title: Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges.
abstract: Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.
authors.affiliation: a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .|b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France .
authors.forename: Pauline
authors.initials: P
authors.lastname: Trémeaux
authors.affiliation: c Centre d'investigation clinique, Santé publique, CHU Grenoble-Alpes , Grenoble , France .|d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and.
authors.forename: Alban
authors.initials: A
authors.lastname: Caporossi
authors.affiliation: e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France.
authors.forename: Marie-Ange
authors.initials: MA
authors.lastname: Thélu
authors.affiliation: d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and.
authors.forename: Michael
authors.initials: M
authors.lastname: Blum
authors.affiliation: e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Leroy
authors.affiliation: a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .|b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France .
authors.forename: Patrice
authors.initials: P
authors.lastname: Morand
authors.affiliation: a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .|b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France .
authors.forename: Sylvie
authors.initials: S
authors.lastname: Larrat
mesh_terms: D016679:Genome, Viral / Q000235:genetics*; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D025202:Molecular Diagnostic Techniques; D058889:Molecular Typing; D000073336:Whole Genome Sequencing / Q000379:methods*
keywords: Sanger sequencing; genotyping; next-generation sequencing; resistance-associated variants