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. STUDY DESIGN: 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.
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. STUDY DESIGN: 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: 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: Natalia Chueca; Isidro Rivadulla; Rubén Lovatti; Gabriel Reina; Ana Blanco; Jose Angel Fernandez-Caballero; Laura Cardeñoso; Javier Rodriguez-Granjer; Miriam Fernandez-Alonso; Antonio Aguilera; Marta Alvarez; Juan Carlos Galán; Federico García Journal: PLoS One Date: 2016-04-20 Impact factor: 3.240