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

Abstract

Hepatitis C virus (HCV) genotype 4 (GT4) is genetically diverse with 17 confirmed and 4 provisional subtypes. In this report, HCV GT4-infected patient samples from Phase 2/3 clinical studies were analysed to characterize global demographics and genetic diversity of GT4 infection among patients treated with ombitasvir (OBV, NS5A inhibitor) plus paritaprevir/r (NS3/4A inhibitor codosed with ritonavir). Among 17 subtypes isolated from GT4-infected patients in the PEARL-I and AGATE-I studies, subtype prevalence by country of enrolment and country of origin suggested that subtypes 4a and 4d were likely circulating in Europe, while heterogeneous GT4 subtypes and a portion of GT4a detected in European and North American countries were likely due to immigration of HCV-infected patients from Africa. The distributions of birth cohort and race were also significantly different across GT4 subtypes 4a, 4d, and non-4a/4d. In addition, phylogenetic analyses of NS5A sequences revealed clustering within subtype 4a which segregated by the patient-reported country of origin and the presence of the L30R/S polymorphism. HCV NS5A sequences derived from GT4a-infected patients who originated from Europe and the United States clustered separately from sequences derived from patients who originated from Egypt, suggesting that genetically distinct strains of subtype 4a may be circulating globally. Finally, NS5A baseline polymorphisms were frequently detected at amino acid positions of interest for the inhibitor-class and OBV retained activity against 37 of 39 NS5A GT4 clinical isolates, with no impact on treatment outcome in the PEARL-I and AGATE-I studies.

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

“…Our data, showing a large over‐representation of patients infected with HCV subtype 4r among those who failed to achieve SVR after DAA‐based therapy in France, as compared to the very low prevalence of this subtype in the country, indicate that HCV subtype 4r is difficult to cure with currently available antiviral drug regimens. These results are in keeping with a Rwandan study showing a 54% SVR rate in patients infected with subtype 4r treated with sofosbuvir and ledipasvir, significantly lower than that with other genotype 4 subtypes (87%‐100%) .…”

“…In France, 12.4% (164 of 1,322) of all patients with chronic hepatitis C (CHC) prospectively included between 2010 and 2014 in a nation‐wide, multicenter cohort study (CO22 HEPATHER) were infected with genotype 4 . 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 …”

“…(13) 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. (21) 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. (22) The aim of this study was to assess the proportion of subtype 4r infections in a population of patients treated for their HCV infection in France who failed to achieve SVR and to virologically characterize their treatment failures.…”

Hepatitis C virus genetic diversity by geographic region within genotype 1-6 subtypes among patients treated with glecaprevir and pibrentasvir

“…Viral RNA isolation, reverse transcriptase (RT)-PCR, and nested PCR were conducted using genotype and subtype-specific primers on >2300 available baseline plasma samples, as previously described in detail for full-length NS3/4A and NS5A genes [ 34 , 35 , 37 – 41 ]. For each sample, HCV genotype was identified by the Versant HCV Genotype Inno-LiPA Assay v2.0 at the time of enrollment in the study, and HCV subtype was subsequently determined by neighbor-joining phylogenetic analysis of full-length NS3/4A and NS5A nucleotide sequences, as described in detail previously [ 40 , 41 ]. The subtype for each sample was assigned based on agreement between NS3/4A and NS5A results when both gene sequences were available, or was based on data from a single gene target when data was not available from both genes.…”

“…NGS analysis of NS3/4A and NS5A amplicons from 2348 baseline samples was conducted by DDL Diagnostic Laboratory (Rijswijk, Netherlands) for studies SURVEYOR-1, -2, ENDURANCE-1, -3, -4, -5/6, and EXPEDITION-1, and by Monogram Biosciences (South San Francisco, CA, USA) for studies ENDURANCE-2 and EXPEDITION-4, using methods that were described in detail previously [ 40 ]. PCR amplicons were purified and quantified by DDL Diagnostic Laboratory using methods previously described [ 40 ]. PCR amplicons were purified, quantified, and normalized by Monogram Biosciences using the AxyPrep Mag PCR Normalizer kit (Corning Life Sciences, Corning, NY).…”