Melanie A Mallory1, Danijela X Lucic2, Mitchell T Sears3, Gavin A Cloherty4, David R Hillyard5. 1. ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA. Electronic address: melanie.mallory@aruplab.com. 2. Abbott Molecular Inc., 1350 E. Touhy Avenue, Des Plaines, IL 60018, USA. Electronic address: danijela.lucic@abbott.com. 3. ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA. Electronic address: mitch.sears@gmail.com. 4. Abbott Molecular Inc., 1350 E. Touhy Avenue, Des Plaines, IL 60018, USA. Electronic address: gavin.cloherty@abbott.com. 5. ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA; University of Utah Department of Pathology, 15 North Medical Drive East, Salt Lake City, UT 84112, USA. Electronic address: hillyadr@aruplab.com.
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.
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.
Authors: Josep Quer; Josep Gregori; Francisco Rodríguez-Frias; Maria Buti; Antonio Madejon; Sofia Perez-del-Pulgar; Damir Garcia-Cehic; Rosario Casillas; Maria Blasi; Maria Homs; David Tabernero; Miguel Alvarez-Tejado; Jose Manuel Muñoz; Maria Cubero; Andrea Caballero; Jose Antonio del Campo; Esteban Domingo; Irene Belmonte; Leonardo Nieto; Sabela Lens; Paloma Muñoz-de-Rueda; Paloma Sanz-Cameno; Silvia Sauleda; Marta Bes; Jordi Gomez; Carlos Briones; Celia Perales; Julie Sheldon; Lluis Castells; Lluis Viladomiu; Javier Salmeron; Angela Ruiz-Extremera; Rosa Quiles-Pérez; Ricardo Moreno-Otero; Rosario López-Rodríguez; Helena Allende; Manuel Romero-Gómez; Jaume Guardia; Rafael Esteban; Javier Garcia-Samaniego; Xavier Forns; Juan Ignacio Esteban Journal: J Clin Microbiol Date: 2014-11-05 Impact factor: 5.948
Authors: V Saludes; A Antuori; B Reinhardt; I Viciana; E Clavijo; L Schreiber; M Tenenbaum; F Rodriguez-Frias; J Quer; L Matas; E Martró Journal: Sci Rep Date: 2019-03-06 Impact factor: 4.379