Commentary: Next-Generation Sequencing: a Diagnostic One-Stop Shop for Hepatitis C?

Abstract

Before starting chronic hepatitis C treatment, the viral genotype/subtype has to be accurately determined and potentially coupled with drug resistance testing. Due to the high genetic variability of the hepatitis C virus, this can be a demanding task that can potentially be streamlined by viral whole-genome sequencing using Hepatitis C virus (HCV) is well-known for its high genetic variability, with seven distinct major HCV genotypes and nearly 70 officially assigned subtypes (1). For this reason, even though revolutionary progress has recently been made with direct-acting antivirals (DAAs) against HCV with high efficacy rates and an improved safety profile, there is still no universal antiviral treatment available that works equally effectively against all HCV genotypes (and especially subtypes) and across all patient populations (2, 3). Recent approval by the U.S. Food and Drug Administration (on 28 June 2016) of the first all-oral, pan-genotypic, single-tablet regimen for treating HCV-infected adults with and without cirrhosis based on a combination of sofosbuvir (NS5B inhibitor) and velpatasvir (pan-genotypic NS5A inhibitor) is an important step forward, but only time will tell whether the excellent results obtained in the clinical trials across all six major HCV genotypes and their subtypes (4, 5) will be reproduced in real-life settings.Accurate determination of the HCV genotype and selected HCV subtypes before treatment initiation has been mandatory for more than 2 decades in order to select the most appropriate treatment regimen and to decide on its duration and the use of ribavirin, and it is here to stay for at least the next few years (6). A few sequencing-based and several non-sequencing-based HCV genotyping assays are commercially available and are used worldwide for routine determination of the HCV genotype and selected subtypes. The non-sequencing-based HCV genotyping assays are mainly founded on reverse hybridization or real-time PCR. Because both assay groups belong to DNA probe-based technologies, they occasionally fail to provide unambiguous results, particularly when the genetic diversity of the target is high, as in the case of HCV. Even with the last versions of commercial non-sequencing-based HCV genotyping assays, the HCV genotype/subtype fails to be assigned in 5 to 10% of patients (7,8). The failure to obtain an unambiguous genotyping result by probe-based assays is frustrating, but it can be overcome by the use of a supplementary test (9). However, more concerning are cases of genotype misclassification because these often remain unnoticed until the clinical consequences of misclassification are evident, for example, after treatment failure with an HCV genotype 1-specific DAA combination. Recent studies have shown a substantial number of HCV genotype/subtype misclassifications, occurring in 2% to more than 50% of patients, depending on the genotyping assay and population studies (9-12). However, it should be stressed that the great majority of misclassifications account for erroneous ...

Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus

“…Since current antiviral therapies are still largely genotype-dependent, an accurate determination of the genotype and subtype is mandatory in clinical settings for treatment planning. Depending on the genotypic assay used, a non-negligible percentage of patients are misclassified regarding genotype and subtype [ 39 – 41 ]. High resolution NGS technologies ensure an accurate determination of HCV subtypes [ 34 , 42 ].…”

The First Complete Genome Sequences of Hepatitis C Virus Subtype 2b from Latin America: Molecular Characterization and Phylogeographic Analysis

“…Despite the revolutionary progress recently made with direct-acting antivirals (DAAs) against HCV, identification of the HCV genotype/subtype remains an important requirement for effective treatment decisions and serves as a good predictor of treatment success [13,14]. Therefore, HCV whole-genome sequencing appears useful for the accurate determination of viral genotypes and resistance-associated substitutions throughout the DAA target genome regions (NS3, NS5A, and NS5B) as well as identifying recombinant or rare viral types [15,16,17].…”