Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.
Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France.
J Med Virol. 2015 Nov;87(11):1921-33. doi: 10.1002/jmv.24261. Epub 2015 Jun 12.
Infection with hepatitis C virus (HCV) represents a major public health concern worldwide. Recent therapeutic advances have been considerable, HCV genotype continuing to guide therapeutic management. Since 2008, HCV genotyping in our clinical microbiology laboratory at university hospitals of Marseille, Southeastern France, has been based on NS3 protease gene population sequencing, to allow concurrent HCV genotype and protease inhibitor (PI) genotypic resistance determinations. We aimed, first, to analyze the genetic diversity of HCV NS3 protease obtained from blood samples collected between 2003 and 2013 from patients monitored at university hospitals of Marseille and detect possible atypical sequences; and, second, to identify NS3 protease amino acid patterns associated with decreased susceptibility to HCV PIs. A total of 1,213 HCV NS3 protease sequences were available in our laboratory sequence database. We implemented a strategy based on bioinformatic tools to determine whether HCV sequences are representative of our local HCV genetic diversity, or divergent. In our 2003-2012 HCV NS3 protease sequence database, we delineated 32 clusters representative of the majority HCV genetic diversity, and 61 divergent sequences. Five of these divergent sequences showed less than 85% nucleotide identity with their top GenBank hit. In addition, among the 294 sequences obtained in 2013, three were divergent relative to these 32 previously delineated clusters. Finally, we detected both natural and on-treatment genotypic resistance to HCV NS3 PIs, including a substantial prevalence of Q80K substitutions associated with decreased susceptibility to simeprevir, a second generation PI.
丙型肝炎病毒 (HCV) 感染是全球主要的公共卫生关注点。近年来治疗方法取得了重大进展，HCV 基因型仍然指导着治疗管理。自 2008 年以来，法国东南部马赛大学附属医院的临床微生物学实验室一直基于 NS3 蛋白酶基因群体测序进行 HCV 基因分型，以同时进行 HCV 基因型和蛋白酶抑制剂 (PI) 基因型耐药性测定。我们的目的首先是分析从 2003 年至 2013 年在马赛大学附属医院监测的患者的血液样本中获得的 HCV NS3 蛋白酶的遗传多样性，并检测可能的非典型序列；其次，确定与 HCV PI 敏感性降低相关的 NS3 蛋白酶氨基酸模式。我们实验室的序列数据库中共有 1213 条 HCV NS3 蛋白酶序列。我们实施了一种基于生物信息学工具的策略，以确定 HCV 序列是否代表我们当地的 HCV 遗传多样性，或者是否存在差异。在我们的 2003-2012 年 HCV NS3 蛋白酶序列数据库中，我们确定了 32 个代表大多数 HCV 遗传多样性的聚类，以及 61 个离散序列。其中 5 个离散序列与它们在 GenBank 中的最佳命中序列的核苷酸同一性小于 85%。此外，在 2013 年获得的 294 个序列中，有 3 个相对于这 32 个先前划定的聚类是离散的。最后，我们检测到 HCV NS3 PI 的天然和治疗相关的基因型耐药性，包括与simeprevir（第二代 PI）敏感性降低相关的大量 Q80K 取代。
