title: Deep sequencing in the management of hepatitis virus infections.
abstract: The hepatitis viruses represent a major public health problem worldwide. Procedures for characterization of the genomic composition of their populations, accurate diagnosis, identification of multiple infections, and information on inhibitor-escape mutants for treatment decisions are needed. Deep sequencing methodologies are extremely useful for these viruses since they replicate as complex and dynamic quasispecies swarms whose complexity and mutant composition are biologically relevant traits. Population complexity is a major challenge for disease prevention and control, but also an opportunity to distinguish among related but phenotypically distinct variants that might anticipate disease progression and treatment outcome. Detailed characterization of mutant spectra should permit choosing better treatment options, given the increasing number of new antiviral inhibitors available. In the present review we briefly summarize our experience on the use of deep sequencing for the management of hepatitis virus infections, particularly for hepatitis B and C viruses, and outline some possible new applications of deep sequencing for these important human pathogens.
authors.affiliation: Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain. Electronic address: josep.quer@vhir.org.
authors.forename: Josep
authors.initials: J
authors.lastname: Quer
authors.affiliation: Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodríguez-Frias
authors.affiliation: Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Roche Diagnostics, S.L., Sant Cugat del Vallés, Spain.
authors.forename: Josep
authors.initials: J
authors.lastname: Gregori
authors.affiliation: Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Tabernero
authors.affiliation: Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain.
authors.forename: Maria Eugenia
authors.initials: ME
authors.lastname: Soria
authors.affiliation: Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
authors.forename: Damir
authors.initials: D
authors.lastname: García-Cehic
authors.affiliation: Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Homs
authors.affiliation: Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
authors.forename: Albert
authors.initials: A
authors.lastname: Bosch
authors.affiliation: Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
authors.forename: Rosa María
authors.initials: RM
authors.lastname: Pintó
authors.affiliation: Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
authors.forename: Juan Ignacio
authors.initials: JI
authors.lastname: Esteban
authors.affiliation: Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
authors.forename: Esteban
authors.initials: E
authors.lastname: Domingo
authors.affiliation: Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
authors.forename: Celia
authors.initials: C
authors.lastname: Perales
mesh_terms: D000818:Animals; D000998:Antiviral Agents / Q000494:pharmacology / Q000627:therapeutic use; D019468:Disease Management; D024882:Drug Resistance, Viral; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D005838:Genotype; D016174:Hepacivirus / Q000187:drug effects / Q000235:genetics; D006515:Hepatitis B virus / Q000187:drug effects / Q000235:genetics; D003698:Hepatitis Delta Virus / Q000187:drug effects / Q000235:genetics; D006518:Hepatitis Viruses / Q000187:drug effects / Q000235:genetics*; D006525:Hepatitis, Viral, Human / Q000175:diagnosis / Q000628:therapy / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D017211:Treatment Failure; D016896:Treatment Outcome
chemical_list: D000998:Antiviral Agents
keywords: Antiviral drug resistance; Hepatic disease; Mutation; Quasispecies; Viral diversity