title: High HCV subtype heterogeneity in a chronically infected general population revealed by high-resolution hepatitis C virus subtyping.
abstract: OBJECTIVE
  This study aimed to characterize the chronically infected general hepatitis C virus (HCV) population in Barcelona using a highly sensitive subtyping method that can identify the 67 recognized HCV subtypes and diagnose mixed infection by various genotypes/subtypes in a single individual. The resulting information has implications for selecting optimal direct-acting antiviral (DAA) treatment for each patient and establishing public healthcare policies in our setting.
  
  
  METHODS
  Consecutive HCV patients (treatment-naïve or interferon-based failures) attending Vall d'Hebron Hospital outpatient clinics from February 2015 to May 2016 (N=1473) were included in the study. Patient samples were characterized using HCV subtyping by next-generation ultra-deep pyrosequencing.
  
  
  RESULTS
  The following genotypes (G) were found: G1 (1126/1473 (76.4%)), G4 (145/1473 (9.8%)), G3 (135/1473 (9.2%)), G2 (51/1473 (3.5%)), and G5 (1/1473 (0.1%)). Twenty-two subtypes were seen: 1b (790/1473 (53.6%)), 1a (332/1473 (22.5%)), 3a (133/1473 (9.0%)), 4d (105/1473 (7.1%)), 4a (29/1473 (2.0%)), and 2c (25/1473 (1.7%)), with 16 low-prevalence subtypes accounting for the remaining 3.0% (44/1473). There was a worrisome 1.0% (15/1473) of mixed infections. G2 (51/1473 (3.5%)) showed a high level of heterogeneity. Analyses by age groups showed a predominance of G1b over G1a (428/506 (84.6%) vs. 24/506 (4.7%)) in patients born before 1950 (N=506/1473), and similar percentages of these subtypes in those born between 1951 and 1975 (N=834/1473) (315/834, 37.8% vs. 266/834, 31.9%) and after 1976 (N=133/1473) (47/133, 35.3% vs. 42/133, 31.6%).
  
  
  CONCLUSIONS
  Subtype distribution showed a higher level of heterogeneity than was expected, particularly for G2. Prevalence of mixed infections was around 1%. HCV subtype distribution related to patient age group suggested that patients born from 1936 to 1975 in our setting should undergo screening for the infection. Next-generation sequencing enabled better classification of candidates for DAA-based treatment.
authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain. Electronic address: frarodri@vhebron.net.
authors.forename: F
authors.initials: F
authors.lastname: Rodriguez-Frias
authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Clinical Microbiology Department, HUVH, Barcelona, Spain.
authors.forename: L
authors.initials: L
authors.lastname: Nieto-Aponte
authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Roche Diagnostics SL, Sant Cugat del Vall_es, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
authors.forename: D
authors.initials: D
authors.lastname: Garcia-Cehic
authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Clinical Microbiology Department, HUVH, Barcelona, Spain.
authors.forename: R
authors.initials: R
authors.lastname: Casillas
authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: D
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authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain.
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authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain.
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authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
authors.forename: Ll
authors.initials: L
authors.lastname: Castells
authors.affiliation: Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
authors.forename: Ll
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authors.lastname: Viladomiu
authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
authors.forename: B
authors.initials: B
authors.lastname: Minguez
authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.initials: S
authors.lastname: Augustin
authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
authors.forename: M
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authors.lastname: Riveiro-Barciela
authors.affiliation: Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
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authors.affiliation: Liver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
authors.forename: R
authors.initials: R
authors.lastname: Esteban
authors.affiliation: Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Clinical Microbiology Department, HUVH, Barcelona, Spain.
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain.
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authors.initials: JI
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authors.affiliation: Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Hepaticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain; Liver Unit, Malalties Hepatiques, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-HUVH), Barcelona, Spain. Electronic address: josep.quer@vhir.org.
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mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D060085:Coinfection / Q000453:epidemiology / Q000821:virology; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000453:epidemiology / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D015995:Prevalence; D013030:Spain / Q000453:epidemiology; D055815:Young Adult
keywords: HCV; Hepatitis C virus; High-resolution HCV subtyping; Mixed infections; Prevalence; Subtypes