title: Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice.
abstract: BACKGROUND
  Hepatitis C virus (HCV) genotyping is mandatory for tailoring dose and duration of pegylated interferon-α plus ribavirin treatment and for deciding on triple therapy eligibility. Additionally, subtyping may play a role in helping to select future treatment regimens that include directly-acting antivirals. However, commercial assays for HCV genotyping fail to identify the genotype/subtype in some cases.
  
  
  OBJECTIVE
  Our aims were (i) to determine the success rate of the commercial genotyping assay Abbott RealTime HCV Genotype II at identifying the genotype and the HCV-1 subtype; and (ii) to phylogenetically characterise the obtained indeterminate results.
  
  
  METHODS
  HCV genotyping results obtained between 2009 and 2012 in a Spanish reference hospital were reviewed. A total of 896 people were genotyped with the Abbott RealTime HCV Genotype II assay. Specimens with an indeterminate result were retrospectively genotyped using the reference method based on the phylogenetic analysis of HCV NS5B sequences.
  
  
  RESULTS
  Using the commercially available assay, an indeterminate HCV genotype result was obtained in 20 of 896 patients (2.2%); these corresponded to genotypes 3a, 3k and 4d. Importantly, 8.6% of all cases where genotype 3 was detected were indeterminate. In addition, the HCV-1 subtype was not assigned in 29 of 533 cases (5.4%).
  
  
  CONCLUSIONS
  The implementation in the clinical microbiology laboratory of the reference method for HCV genotyping allows indeterminate genotype/subtype results to be interpreted and may lead to the identification of previously uncharacterised subtypes.
authors.affiliation: Microbiology Service, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
authors.forename: Victoria
authors.initials: V
authors.lastname: González
authors.forename: Meissiner
authors.initials: M
authors.lastname: Gomes-Fernandes
authors.forename: Elisabet
authors.initials: E
authors.lastname: Bascuñana
authors.forename: Sònia
authors.initials: S
authors.lastname: Casanovas
authors.forename: Verónica
authors.initials: V
authors.lastname: Saludes
authors.forename: Elena
authors.initials: E
authors.lastname: Jordana-Lluch
authors.forename: Lurdes
authors.initials: L
authors.lastname: Matas
authors.forename: Vicenç
authors.initials: V
authors.lastname: Ausina
authors.forename: Elisa
authors.initials: E
authors.lastname: Martró
mesh_terms: D000328:Adult; D005260:Female; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000175:diagnosis* / Q000821:virology*; D006761:Hospitals; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D011933:Reagent Kits, Diagnostic; D017422:Sequence Analysis, DNA; D013030:Spain; D017361:Viral Nonstructural Proteins / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D011933:Reagent Kits, Diagnostic; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase
keywords: Genotyping; Hepatitis C virus; Phylogenetic analysis; Real-time PCR; Subtyping