Investigation of drug resistance against protease, reverse transcriptase, and integrase inhibitors by next-generation sequencing in HIV-positive patients

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dc.contributor.authorTekin, Duygu
dc.contributor.authorGokengin, Deniz
dc.contributor.authorOnay, Huseyin
dc.contributor.authorErensoy, Selda
dc.contributor.authorSertoz, Ruchan
dc.date.accessioned2020-12-01T11:57:48Z
dc.date.available2020-12-01T11:57:48Z
dc.date.issued2020
dc.departmentEge Üniversitesien_US
dc.description.abstractOur aim was to investigate the mutations in protease (PR), reverse transcriptase (RT), and integrase (IN) gene regions in human immunodeficiency virus (HIV) using a single amplicon via next-generation sequencing (NGS). the study included plasma samples from 49 HIV-1-positive patients, which were referred for HIV-1 drug resistance testing during 2017. A nested polymerase chain reaction (PCR) was performed after the RNA extraction and one-step reverse transcription stages. the sequencing of the HIV genome in the PR, RT, and IN gene regions was carried out using MiSeq NGS technology. Sanger sequencing (SS) was used to analyze resistance mutations in the PR and RT gene regions using a ViroSeq HIV-1 Genotyping System. PCR products were analyzed with an ABI3500 GeneticAnalyzer (Applied Biosystems). Resistance mutations detected with NGS at frequencies above 20% were identical to the SS results. Resistance to at least one antiretroviral (ARV) drug was 22.4% (11 of 49) with NGS and 10.2% (5 of 49) with SS. At least one low-frequency resistance mutation was detected in 18.3% (9 of 49) of the samples. Low-frequency resistance mutations resulted in virological failure in only one patient. the cost of the analyses was reduced by sample pooling and multiplex analysis using the MiSeq system. This is the first study in Turkey to use NGS technologies for the detection of resistance mutations in all three gene (PR, RT, IN) regions using a single amplicon. Our findings suggest that NGS is more sensitive and cost-effective than the SS method.en_US
dc.identifier.doi10.1002/jmv.26582en_US
dc.identifier.issn0146-6615
dc.identifier.issn1096-9071
dc.identifier.pmid33026651en_US
dc.identifier.scopus2-s2.0-85094184849en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1002/jmv.26582
dc.identifier.urihttps://hdl.handle.net/11454/61815
dc.identifier.wosWOS:000585023500001en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherWileyen_US
dc.relation.ispartofJournal of Medical Virologyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectanti&#8208en_US
dc.subjectretrovirus drugen_US
dc.subjectantiviral agentsen_US
dc.subjecthuman immunodeficiency virusen_US
dc.subjectintegrase inhibitorsen_US
dc.subjectnon&#8208en_US
dc.subjectnucleoside reverse transcriptase inhibitoren_US
dc.subjectnucleoside analog reverse transcriptaseen_US
dc.subjectprotease inhibitoren_US
dc.subjectvirus classificationen_US
dc.titleInvestigation of drug resistance against protease, reverse transcriptase, and integrase inhibitors by next-generation sequencing in HIV-positive patientsen_US
dc.typeArticleen_US

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