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Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience.

dc.contributor.authorDel-Campo, Jose A
dc.contributor.authorParra-Sanchez, Manuel
dc.contributor.authorFigueruela, Blanca
dc.contributor.authorGarcia-Rey, Silvia
dc.contributor.authorQuer, Josep
dc.contributor.authorGregori, Josep
dc.contributor.authorBernal, Samuel
dc.contributor.authorGrande, Lourdes
dc.contributor.authorPalomares, Jose C
dc.contributor.authorRomero-Gomez, Manuel
dc.contributor.funderAndalusian Government
dc.contributor.funderInstituto de Salud Carlos III
dc.contributor.funderEuropean Regional Development Fund (ERDF)
dc.date.accessioned2023-01-25T10:02:06Z
dc.date.available2023-01-25T10:02:06Z
dc.date.issued2017-12-15
dc.description.abstractThe effectiveness of the new generation of hepatitis C treatments named direct-acting antiviral agents (DAAs) depends on the genotype, subtype, and resistance-associated substitutions present in individual patients. The aim of this study was to evaluate a massive sequencing platform for the analysis of genotypes and subtypes of hepatitis C virus (HCV) in order to optimize therapy. A total of 84 patients with hepatitis C were analyzed. The routine genotyping methodology for HCV used at the study institution (Versant HCV Assay, LiPA) was compared with a deep sequencing platform (454/GS-Junior and Illumina MiSeq). The mean viral load in these HCV patients was 6.89×106±7.02×105. Viral genotypes analyzed by LiPA were distributed as follows: 26% genotype 1a (22/84), 55% genotype 1b (46/84), 1% genotype 1 (1/84), 2.5% genotype 3 (2/84), 6% genotype 3a (5/84), 6% genotype 4a/c/d (5/84). When analyzed by deep sequencing, the samples were distributed as follows: 27% genotype 1a (23/84), 56% genotype 1b (47/84), 8% genotype 3a (7/84), 5% genotype 4d (4/84), 2.5% genotype 4f (2/84). Six of the 84 patients (7%) were infected with more than one subtype. Among these, 33% (2/6) failed DAA-based triple therapy. The detection of mixed infection could explain some treatment failures. Accurate determination of viral genotypes and subtypes would allow optimal patient management and improve the effectiveness of DAA therapy.
dc.identifier.citationDel Campo JA, Parra-Sánchez M, Figueruela B, García-Rey S, Quer J, Gregori J, et al, Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience. Int J Infect Dis. 2018 Feb;67:114-117.
dc.identifier.doi10.1016/j.ijid.2017.12.016
dc.identifier.essn1878-3511
dc.identifier.pmcPMC5812776
dc.identifier.pmid29253705
dc.identifier.unpaywallURLhttp://www.ijidonline.com/article/S1201971217303284/pdf
dc.identifier.urihttp://hdl.handle.net/10668/11923
dc.journal.titleInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
dc.journal.titleabbreviationInt J Infect Dis
dc.language.isoen
dc.organizationInstituto de Biomedicina de Sevilla-IBIS
dc.organizationHospital Universitario Virgen del Rocío
dc.page.number114-117
dc.provenanceRealizada la curación de contenido 27/05/2025.
dc.publisherElsevier Ltd
dc.pubmedtypeJournal Article
dc.relation.projectIDPI0892-2012
dc.relation.projectIDPI14/01349
dc.relation.projectIDPI16/00337
dc.relation.publisherversionhttps://linkinghub.elsevier.com/retrieve/pii/S1201-9712(17)30328-4
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.accessRightsopen access
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectDeep sequencing
dc.subjectDirect-acting antivirals
dc.subjectHCV
dc.subjectMixed infection
dc.subjectNGS
dc.subject.decsGenotipo
dc.subject.decsHepatitis C
dc.subject.decsEfectividad
dc.subject.decsHepacivirus
dc.subject.decsCoinfección
dc.subject.decsCarga Viral
dc.subject.decsAntivirales
dc.subject.meshAdult
dc.subject.meshCoinfection
dc.subject.meshFemale
dc.subject.meshGenotype
dc.subject.meshHepacivirus
dc.subject.meshHepatitis C
dc.subject.meshHigh-Throughput Nucleotide Sequencing
dc.subject.meshHumans
dc.subject.meshMale
dc.subject.meshMiddle Aged
dc.subject.meshSequence Analysis, DNA
dc.subject.meshViral Load
dc.subject.meshViral Nonstructural Proteins
dc.titleHepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience.
dc.typeresearch article
dc.type.hasVersionVoR
dc.volume.number67
dspace.entity.typePublication

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