Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed

Abstract

We evaluated the transition of dominant resistance-associated substitutions (RASs) in hepatitis C virus during long-term follow-up after the failure of DAAs (direct acting antivirals)-based therapy. RASs in non-structure (NS)3/4A, NS5A, NS5B, and deletions in NS5A from 20 patients who failed simeprevir/pegylated-interferon/ribavirin (SMV/PEG-IFN/RBV) and 25 patients who failed daclatasvir/asunaprevir (DCV/ASV) treatment were examined by direct sequencing. With respect to SMV/PEG-IFN/RBV treatment, RAS was detected at D168 in NS3/4A but not detected in NS5A and NS5B at treatment failure in 16 of 20 patients. During the median follow-up period of 64 weeks, the RAS at D168 became less dominant in 9 of 16 patients. Among 25 DCV/ASV failures, RASs at D168, L31, and Y93 were found in 57.1%, 72.2%, and 76.9%, respectively. NS5A deletions were detected in 3 of 10 patients treated previously with SMV/PEG-IFN/RBV. The number of RASs in the breakthrough patients exceeded that in relapsers (mean 3.9 vs. 2.7, p < 0.05). RAS at D168 in NS3/4A became less dominant in 6 of 15 patients within 80 weeks. Y93H emerged at the time of relapse, then decreased gradually by 99% at 130 weeks post-treatment. Emerged RASs were associated with the clinical course of treatment and could not be detected during longer follow-up.

The presence of multiple NS5A RASs is associated with the outcome of sofosbuvir and ledipasvir therapy in NS5A inhibitor‐naïve patients with chronic HCV genotype 1b infection in a real‐world cohort

“…First, it was a single‐centre study and only involved Japanese patients with chronic HCV genotype 1b infection. Second, we could not detect <20.0%‐25.0% of the mutations related to amino acid substitutions because an ultradeep sequencing method was not used. However, in previous studies, NS5A RASs were generally examined by direct‐sequencing methods because the predominant RASs are associated with the outcome of DAA therapy.…”

“…Serum samples were obtained from the patients before treatment. Amino acids sequences in the NS5A region of HCV genotype 1 were examined as described previously . In detail, RNA was extracted from 140 μL serum using a commercial kit (QIAmp viral RNA mini kit, Qiagen, Hilden, Germany).…”

Ribavirin induces hepatitis C virus genome mutations in chronic hepatitis patients who failed to respond to prior daclatasvir plus asunaprevir therapy

“…NS3/4A protease‐resistant HCV variants have reduced fitness, as estimated by viral replicative ability and production of infectious progeny . In contrast to NS3 RAVs, treatment‐emergent NS5A RAVs do not appear to compromise fitness and are known to persist for a long time . It is possible that RBV‐induced transitions may be suppressed among treatment‐emergent NS5A RAVs due to high viral fitness.…”

“…31,32 In contrast to NS3 RAVs, treatmentemergent NS5A RAVs do not appear to compromise fitness and are known to persist for a long time. 29,33,34 It is possible that RBV- Induction of G-to-A hypermutation in human immunodeficiency virus and HBV has been reported as part of host innate immunity against virus infection; hypermutation of HBV was induced in hepatocytes, and expression of APOBEC3G protein in liver cellderived cell lines increased hypermutation. 35 On the other hand, there are few reports about APOBEC3G and hypermutation in HCV.…”

HCV Genotyping with Concurrent Profiling of Resistance-Associated Variants by NGS Analysis

“…Targeted assays had been previously developed to identify a specific RAV [27,28]. RAVs which are found at levels with at least 15% variant frequency, at baseline, are known to confer resistance to certain DAAs [29], and therefore may impact on the effectiveness of DAA treatment [30]. Vela NGS targets relevant RAVs in three non-structural gene segments (NS3, NS5A and NS5B) of HCV 1a and 1b, and although the RAV profiling is comprehensive but not exhaustive due to the assay design, any baseline RAVs present in any of these DAA target genes, can affect the therapeutic effectiveness [31].…”