Geno2pheno[HCV] – A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents

Abstract

The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR) rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs). RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2pheno[HCV] (g2p[HCV]) to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir), the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir), and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir). Upon submission of up to eight sequences, g2p[HCV] aligns the input sequences, identifies the genomic region(s), predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2p[HCV] offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant, phenotypic cell culture assays obtained from patients’ virus variants.

Prevalence of NS5A resistance associated substitutions in patients with hepatitis C virus genotypes 1a and 3: Impact on current therapeutic strategies

“…Nucleotide sequences were assembled using the Variant Reporter version 1.0 software (Thermo Fisher Scientific) and aligned with reference sequences (GeneBank accession numbers AF009606 for HCV G1a and D17763 for HCV G3). NS5A sequences were analyzed using geno2pheno (HCV) algorithm for the identification of NS5A RASs considering the clinically relevant RASs for the analysis: M28A/G/T, Q30D/E/H/G/K/L/R, L31M/V/F, H58D, and Y93C/H/N/S for G1a and Y93H for G3 accordingly to the last updated guidelines of the American Association for the Study of Liver Diseases (AASLD) and the European Association for the Study of the Liver (EASL)…”

Hepatitis C infection and renal cell carcinoma: A systematic review and meta-analysis

“…In the new era of treatment of HCV infection, direct-acting antiviral agents have been demonstrated to be effective therapy and increasingly used[31]. These agents may potentially decrease the incidence of RCC in HCV patients in the long term.…”

NS3 Variability in Hepatitis C Virus Genotype 1A Isolates from Liver Tissue and Serum Samples of Treatment-Naïve Patients with Chronic Hepatitis C

“…Serum HCV RNA levels were quantified in each sample using the commercial assays COBAS Ampliprep/COBAS TaqMan HCV Quantitative Test v2.0 (Roche Diagnostics, Mannheim, Germany) with a lower limit of detection of 15 IU/mL. HCV genotype/subtypes were determined at screening by Versant LIPA v2 assay (Siemens Healthcare Diagnostics, Milan, Italy) and also confirmed by sequencing analysis of the NS5A, NS5B, and NS3/4A viral regions followed by alignment search tool (Geno2pheno) analysis [18].…”