Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype

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 phylogeneti...

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Detalles Bibliográficos
Autores: von Massow, Georg, Garcia-Cehic, Damir, Gregori, Josep, Rodriguez-Frias, Francisco, Dolores Macia, Maria, Escarda Gelabert, Ana, Ignacio Esteban, Juan, Quer, Josep
Tipo de recurso: artículo
Fecha de publicación:2019
País:España
Institución:Instituto de Salud Carlos III (ISCIII)
Repositorio:Repisalud
Idioma:inglés
OAI Identifier:oai:repisalud.isciii.es:20.500.12105/22679
Acceso en línea:https://hdl.handle.net/20.500.12105/22679
Access Level:acceso abierto
Palabra clave:Subtype
Direct-acting antivirals
HCV
Genotype 1
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spelling Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtypevon Massow, GeorgGarcia-Cehic, DamirGregori, JosepRodriguez-Frias, FranciscoDolores Macia, MariaEscarda Gelabert, AnaIgnacio Esteban, JuanQuer, JosepSubtypeDirect-acting antiviralsHCVGenotype 1Hepatitis 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.Dove Medical Press20242024-09-1020192019-01-0120192019-01-01research articlehttp://purl.org/coar/resource_type/c_2df8fbb1info:eu-repo/semantics/articlehttps://hdl.handle.net/20.500.12105/22679reponame:Repisaludinstname:Instituto de Salud Carlos III (ISCIII)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial 3.0 Unportedhttps://creativecommons.org/licenses/by-nc/3.0/info:eu-repo/semantics/openAccessoai:repisalud.isciii.es:20.500.12105/226792026-06-12T12:43:37Z
dc.title.none.fl_str_mv Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
title Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
spellingShingle Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
von Massow, Georg
Subtype
Direct-acting antivirals
HCV
Genotype 1
title_short Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
title_full Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
title_fullStr Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
title_full_unstemmed Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
title_sort Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype
dc.creator.none.fl_str_mv von Massow, Georg
Garcia-Cehic, Damir
Gregori, Josep
Rodriguez-Frias, Francisco
Dolores Macia, Maria
Escarda Gelabert, Ana
Ignacio Esteban, Juan
Quer, Josep
author von Massow, Georg
author_facet von Massow, Georg
Garcia-Cehic, Damir
Gregori, Josep
Rodriguez-Frias, Francisco
Dolores Macia, Maria
Escarda Gelabert, Ana
Ignacio Esteban, Juan
Quer, Josep
author_role author
author2 Garcia-Cehic, Damir
Gregori, Josep
Rodriguez-Frias, Francisco
Dolores Macia, Maria
Escarda Gelabert, Ana
Ignacio Esteban, Juan
Quer, Josep
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv
dc.subject.none.fl_str_mv Subtype
Direct-acting antivirals
HCV
Genotype 1
topic Subtype
Direct-acting antivirals
HCV
Genotype 1
description 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.
publishDate 2019
dc.date.none.fl_str_mv 2019
2019-01-01
2019
2019-01-01
2024
2024-09-10
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/20.500.12105/22679
url https://hdl.handle.net/20.500.12105/22679
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 3.0 Unported
https://creativecommons.org/licenses/by-nc/3.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 3.0 Unported
https://creativecommons.org/licenses/by-nc/3.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Dove Medical Press
publisher.none.fl_str_mv Dove Medical Press
dc.source.none.fl_str_mv reponame:Repisalud
instname:Instituto de Salud Carlos III (ISCIII)
instname_str Instituto de Salud Carlos III (ISCIII)
reponame_str Repisalud
collection Repisalud
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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