Ramos Diogo, Pinto Miguel, Sousa Coutinho Rodrigo, Silva Carolina, Quina Miriam, Gomes João Paulo, Pádua Elizabeth
Reference Laboratory of HIV and Hepatitis B and C, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal.
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, P-1649-016 Lisbon, Portugal.
Pathogens. 2023 May 24;12(6):754. doi: 10.3390/pathogens12060754.
Hepatitis C virus (HCV) is associated with liver damage and an increased progression rate to cirrhosis and hepatocellular carcinoma. In Portugal, it is prevalent in vulnerable populations such as injection drug users (IDU). HCV is characterized by a high intra-host variability, and the selecting driving forces could select variants containing resistance-associated substitutions (RAS) that reduce treatment effectiveness. The main goal of this study was to analyze the sequence variation of NS5A in treatment-naïve IDU. The epidemiological and clinical status of hepatitis C were analyzed, and samples were sequenced by Sanger and Next-Generation sequencing (NGS) to assess RAS and confirm HCV subtypes. Phylogenetic classification was concordant: 1a, 52.4%; 1b, 10.7%; 3a, 20.2%; 4a, 8.3%; 4d, 7.1%; and one 2k/1b recombinant. A 1a/3a mixed infection was detected by NGS. RAS were found in 34.5% (29/84) of samples using Sanger sequencing, while in 42.9% (36/84) using NGS. In sequences from subtypes 1a and 1b, RAS K24R, M28V, Q30H/R, H58D/P/Q/R, and RAS L31M and P58S were detected, respectively. In subtype 3a, RAS A30S/T, Y93H and polymorphisms in position 62 were identified. Additionally, RAS P58L was detected in genotype 4. The strategy used for the molecular survey of baseline HCV resistance is of particular importance to achieve treatment effectiveness and contribute to the elimination of hepatitis C.
丙型肝炎病毒（HCV）与肝损伤以及肝硬化和肝细胞癌的进展速度加快有关。在葡萄牙，它在注射吸毒者（IDU）等弱势群体中很普遍。HCV的特点是宿主内变异性高，选择驱动力可能会选择含有降低治疗效果的耐药相关替代（RAS）的变体。本研究的主要目的是分析初治IDU中NS5A的序列变异。分析了丙型肝炎的流行病学和临床状况，并通过桑格测序和下一代测序（NGS）对样本进行测序，以评估RAS并确认HCV亚型。系统发育分类结果一致：1a型，52.4%；1b型，10.7%；3a型，20.2%；4a型，8.3%；4d型，7.1%；以及一个2k/1b重组体。通过NGS检测到1a/3a混合感染。使用桑格测序法在34.5%（29/84）的样本中发现了RAS，而使用NGS法在42.9%（36/84）的样本中发现了RAS。在1a型和1b型亚型的序列中，分别检测到了RAS K24R、M28V、Q30H/R、H58D/P/Q/R以及RAS L31M和P58S。在3a型亚型中，鉴定出了RAS A30S/T、Y93H以及62位的多态性。此外，在4型基因型中检测到了RAS P58L。用于基线HCV耐药性分子检测的策略对于实现治疗效果和促进丙型肝炎的消除尤为重要。
