Thesis (MScMedSc)--Stellenbosch University, 2013. / Bibliography / The efficiency in which HIV-1 can infect, spread and evade the attack of therapeutic
agents can be attributed to a high mutation rate and frequent recombination events.
These factors have collectively contributed to the diversity observed in HIV-1 and
resulted in a multitude of subtypes, sub-subtypes, circulating recombinant forms
(CRF’s) and unique recombinant forms (URF’s). The aim of this study was to
investigate HIV-1 diversity in Cape Town using a small cohort of treatment naive
patients being investigated for HIV Associated Neurocognitive Disorders (HAND).
Four different genomic domains: gag, pol, accessory and gp41 genes were
sequenced to subtype the virus. HIV-1 tat was further investigated because the
dicysteine motif has been reported to play a role in HAND. Viral RNA and proviral
DNA was extracted from 64 patients and used for the amplification and sequencing
of the genes. Rega and jpHMM online tools were used to identify HIV-1 subtypes
and recombinants while Neighbor-joining phylogenetic trees were constructed for
phylogenetic analysis. The pol gene was further investigated using SCUEAL to
detect possible intra-subtype recombination and was also screened for the presence
of transmitted drug resistance. In addition tat sequence datasets retrieved from the
Los Alamos sequence database were investigated and compared with the newly
generated sequences for the detection of point mutations and amino acid signature
patterns. Sequencing identified most of the samples as subtype C; however six inter-subtype
recombinants (AE, A1G, A1CU and two BC) and 9 intra-subtype C recombinants
were identified. In addition 13% of pol sequences were identified with resistance
mutations. Signature pattern analysis identified a high level of variability in the tat
sequences: 68% were identified with C30S31; 29% with the C30C31 mutation and a
single sequence with a novel mutation C30A31. Functional analysis of these
mutations indicated that all mutations investigated were capable of inducing
apoptosis in cell culture. The C30C31 mutation generated the highest level of
apoptosis, closely followed by the C30A31 mutation. However no statistical
significance could be detected between tat mutations and the observed levels of
apoptosis.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/80187 |
| Date | 03 1900 |
| Creators | Isaacs, Shahieda |
| Contributors | Engelbrecht, Susan, Glashoff, Richard, Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | English |
| Type | Thesis |
| Format | 121 p. : ill. |
| Rights | Stellenbosch University |
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