Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure
Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure
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DOI：
10.1016/j.antiviral.2019.104694
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发表时间：
2020-02-01
影响因子：
7.6
通讯作者：
Quer, Josep
中科院分区：
文献类型：
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作者：
Chen, Qian;Perales, Celia;Quer, Josep
一部分丙型肝炎病毒（HCV）感染的患者无法使用直接作用的抗病毒（DAA）治疗方案，通常是因为耐药相关替代（RAS）。本研究的目的是描述DAA治疗失败的大型患者队列的耐药特征，并调查HCV亚型与失败之间的关系，以帮助优化这些患者的管理。设计了一种基于深度测序的新的标准化HCV-RAS检测方案，并应用于220份来自DAA治疗失败患者的先前亚型样本，在39家西班牙医院收集。大多数患者接受了基于DAA的无干扰素（IFN）方案; 79%的患者接受了含索非布韦的治疗失败。用亚型特异性引物分析非结构蛋白（NS）3、NS 5A和NS 5 B（DAA靶区）的基因组区域，发现病毒亚型分布如下：（G）1型占62.7%，G3 a型占21.4%，G4 d型占12.3%，G2型占1.8%，混合感染占1.8%。总体而言，88.6%的患者携带至少1种RAS，19%的患者携带突变谱中频率低于20%的RAS。有和没有利巴韦林治疗之间的RAS选择没有差异。无论接受何种治疗，每种HCV亚型均显示特定类型的RAS。值得注意的是，在18.6%治疗失败的患者的靶蛋白中没有检测到RAS，并且30.4%的患者在不是他们接受的抑制剂的靶蛋白中具有RAS。利巴韦林的使用并不影响失败时RAS的类型或数量。RAS出现的亚型特异性模式强调了准确的HCV亚型分型的重要性。“靶外”RAS的频率表明需要在所有三个DAA靶区域进行RAS筛查。
A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients.A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) alpha-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers.Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received.HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of "extra-target" RAS suggests the need for RAS screening in all three DAA target regions.