和功能的特异性抑制剂在全球范围内的出现，这种情况正在发生变化。这些新药可能产生不同的抗病毒反应和耐药谱。因此，准确分类 HCV 基因型和亚型至关重要。我们开发了一种“内部”方法来改进 HCV 亚型鉴定，并将结果与在葡萄牙广泛使用的第二代线探针分析 (LiPA) 进行了比较。对来自 72 名慢性 HCV 感染囚犯和参考样本的 HCV 的 C/E1 和 NS5B 基因组区域进行了系统发育分析。虽然 LiPA 被认为是一种很好的基因分型方法，但与“内部”方法相比，只有 47.2%的病例被分为亚型，而只有 95.8%的病例被分为亚型。在 88.9%的样本中获得了 C/E1 和 NS5B 区域的分子数据。23 例 1a 亚型中有 2 例被 LiPA 错误分类为 1b 亚型。在 C/E1 中发现了 2 个 RF1_2k/1b 假定重组体，2 个潜在的基因型间重组体 1b/4a 和 3a/4a，以及在 NS5B 中发现了 1 个潜在的基因型内重组体 2q/2k 和 2k/2a。“内部”方法能够准确地对 HCV 进行亚型鉴定，在某些情况下还可以检测到重组病毒或双重 HCV 感染。计划对这些潜在的重组病毒进行全长基因组分析以进行特征描述。
