TY - JOUR
T1 - Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
AU - von Massow, Georg
AU - Garcia-Cehic, Damir
AU - Gregori, Josep
AU - Rodriguez-Frias, Francisco
AU - Macià, María Dolores
AU - Escarda, Ana
AU - Esteban, Juan Ignacio
AU - Quer, Josep
PY - 2019/1/1
Y1 - 2019/1/1
N2 - © 2019 von Massow et al. Hepatitis C virus (HCV) is a highly variable infectious agent, classified into 8 genotypes and 86 subtypes. Our laboratory has implemented an in-house developed high-resolution HCV subtyping method based on next-generation sequencing (NGS) for error-free classification of the virus using phylogenetic analysis and analysis of genetic distances in sequences from patient samples compared to reference sequences. During routine diagnostic, a sample from an Equatorial Guinea patient could not be classified into any of the existing subtypes. The whole genome was analyzed to confirm that the new isolate could be classified as a new HCV subtype. In addition, naturally occurring resistance-associated substitutions (RAS) were analyzed by NGS. Whole-genome analysis based on p-distances suggests that the sample belongs to a new HCV genotype 1 subtype. Several RAS in the NS3 (S122T, D168E and I170V) and NS5A protein (Q(1b)24K, R(1b)30Q and Y93L+Y93F) were found, which could limit the use of some inhibitors for treating this subtype. RAS studies of new subtypes are of great interest for tailoring treatment, as no data on treatment efficacy are reported. In our case, the patient has not yet been treated, and the RAS report will be used to design the most effective treatment.
AB - © 2019 von Massow et al. Hepatitis C virus (HCV) is a highly variable infectious agent, classified into 8 genotypes and 86 subtypes. Our laboratory has implemented an in-house developed high-resolution HCV subtyping method based on next-generation sequencing (NGS) for error-free classification of the virus using phylogenetic analysis and analysis of genetic distances in sequences from patient samples compared to reference sequences. During routine diagnostic, a sample from an Equatorial Guinea patient could not be classified into any of the existing subtypes. The whole genome was analyzed to confirm that the new isolate could be classified as a new HCV subtype. In addition, naturally occurring resistance-associated substitutions (RAS) were analyzed by NGS. Whole-genome analysis based on p-distances suggests that the sample belongs to a new HCV genotype 1 subtype. Several RAS in the NS3 (S122T, D168E and I170V) and NS5A protein (Q(1b)24K, R(1b)30Q and Y93L+Y93F) were found, which could limit the use of some inhibitors for treating this subtype. RAS studies of new subtypes are of great interest for tailoring treatment, as no data on treatment efficacy are reported. In our case, the patient has not yet been treated, and the RAS report will be used to design the most effective treatment.
KW - Direct-acting antivirals
KW - Genotype 1
KW - HCV
KW - Subtype
U2 - https://doi.org/10.2147/IDR.S195441
DO - https://doi.org/10.2147/IDR.S195441
M3 - Article
C2 - 31118701
SN - 1178-6973
VL - 12
SP - 947
EP - 955
JO - Infection and Drug Resistance
JF - Infection and Drug Resistance
ER -
