title: Characterization of Samples Identified as Hepatitis C Virus Genotype 1 without Subtype by Abbott RealTime HCV Genotype II Assay Using the New Abbott HCV Genotype Plus RUO Test.
abstract: Hepatitis C virus (HCV) genotyping continues to be relevant for therapeutic strategies. Some samples are reported as genotype 1 (gt 1) without subtype by the Abbott RealTime HCV Genotype II (GT II) test. To characterize such samples further, the Abbott HCV Genotype Plus RUO (Plus) assay, which targets the core region for gt 1a, gt 1b, and gt 6 detection, was evaluated as a reflex test in reference to NS5B or 5'-untranslated region (UTR)/core region sequencing. Of 3,626 routine samples, results of gt 1 without subtype were received for 171 samples (4.7%), accounting for 11.5% of gt 1 specimens. The Plus assay and sequencing were applied to 98 of those samples. NS5B or 5'-UTR/core region sequencing was successful for 91/98 specimens (92.9%). Plus assay and sequencing results were concordant for 87.9% of specimens (80/91 samples). Sequencing confirmed Plus assay results for 82.6%, 85.7%, 100%, and 89.3% of gt 1a, gt 1b, gt 6, and non-gt 1a/1b/6 results, respectively. Notably, 12 gt 6 samples that had been identified previously as gt 1 without subtype were assigned correctly here; for 25/28 samples reported as "not detected" by the Plus assay, sequencing identified the samples as gt 1 with subtypes other than 1a/1b. The genetic variability of HCV continues to present challenges for the current genotyping platforms regardless of the applied methodology. Samples identified by the GT II assay as gt 1 without subtype can be further resolved and reliably characterized by the new Plus assay.
authors.affiliation: Virologie AP-HP Hôpital Paul Brousse, Villejuif, France.
authors.forename: Camelia
authors.initials: C
authors.lastname: Mokhtari
authors.affiliation: Biomnis, Ivry sur Seine, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Ebel
authors.affiliation: Abbott GmbH & Co. KG, Wiesbaden, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Reinhardt
authors.affiliation: Biomnis, Ivry sur Seine, France.
authors.forename: Sandra
authors.initials: S
authors.lastname: Merlin
authors.affiliation: Virologie AP-HP Hôpital Paul Brousse, Villejuif, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Proust
authors.affiliation: Virologie AP-HP Hôpital Paul Brousse, Villejuif, France anne-marie.roque@aphp.fr.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Roque-Afonso
mesh_terms: D020121:5' Untranslated Regions; D005838:Genotype; D060005:Genotyping Techniques; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000175:diagnosis* / Q000821:virology*; D006801:Humans; D011933:Reagent Kits, Diagnostic; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D017361:Viral Nonstructural Proteins / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D020121:5' Untranslated Regions; D011933:Reagent Kits, Diagnostic; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase