Evaluation of the Abbott RealTime HCV genotype II RUO (GT II) assay with reference to 5′UTR, core and NS5B sequencing

• Published in: Journal of clinical virology Vol. 60; no. 1; pp. 22 - 26
• Main Authors: Mallory, Melanie A, Lucic, Danijela X, Sears, Mitchell T, Cloherty, Gavin A, Hillyard, David R
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.05.2014
• Subjects: Allergy and Immunology; DNA sequencing; Genotyping; Hepatitis C virus; Infectious Disease; Real-time PCR; protease inhibitor; Genotyping; Real-time PCR; hepatitis C virus; PI; HCV; DNA sequencing; Hepatitis C virus
• ISSN: 1386-6532; 1873-5967
• DOI: 10.1016/j.jcv.2014.02.006

Abstract Background HCV genotyping is a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. Objective To evaluate the concordance between the Abbott GT II assay and genotyping by sequencing subregions of the HCV 5′UTR, core and NS5B. Study design The Abbott assay was used to genotype 127 routine patient specimens and 35 patient specimens with unusual subtypes and mixed infection. Abbott results were compared to genotyping by 5′UTR, core and NS5B sequencing. Sequences were genotyped using the NCBI non-redundant database and the online genotyping tool COMET. Results Among routine specimens, core/NS5B sequencing identified 93 genotype 1s, 13 genotype 2s, 15 genotype 3s, three genotype 4s, two genotype 6s and one recombinant specimen. Genotype calls by 5′UTR, core, NS5B sequencing and the Abbott assay were 97.6% concordant. Core/NS5B sequencing identified two discrepant samples as genotype 6 (subtypes 6l and 6u) while Abbott and 5′UTR sequencing identified these samples as genotype 1 with no subtype. The Abbott assay subtyped 91.4% of genotype 1 specimens. Among the 35 rare specimens, the Abbott assay inaccurately genotyped 3k, 6e, 6o, 6q and one genotype 4 variant; gave indeterminate results for 3g, 3h, 4r, 6m, 6n, and 6q specimens; and agreed with core/NS5B sequencing for mixed specimens. Conclusions The Abbott assay is an automated HCV genotyping method with improved accuracy over 5′UTR sequencing. Samples identified by the Abbott assay as genotype 1 with no subtype may be rare subtypes of other genotypes and thus require confirmation by another method.