Drug resistance genotyping and phylogenetic analysis of HIV in chronically infected antiretroviral naive patients

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dc.contributor.advisor Bessong, Pascal Obong
dc.contributor.advisor Traore, Afsatou Ndama
dc.contributor.author Baloyi, Tlangelani
dc.date 2018
dc.date.accessioned 2019-06-05T09:58:16Z
dc.date.available 2019-06-05T09:58:16Z
dc.date.issued 2019-05-18
dc.identifier.citation Baloyi, Tlangelani (2018) Drug resistance genotyping and phylogenetic analysis of HIV in chronically infected antiretroviral naive patients, University of Venda, South Africa.<http://hdl.handle.net/11602/1342>.
dc.identifier.uri http://hdl.handle.net/11602/1342
dc.description MSc (Microbiology) en_US
dc.description Department of Microbiology
dc.description.abstract Background: Antiretroviral treatment (ART) has grown to be one of the most effective tool in the fight to control HIV/AIDS morbidity and mortality worldwide. However, due to the emergence of drug resistant HIV, ART efficacy can be jeopardized. Drug resistant HIV strain has a potential of becoming a major public threat, as its limit treatment options on people living with HIV. With several findings worldwide reporting drug resistant HIV to be currently being transmitted to ART-naïve persons, measures have been taken to genotype drug resistant HIV prior to treatment initiation. However, in resource limited countries such measures are not executed especially in public sectors due to the costs associated with the required assays for genotyping. Objective: The objectives of the study was to establish a deep sequencing protocol (Next Generation Sequencing-NGS) using an Illumina MiniSeq Platform and subsequently apply it to genotype HIV in chronically infected drug naïve persons for resistance mutations and viral genotypes Methods: HIV positive Individuals without any exposure to ART (Treatment-naive) were recruited. Partial pol fragment (complete protease and ~1104bp reverse transcriptase) were amplified and purified. Libraries were prepared using Nextera XT library preparation kit, fragmented, tagmented, pooled and denatured then sequenced with Illumina MiniSeq instrument. Consensus sequences were derived, aligned and phylogenetically analysed. The Stanford HIV Drug Resistance Algorithm was used to infer the presence of drug resistant mutants, at the viral minority and majority population levels. Results and discussion: An NGS protocol to generate nucleotide sequences for drug resistance inference was established. No major drug resistance mutations were detected against protease, reverse transcriptase inhibitors in the study subjects investigated. Nevertheless, V179D change was observed in one patient (8.3%). V179D has been shown to impact a low-level resistance to NNRTI. On the other hand, several secondary and unusual mutations at known drug sites were detected even at minority threshold level of <20%. Conclusion: No major drug resistance mutations was detected in the drug naïve study population. This finding suggests that there is no risk of treatment failure to the investigated subjects, however it is important to assess the potential phenotypic v | P a g e significance of the identified secondary resistance mutations in the context of HIV-1 subtype C. The established NGS protocol should be applied in subsequent HIV drug resistance studies. en_US
dc.description.sponsorship NRF en_US
dc.format.extent 1 online resource (xii, )
dc.language.iso en en_US
dc.rights University if Venda
dc.subject HIV-1 Subtype C. en_US
dc.subject Next generation sequencing en_US
dc.subject Drug resistance mutations en_US
dc.subject Treatment naive patients en_US
dc.subject South Africa en_US
dc.subject.ddc 616.9792010968
dc.subject.lcsh AIDS (Disease) -- South Africa
dc.subject.lcsh AIDS (Disease) -- Prevention
dc.subject.lcsh HIV-positive persons -- South Africa
dc.subject.lcsh AIDS (Disease) -- Patients -- South Africa
dc.subject.lcsh Patients -- South Africa
dc.subject.lcsh HIV infections -- South Africa
dc.title Drug resistance genotyping and phylogenetic analysis of HIV in chronically infected antiretroviral naive patients en_US
dc.type Dissertation en_US

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