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Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba

2015-02-11Artigo científico Acesso aberto
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dc.contributor.authorAlemán, Yoan
dc.contributor.authorVinken, Lore
dc.contributor.authorKourí, Vivian
dc.contributor.authorPérez, Lissette
dc.contributor.authorÁlvarez, Alina
dc.contributor.authorAbrahantes, Yeissel
dc.contributor.authorFonseca, Carlos
dc.contributor.authorPérez, Jorge
dc.contributor.authorCorrea, Consuelo
dc.contributor.authorSoto, Yudira
dc.contributor.authorSchrooten, Yoeri
dc.contributor.authorVandamme, Anne Mieke
dc.contributor.authorVan Laethem, Kristel
dc.contributor.institutionInstituto de Higiene e Medicina Tropical (IHMT)
dc.contributor.institutionTB, HIV and opportunistic diseases and pathogens (THOP)
dc.contributor.institutionGlobal Health and Tropical Medicine (GHTM)
dc.contributor.pblPLOS - Public Library of Science
dc.date.accessioned2018-05-14T22:01:18Z
dc.date.available2018-05-14T22:01:18Z
dc.date.issued2015-02-11
dc.descriptionPMID: 25671421 WOS:000349545300039
dc.description.abstractAs commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7%to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the inhouse procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent230436
dc.identifier.doi10.1371/journal.pone.0117176
dc.identifier.issn1932-6203
dc.identifier.otherPURE: 1224568
dc.identifier.otherPURE UUID: 909c9bc2-ebef-4c5b-98d4-57d7c029da91
dc.identifier.otherScopus: 84923036608
dc.identifier.otherWOS: 000349545300039
dc.identifier.otherPubMed: 25671421
dc.identifier.urihttp://www.scopus.com/inward/record.url?scp=84923036608&partnerID=8YFLogxK
dc.identifier.urlhttps://www.scopus.com/pages/publications/84923036608
dc.language.isoeng
dc.peerreviewedyes
dc.subjectGeneral Agricultural and Biological Sciences
dc.subjectGeneral Biochemistry,Genetics and Molecular Biology
dc.subjectGeneral Medicine
dc.subjectSDG 3 - Good Health and Well-being
dc.titlePerformance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cubaen
dc.typejournal article
degois.publication.issue2
degois.publication.titlePLoS ONE
degois.publication.volume10
dspace.entity.typePublication
rcaap.rightsopenAccess

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