RT Journal Article
T1 High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods.
A1 Quer, Josep
A1 Gregori, Josep
A1 Rodríguez-Frias, Francisco
A1 Buti, Maria
A1 Madejon, Antonio
A1 Perez-del-Pulgar, Sofia
A1 Garcia-Cehic, Damir
A1 Casillas, Rosario
A1 Blasi, Maria
A1 Homs, Maria
A1 Tabernero, David
A1 Alvarez-Tejado, Miguel
A1 Muñoz, Jose Manuel
A1 Cubero, Maria
A1 Caballero, Andrea
A1 del Campo, Jose Antonio
A1 Domingo, Esteban
A1 Belmonte, Irene
A1 Nieto, Leonardo
A1 Lens, Sabela
A1 Muñoz-de-Rueda, Paloma
A1 Sanz-Cameno, Paloma
A1 Sauleda, Silvia
A1 Bes, Marta
A1 Gomez, Jordi
A1 Briones, Carlos
A1 Perales, Celia
A1 Sheldon, Julie
A1 Castells, Lluis
A1 Viladomiu, Lluis
A1 Salmeron, Javier
A1 Ruiz-Extremera, Angela
A1 Quiles-Pérez, Rosa
A1 Moreno-Otero, Ricardo
A1 López-Rodríguez, Rosario
A1 Allende, Helena
A1 Romero-Gómez, Manuel
A1 Guardia, Jaume
A1 Esteban, Rafael
A1 Garcia-Samaniego, Javier
A1 Forns, Xavier
A1 Esteban, Juan Ignacio
K1 Técnicas de genotipaje
K1 Hepacivirus
K1 Humanos
K1 Filogenia
K1 Juego de reactivos para diagnóstico
K1 Proteínas no estructurales virales
AB Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.
PB American Society for Microbiology
SN 0095-1137
YR 2015
FD 2015-01
LK http://hdl.handle.net/10668/2505
UL http://hdl.handle.net/10668/2505
LA en
NO Quer J, Gregori J, Rodríguez-Frias F, Buti M, Madejon A, Perez-del-Pulgar S, et al. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. J Clin Microbiol. 2015; 53(1):219-26
NO Journal Article; Research Support, Non-U.S. Gov't;                                        Corrección: Volume 53, no. 1, p. 219–226, 2015. Page 221, Table 1: The sequence for primer 13N5Bo8254 should read “GTTGTAAAACGACGGCCAGTCNTAYGAYACCMGNTGYTTTGACTC.”
DS RISalud
RD Apr 5, 2025