Resistance characterization of ledipasvir and velpatasvir in hepatitis C virus genotype 4

Abstract

HCV genotype 4 (GT4) has often been overlooked in drug development, even though it infects ~20 million people worldwide. Ledipasvir/sofosbuvir and sofosbuvir/velpatasvir were highly efficacious in GT4 HCV-infected patients from GS-US-337-1119 and GS-US-342-1138. Here, we characterize the resistance profile of ledipasvir (LDV) and velpatasvir (VEL) in patients with GT4 HCV infection. NS5A deep-sequencing was performed for 454 patients infected with HCV GT4 at baseline, including 44 patients enrolled in GS-US-337-1119 and 116 patients enrolled in GS-US-342-1138, and at relapse for patients with virologic failure. LDV and VEL susceptibilities of 56 patient isolates were determined. In GS-US-337-1119, SVR12 rates were 100% for all subtypes except 4b and 4r. Phenotypic assessment of 56 HCV NS5A patient isolates from various GT4 subtypes indicated that LDV had high potency for the common subtypes 4a/d, and subtypes 4c/f/k/l/m/n/o/p/r/t despite the presence of resistance-associated substitutions (RASs). For the rare GT4b, LDV median EC was higher, but with a broad range of individual values. Importantly, all GT4b isolates tested had 2-4 NS5A RASs, some including Y93H. Similarly, the 2 GT4r infected patients who had virologic relapse had rare triple RASs. Reversion of these substitutions to the consensus residue significantly increased LDV susceptibility. In GS-US-342-1138, all patients achieved SVR12, regardless of their subtype or presence of RASs. In vitro data confirmed that VEL is potent against all GT4 isolates tested. LDV and VEL are potent antiviral drugs, estimated to be effective against >95% and >99%, respectively, of GT4 HCV isolates.

Characterization of demographics and NS5A genetic diversity for hepatitis C virus genotype 4‐infected patients with or without cirrhosis treated with ombitasvir/paritaprevir/ritonavir

“…High SVR12 rates of 96.2% or 95.4% were reported in HCV GT4‐infected patients treated with either OBV/PTV/r (n = 122) or SOF/LDV (n = 130), respectively, with or without RBV in a real‐world setting, but an analysis of the prevalence of NS5A baseline polymorphisms was not included in the study results . Another study reported SVR12 rates of 93% (41/44) in GT4‐infected patients treated with SOF/LDV, which included 25 patients with baseline polymorphisms L28M and/or L30R/S in NS5A; all 3 virologic failures had L28M/V with or without L30R in NS5A at baseline, which corresponds with a 37‐ to 67‐fold change in LDV activity against L28M/V and L30R in GT4 . In our combined cohort analysis, SVR12 rates of 98.9% (94/95) were observed for HCV GT4‐infected patients with an NS5A polymorphism at baseline treated with OBV/PTV/r plus RBV in the PEARL‐I and AGATE‐I studies, indicating that there was no impact of NS5A baseline polymorphisms on treatment outcome, even though 35.8% (95/265, excluding the common T/P58 polymorphism in GT4d) of the patient sequences had an NS5A polymorphism at a resistance‐associated amino acid position; this included 78 patients with L28M and/or L30R/S in NS5A (not counting subtype 4d where R30 is wild‐type).…”

Frequent Antiviral Treatment Failures in Patients Infected With Hepatitis C Virus Genotype 4, Subtype 4r

“…Briefly, HCV RNA was extracted with the QIASymphony DSP Virus/Pathogen kit on a QIASymphony device (Qiagen GmbH, Hilden, Germany), according to the manufacturer's instructions. Complementary DNA synthesis was performed with the OneStep RT‐PCR kit (Qiagen GmbH) with sets of primers adapted to the viral regions targeted . Nested PCR was then performed with common primers and, when necessary, genotype‐specific primers.…”

“…In the pooled PEARL‐I and AGATE‐I studies, clinical trials including patients treated with ombitasvir/paritaprevir/ritonavir, only 1 of 101 French genotype 4–infected patients was infected with subtype 4r . In the pooled GS‐US‐337‐1119 and ASTRAL‐1 trials, which included patients from Europe and the United States treated with sofosbuvir/ledipasvir and sofosbuvir/velpatasvir, respectively, 5 of 160 genotype 4–infected patients (i.e., 3.1%) were infected with subtype 4r …”

HCV genotype 4, 5 and 6: Distribution of viral subtypes and sustained virologic response rates in clinical trials of approved direct‐acting antiviral regimens

“…Extensive HCV genetic variability exists at multiple key NS5A resistance‐associated amino acid positions, both across and within different HCV subtypes . Recent studies have shown that reduced susceptibility to ledipasvir for some GT 4b and 4r isolates is associated with the presence of NS5A resistance‐associated substitutions, which may explain occurrences of ledipasvir/sofosbuvir virologic failure among patients with these subtypes . Nevertheless, more data are needed with various NS5A inhibitor‐containing regimens before we can draw firm conclusions about the impact of NS5A genetic variability on treatment outcomes for patients with GT 4b, 4r and other less common subtypes.…”

“…Cell culture studies demonstrated antiviral activity of each drug component against each approved GT, with data generally demonstrating consistent activity across several representative subtypes of GT 4 and 6. Although it is not feasible to capture all of the genetic diversity of GT 4 and 6 subtypes in cell culture studies and clinical trials, antiviral activity generally has been demonstrated, at minimum, across the most common representative subtypes of GT 4 and 6…”