Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Detalhes bibliográficos
Autor(a) principal: Christensen, Kasper T.
Data de Publicação: 2022
Outros Autores: Pierard, Florian, Beuselinck, Kurt, Bonsall, David, Bowden, Rory, Lagrou, Katrien, Nevens, Frederik, Schrooten, Yoeri, Simmonds, Peter, Vandamme, Anne Mieke, Van Wijngaerden, Eric, Dierckx, Tim, Cuypers, Lize, Van Laethem, Kristel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/147814
Resumo: Funding Information: This work and KTC were supported by grants from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO) ( G069214 , G0B2317N , 1S38819N ). LC acknowledges FWO travel grant for a research visit at University of Oxford ( V431117N ). The authors thank the staff in Oxford in their support of the laboratory work and the donation of the probes used for enrichment of HCV. Publisher Copyright: © 2022 Elsevier B.V.
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spelling Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohortAntiviral resistanceFull genomeHepatitis C virusLiPANext-generation sequencingTreatment failureQR355 VirologyR MedicineVirologyInfectious DiseasesApplied Microbiology and BiotechnologySDG 3 - Good Health and Well-beingSDG 9 - Industry, Innovation, and InfrastructureFunding Information: This work and KTC were supported by grants from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO) ( G069214 , G0B2317N , 1S38819N ). LC acknowledges FWO travel grant for a research visit at University of Oxford ( V431117N ). The authors thank the staff in Oxford in their support of the laboratory work and the donation of the probes used for enrichment of HCV. Publisher Copyright: © 2022 Elsevier B.V.Background: Although most currently used regimens for Hepatitis C virus (HCV) infections can be initiated without prior knowledge of genotype and subtype, genotyping is still useful to identify patients who might benefit from a personalized treatment due to resistance to direct-acting antivirals (DAA). Objectives: To assess the utility of full-genome next-generation sequencing (FG-NGS) for HCV genotyping. Study design: 138 HCV plasma samples previously genotyped by VERSANT HCV Genotype Assay (LiPA) were subjected to FG-NGS and phylogenetically genotyped Genome Detective. Consensuses were analysed by HCV-GLUE for resistance-associated substitutions (RASs) and their impact on treatment response was investigated. Results: 102/138 (73.9%) samples were sequenced to a genome coverage and depth of >90% of the HCV open reading frame covered by >100 reads/site. Concordant genotype and subtype results were assigned in 97.1% and 79.4% of samples, respectively. FG-NGS resolved the subtype of 13.7% samples that had ambiguous calls by LiPA and identified one dual infection and one recombinant strain. At least one RAS was found for the HCV genes NS3, NS5A, and NS5B in 2.91%, 36.98% and 27.3% samples, respectively. Irrespective of the observed RAS, all patients responded well to DAA treatment, except for HCV1b-infected patients treated with Zepatier (33.3% failure rate (5/15)). Conclusion: While LiPA and FG-NGS showed overall good concordance, FG-NGS improved specificity for subtypes, recombinant and mixed infections. FG-NGS enabled the detection of RAS, but its predictive value for treatment outcome in DAA-naïve patients remains uncertain. With additional refinements, FG-NGS may be the way forward for HCV genotyping.Instituto de Higiene e Medicina Tropical (IHMT)Global Health and Tropical Medicine (GHTM)TB, HIV and opportunistic diseases and pathogens (THOP)Universidade NOVA de LisboaRUNChristensen, Kasper T.Pierard, FlorianBeuselinck, KurtBonsall, DavidBowden, RoryLagrou, KatrienNevens, FrederikSchrooten, YoeriSimmonds, PeterVandamme, Anne MiekeVan Wijngaerden, EricDierckx, TimCuypers, LizeVan Laethem, Kristel2023-01-18T22:17:29Z2022-102022-10-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/147814eng1386-6532PURE: 50787197https://doi.org/10.1016/j.jcv.2022.105252info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:29:04Zoai:run.unl.pt:10362/147814Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:53:05.610783Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
title Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
spellingShingle Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
Christensen, Kasper T.
Antiviral resistance
Full genome
Hepatitis C virus
LiPA
Next-generation sequencing
Treatment failure
QR355 Virology
R Medicine
Virology
Infectious Diseases
Applied Microbiology and Biotechnology
SDG 3 - Good Health and Well-being
SDG 9 - Industry, Innovation, and Infrastructure
title_short Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
title_full Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
title_fullStr Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
title_full_unstemmed Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
title_sort Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort
author Christensen, Kasper T.
author_facet Christensen, Kasper T.
Pierard, Florian
Beuselinck, Kurt
Bonsall, David
Bowden, Rory
Lagrou, Katrien
Nevens, Frederik
Schrooten, Yoeri
Simmonds, Peter
Vandamme, Anne Mieke
Van Wijngaerden, Eric
Dierckx, Tim
Cuypers, Lize
Van Laethem, Kristel
author_role author
author2 Pierard, Florian
Beuselinck, Kurt
Bonsall, David
Bowden, Rory
Lagrou, Katrien
Nevens, Frederik
Schrooten, Yoeri
Simmonds, Peter
Vandamme, Anne Mieke
Van Wijngaerden, Eric
Dierckx, Tim
Cuypers, Lize
Van Laethem, Kristel
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Instituto de Higiene e Medicina Tropical (IHMT)
Global Health and Tropical Medicine (GHTM)
TB, HIV and opportunistic diseases and pathogens (THOP)
Universidade NOVA de Lisboa
RUN
dc.contributor.author.fl_str_mv Christensen, Kasper T.
Pierard, Florian
Beuselinck, Kurt
Bonsall, David
Bowden, Rory
Lagrou, Katrien
Nevens, Frederik
Schrooten, Yoeri
Simmonds, Peter
Vandamme, Anne Mieke
Van Wijngaerden, Eric
Dierckx, Tim
Cuypers, Lize
Van Laethem, Kristel
dc.subject.por.fl_str_mv Antiviral resistance
Full genome
Hepatitis C virus
LiPA
Next-generation sequencing
Treatment failure
QR355 Virology
R Medicine
Virology
Infectious Diseases
Applied Microbiology and Biotechnology
SDG 3 - Good Health and Well-being
SDG 9 - Industry, Innovation, and Infrastructure
topic Antiviral resistance
Full genome
Hepatitis C virus
LiPA
Next-generation sequencing
Treatment failure
QR355 Virology
R Medicine
Virology
Infectious Diseases
Applied Microbiology and Biotechnology
SDG 3 - Good Health and Well-being
SDG 9 - Industry, Innovation, and Infrastructure
description Funding Information: This work and KTC were supported by grants from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO) ( G069214 , G0B2317N , 1S38819N ). LC acknowledges FWO travel grant for a research visit at University of Oxford ( V431117N ). The authors thank the staff in Oxford in their support of the laboratory work and the donation of the probes used for enrichment of HCV. Publisher Copyright: © 2022 Elsevier B.V.
publishDate 2022
dc.date.none.fl_str_mv 2022-10
2022-10-01T00:00:00Z
2023-01-18T22:17:29Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/147814
url http://hdl.handle.net/10362/147814
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1386-6532
PURE: 50787197
https://doi.org/10.1016/j.jcv.2022.105252
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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