ArticleJournal of clinical microbiology2015
High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods.
Erratum issuedOpen access · bronzeAbstract read
In one paragraph
Article in Journal of clinical microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 39 papers.
0numbers the graph read from it
0cells of the map it votes in
39citing papers in PubMed
5.4field-weighted citation impact, top 3% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 83 citations in OpenAlex.
- Deep Sequencing Analysis of Hepatitis C Virus Subtypes and Resistance-Associated Substitutions in Genotype 4 Patients Resistant to Direct-Acting Antiviral (DAA) Treatment in Egypt.International journal of molecular sciences · 2025Article
- Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance.Animals : an open access journal from MDPI · 2023Article
- SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations.Pathogens (Basel, Switzerland) · 2022Article
- Review
- Adaptive Immune Responses, Immune Escape and Immune-Mediated Pathogenesis during HDV Infection.Viruses · 2022Review
- Prevalence of Hepatitis C Virus Infection, Genotypes and Subtypes in Migrants from Pakistan in Barcelona, Spain.Infection and drug resistance · 2022Article
- Identification and characterization of mixed infections ofFrontiers in microbiology · 2022Article
- Article
- Utility of the CobasDiagnostics (Basel, Switzerland) · 2021Article
- Molecular characterization of hepatitis C virus in liver disease patients in Botswana: a retrospective cross-sectional study.BMC infectious diseases · 2019Article
- The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid.Genome biology and evolution · 2019Article
- Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing.Scientific reports · 2019Article
- Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay.Scientific reports · 2019Article
- Deep-sequencing study of HCV G4a resistance-associated substitutions in Egyptian patients failing DAA treatment.Infection and drug resistance · 2019Article
- Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype.Infection and drug resistance · 2019Article
- Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus.BMC infectious diseases · 2018Article
- Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8Journal of virology · 2018Article
- A novel standardized deep sequencing-based assay for hepatitis C virus genotype determination.Scientific reports · 2018Article
- Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2018Article
- Relapse or reinfection after failing hepatitis C direct acting antiviral treatment: Unravelled by phylogenetic analysis.PloS one · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
42 authors at 13 institutions in 1 country.
Josep QuerLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain josep.quer@vhir.org jignacio.esteban@ciberehd.org.
Josep GregoriLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Roche Diagnostics SL, Barcelona, Spain.
Francisco Rodríguez-FriasCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Maria ButiLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain.
Antonio MadejonCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain.
Sofia Perez-del-PulgarCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain.
Damir Garcia-CehicLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
Rosario CasillasCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Maria BlasiCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Maria HomsCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
David TaberneroCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Miguel Alvarez-TejadoRoche Diagnostics SL, Barcelona, Spain.
Jose Manuel MuñozRoche Diagnostics SL, Barcelona, Spain.
Maria CuberoLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
Andrea CaballeroBiochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Jose Antonio del CampoCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Virgen de Valme, Seville, Spain.
Esteban DomingoCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.
Irene BelmonteBiochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Leonardo NietoBiochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain.
Sabela LensCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain.
Paloma Muñoz-de-RuedaCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain.
Paloma Sanz-CamenoCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain.
Silvia SauledaCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain.
Marta BesCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain.
Jordi GomezCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain CSIC, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain.
Carlos BrionesCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Astrobiología (CSIC-INTA), Madrid, Spain.
Celia PeralesCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.
Julie SheldonCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.
Lluis CastellsLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain.
Lluis ViladomiuLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
Javier SalmeronCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain.
Angela Ruiz-ExtremeraCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain.
Rosa Quiles-PérezCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain.
Ricardo Moreno-OteroCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain.
Rosario López-RodríguezCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain.
Helena AllendePathological Anatomy Department, VHIR-HUVH, Barcelona, Spain.
Manuel Romero-GómezCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Virgen de Valme, Seville, Spain.
Jaume GuardiaLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain.
Rafael EstebanLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain.
Javier Garcia-SamaniegoCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain.
Xavier FornsCentro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain.
Juan Ignacio EstebanLiver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain josep.quer@vhir.org jignacio.esteban@ciberehd.org.
Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas · ESInstituto de Salud Carlos III · ESRoche (Spain) · ESVall d'Hebron Institut de Recerca · ESConsorci Institut D'Investigacions Biomediques August Pi I Sunyer · ESHospital Clínic de Barcelona · ESHospital Universitario de La Princesa · ESHospital Universitario de Valme · ESHospital Universitario La Paz · ESInstitut Català de la Salut · ESInstituto de Investigación Biosanitaria de Granada · ESInstituto de Parasitología y Biomedicina "López - Neyra" · ESUniversidad Autónoma de Madrid · ES
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.
Indexed as
GenotypeHigh-Throughput Nucleotide SequencingPhylogenyGenotyping TechniquesHepacivirusHepatitis CHumansReagent Kits, DiagnosticRNA-Dependent RNA PolymeraseViral Nonstructural ProteinsNS-5 protein, hepatitis C virusReagent Kits, DiagnosticRNA-Dependent RNA PolymeraseViral Nonstructural Proteins
Identifiers
What OpenQuestion holds
Textmetadata
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.