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Phylogenetic analysis of HIV-1 in Mpumalanga
Thesis (MScMedSc)--Stellenbosch University, 2013.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2013
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| _version_ | 1867613919165546496 |
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| access_status_str | Open Access |
| author | Msimanga, Wela Patrick |
| author2 | Engelbrecht, Susan |
| author_browse | Engelbrecht, Susan Msimanga, Wela Patrick |
| author_facet | Engelbrecht, Susan Msimanga, Wela Patrick |
| author_sort | Msimanga, Wela Patrick |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScMedSc)--Stellenbosch University, 2013. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/80344 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:47.401Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2013 |
| publishDateRange | 2013 |
| publishDateSort | 2013 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/80344 Phylogenetic analysis of HIV-1 in Mpumalanga Msimanga, Wela Patrick Engelbrecht, Susan Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology. HIV-1 diversity Phylogeny HIV infections -- South Africa -- Mpumalanga Dissertations -- Medical virology Theses -- Medical virology Thesis (MScMedSc)--Stellenbosch University, 2013. The 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. 2013-02-26T14:10:45Z 2013-03-15T07:46:23Z 2013-02-26T14:10:45Z 2013-03-15T07:46:23Z 2013-03 Thesis http://hdl.handle.net/10019.1/80344 en_ZA Stellenbosch University 144 p. : ill. application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | HIV-1 diversity Phylogeny HIV infections -- South Africa -- Mpumalanga Dissertations -- Medical virology Theses -- Medical virology Msimanga, Wela Patrick Phylogenetic analysis of HIV-1 in Mpumalanga |
| title | Phylogenetic analysis of HIV-1 in Mpumalanga |
| title_full | Phylogenetic analysis of HIV-1 in Mpumalanga |
| title_fullStr | Phylogenetic analysis of HIV-1 in Mpumalanga |
| title_full_unstemmed | Phylogenetic analysis of HIV-1 in Mpumalanga |
| title_short | Phylogenetic analysis of HIV-1 in Mpumalanga |
| title_sort | phylogenetic analysis of hiv 1 in mpumalanga |
| topic | HIV-1 diversity Phylogeny HIV infections -- South Africa -- Mpumalanga Dissertations -- Medical virology Theses -- Medical virology |
| url | http://hdl.handle.net/10019.1/80344 |
| work_keys_str_mv | AT msimangawelapatrick phylogeneticanalysisofhiv1inmpumalanga |