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Phylogenetic analysis of HIV-1 in Mpumalanga

dc.contributor.advisorEngelbrecht, Susanen_ZA
dc.contributor.authorMsimanga, Wela Patricken_ZA
dc.contributor.otherStellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology.en_ZA
dc.date.accessioned2013-02-26T14:10:45Zen_ZA
dc.date.accessioned2013-03-15T07:46:23Z
dc.date.available2013-02-26T14:10:45Zen_ZA
dc.date.available2013-03-15T07:46:23Z
dc.date.issued2013-03en_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/80344
dc.descriptionThesis (MScMedSc)--Stellenbosch University, 2013.en_ZA
dc.description.abstractThe diversity of HIV-1 sequences derived from patients in Bushbuckridge, Mpumalanga, was investigated. The gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 51 patients were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was assigned using the LANL QC (RIP), REGA and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Most of the sequences, that is 89%, belonged to HIV-1 subtype C. LANL QC (RIP), REGA, jpHMM also detected recombinants in 11% of the sequences. One of the isolates could only have the env gp41 gene fragment amplified and sequenced, which was determined to be HIV-1 subtype B. Phylogenetic analysis using the Neighbor-Joining and Maximum Likelihood methods from MEGA v 5 showed that, except for the env gp41 designated as a subtype B, all sequences in the study clustered with HIV-1 subtype C. Significantly, phylogenetic analysis showed that not only are the Bushbuckridge, Mpumalanga sequences related to HIV-1 subtype C sequences from southern Africa, India, Ethiopia and Brazil, but it is possible there has been multiple introductions of HIV-1 in the province. SDRMs were observed in two samples.en_ZA
dc.format.extent144 p. : ill.
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.subjectHIV-1 diversityen_ZA
dc.subjectPhylogenyen_ZA
dc.subjectHIV infections -- South Africa -- Mpumalangaen_ZA
dc.subjectDissertations -- Medical virologyen_ZA
dc.subjectTheses -- Medical virologyen_ZA
dc.titlePhylogenetic analysis of HIV-1 in Mpumalangaen_ZA
dc.typeThesisen_ZA
dc.rights.holderStellenbosch University


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