Abstract
The objective was to develop a method of HCV genome sequencing that allowed simultaneous genotyping and NS5A inhibitor resistance profiling. In order to validate the use of a unique RT-PCR for genotypes 1–5, 142 plasma samples from patients infected with HCV were analysed. The NS4B-NS5A partial region was successfully amplified and sequenced in all samples. In parallel, partial NS3 sequences were analyzed obtained for genotyping. Phylogenetic analysis showed concordance of genotypes and subtypes with a bootstrap >95% for each type cluster. NS5A resistance mutations were analyzed using the Geno2pheno [hcv] v0.92 tool and compared to the list of known Resistant Associated Substitutions recently published. In conclusion, this tool allows determination of HCV genotypes, subtypes and identification of NS5A resistance mutations. This single method can be used to detect pre-existing resistance mutations in NS5A before treatment and to check the emergence of resistant viruses while undergoing treatment in major HCV genotypes (G1-5) in the EU and the US
Highlights
Chronic HCV infection, recently re-estimated to affect between 64 and 103 million people worldwide [1] is a major public health problem
HCV Direct-Acting Antiviral Agents (DAAs) therapy represents a revolution in HCV treatment [13,14].Today, some DAAs do not have a pangenotypic action and experts define different combinations according to HCV genotype
HCV genotype determination is always recommended before starting a new DAA treatment
Summary
Chronic HCV infection, recently re-estimated to affect between 64 and 103 million people worldwide [1] is a major public health problem. Before 2011, standard treatment consisted of Pegylated Interferon (PEGINF) and ribavirin (R). This treatment allowed viral eradication in only 40–50% of patients with genotype 1 (the more frequent genotype) and 80% in HCV genotype 2 (the easiest genotype to treat with this combination) [2]. Increasing knowledge of HCV molecular biology, the establishment of robust HCV replication models and cell culture systems have enabled the development of Direct-Acting Antiviral Agents (DAAs) to treat HCV infection.
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