Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing
Articolo
Data di Pubblicazione:
2022
Citazione:
Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing / D. Bradshaw, D.F. Bibby, C.F. Manso, R. Piorkowska, H. Mohamed, J. Ledesma, L. Bubba, Y.T. Chan, S.L. Ngui, S. Carne, J.L. Mbisa. - In: CLINICAL MICROBIOLOGY AND INFECTION. - ISSN 1198-743X. - 28:3(2022 Mar), pp. 405-409. [10.1016/j.cmi.2021.06.042]
Abstract:
Objectives: We sought to evaluate clinically a hepatitis C virus (HCV) whole-genome, next-generation sequencing (NGS) pipeline that is agnostic to viral genotype. Methods: Performance of the NGS pipeline was assessed through comparison of results with Sanger sequencing (SS) of partial HCV genomes. Results: There was 98.7% (376/381) concordance for viral subtype between SS and NGS. The positive and negative per cent agreements for determination of resistance-associated substitutions were 97.8% (95% CI 92.5–99.4%) and 99.9% (95% CI 99.5–100.0%), respectively. The NGS pipeline was also able to detect novel subtypes, mixtures, recombinants, transiently occurring resistance mutations and distinguish re-infection with the same subtype from relapse. Discussion: Particular scenarios where NGS may be used include settings without universal access to pan-genotypic antiviral regimens, those infected with a ‘rare’ subtype or who have been failed by first-line therapy, and in cases of suspected re-infection.
Tipologia IRIS:
01 - Articolo su periodico
Keywords:
Clinical evaluation; Genotyping; Hepatitis C virus (HCV); Resistance testing; Whole-genome sequencing
Elenco autori:
D. Bradshaw, D.F. Bibby, C.F. Manso, R. Piorkowska, H. Mohamed, J. Ledesma, L. Bubba, Y.T. Chan, S.L. Ngui, S. Carne, J.L. Mbisa
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