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2015-10-15Zeitschriftenartikel DOI: 10.1371/journal.pone.0140809
Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission
dc.contributor.authorHauser, Andrea
dc.contributor.authorKücherer, Claudia
dc.contributor.authorKunz, Andrea
dc.contributor.authorDabrowski, Piotr Wojtek
dc.contributor.authorRadonić, Aleksandar
dc.contributor.authorNitsche, Andreas
dc.contributor.authorTheuring, Stefanie
dc.contributor.authorBannert, Norbert
dc.contributor.authorSewangi, Julius
dc.contributor.authorMbezi, Paulina
dc.contributor.authorDugange, Festo
dc.contributor.authorHarms, Gundel
dc.contributor.authorMeixenberger, Karolin
dc.date.accessioned2018-05-07T18:40:45Z
dc.date.available2018-05-07T18:40:45Z
dc.date.created2015-12-09
dc.date.issued2015-10-15none
dc.identifier.otherhttp://edoc.rki.de/oa/articles/reYYJ2uxiK7dQ/PDF/22dwXmiRgYKH2.pdf
dc.identifier.urihttp://edoc.rki.de/176904/2202
dc.description.abstractBackground: Pregnant HIV-infected women were screened for the development of HIV-1 drug resistance after implementation of a triple-antiretroviral transmission prophylaxis as recommended by the WHO in 2006. The study offered the opportunity to compare amplicon-based 454 ultra-deep sequencing (UDS) and allele-specific real-time PCR (ASPCR) for the detection of drug-resistant minor variants in the HIV-1 reverse transcriptase (RT). Methods: Plasma samples from 34 Tanzanian women were previously analysed by ASPCR for key resistance mutations in the viral RT selected by AZT, 3TC, and NVP (K70R, K103N, Y181C, M184V, T215Y/F). In this study, the RT region of the same samples was investigated by amplicon-based UDS for resistance mutations using the 454 GS FLX System. Results: Drug-resistant HIV-variants were identified in 69% (20/29) of women by UDS and in 45% (13/29) by ASPCR. The absolute number of resistance mutations identified by UDS was twice that identified by ASPCR (45 vs 24). By UDS 14 of 24 ASPCR-detected resistance mutations were identified at the same position. The overall concordance between UDS and ASPCR was 61.0% (25/41). The proportions of variants quantified by UDS were approximately 2–3 times lower than by ASPCR. Amplicon generation from samples with viral loads below 20,000 copies/ml failed more frequently by UDS compared to ASPCR (limit of detection = 650 copies/ml), resulting in missing or insufficient sequence coverage. Conclusions: Both methods can provide useful information about drug-resistant minor HIV-1 variants. ASPCR has a higher sensitivity than UDS, but is restricted to single resistance mutations. In contrast, UDS is limited by its requirement for high viral loads to achieve sufficient sequence coverage, but the sequence information reveals the complete resistance patterns within the genomic region analysed. Improvements to the UDS limit of detection are in progress, and UDS could then facilitate monitoring of drug-resistant minor variants in the HIV-1 quasispecies.eng
dc.language.isoeng
dc.publisherRobert Koch-Institut, Infektionskrankheiten / Erreger
dc.subjectHumanseng
dc.subjectFemaleeng
dc.subjectAnti-HIV Agents/therapeutic useeng
dc.subjectHIV Infections/virologyeng
dc.subjectHIV-1/geneticseng
dc.subjectMutationeng
dc.subjectHIV Infections/drug therapyeng
dc.subjectAlleleseng
dc.subjectTreatment Failureeng
dc.subjectHIV Infections/diagnosiseng
dc.subjectDrug Resistance Viral/geneticseng
dc.subjectPregnancyeng
dc.subjectPregnancy Complications Infectious/drug therapyeng
dc.subjectPregnancy Complications Infectious/virologyeng
dc.subjectHigh-Throughput Nucleotide Sequencing/methodseng
dc.subjectReal-Time Polymerase Chain Reaction/methodseng
dc.subjectInfectious Disease Transmissioneng
dc.subjectVertical/prevention & controleng
dc.subjectPost-Exposure Prophylaxis/methodseng
dc.subjectPregnancy Complications Infectious/classificationeng
dc.subjectPregnancy Complications Infectious/diagnosiseng
dc.subjectPrognosiseng
dc.subjectTanzaniaeng
dc.subject.ddc610 Medizin
dc.titleComparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission
dc.typeperiodicalPart
dc.identifier.urnurn:nbn:de:0257-10042087
dc.identifier.doi10.1371/journal.pone.0140809
dc.identifier.doihttp://dx.doi.org/10.25646/2127
local.edoc.container-titlePLoS ONE
local.edoc.container-textHauser A, Kuecherer C, Kunz A, Dabrowski PW, Radonić A, Nitsche A, et al. (2015) Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission. PLoS ONE 10(10): e0140809.
local.edoc.fp-subtypeArtikel
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140809
local.edoc.container-publisher-namePublic Library of Science
local.edoc.container-volume10
local.edoc.container-issue10
local.edoc.container-year2015

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