Browsing by Author "Isaacs, Shahieda"

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    The apoptotic potential of different HIV-1 subtype C Tat mutations in cell culture
    (Stellenbosch : Stellenbosch University, 2013-03) Isaacs, Shahieda; Engelbrecht, Susan; Glashoff, Richard; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology.
    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.
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    HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa
    (Public Library of Science, 2014-03) Jacobs, Graeme Brendon; Wilkinson, Eduan; Isaacs, Shahieda; Spies, Georgina; De Oliveira, Tulio; Seedat, Soraya; Engelbrecht, Susan
    South Africa has the largest worldwide HIV/AIDS population with 5.6 million people infected and at least 2 million people on antiretroviral therapy. The majority of these infections are caused by HIV-1 subtype C. Using genotyping methods we characterized HIV-1 subtypes of the gag p24 and pol PR and RT fragments, from a cohort of female participants in the Western Cape Province, South Africa. These participants were recruited as part of a study to assess the combined brain and behavioural effects of HIV and early childhood trauma. The partial HIV-1 gag and pol fragments of 84 participants were amplified by PCR and sequenced. Different online tools and manual phylogenetic analysis were used for HIV-1 subtyping. Online tools included: REGA HIV Subtyping tool version 3; Recombinant Identification Program (RIP); Context-based Modeling for Expeditious Typing (COMET); jumping profile Hidden Markov Models (jpHMM) webserver; and subtype classification using evolutionary algorithms (SCUEAL). HIV-1 subtype C predominates within the cohort with a prevalence of 93.8%. We also show, for the first time, the presence of circulating BC strains in at least 4.6% of our study cohort. In addition, we detected transmitted resistance associated mutations in 4.6% of analysed sequences. With tourism and migration rates to South Africa currently very high, we are detecting more and more HIV-1 URFs within our study populations. It is stil unclear what role these unique strains will play in terms of long term antiretroviral treatment and what challenges they will pose to vaccine development. Nevertheless, it remains vitally important to monitor the HIV-1 diversity in South Africa and worldwide as the face of the epidemic is continually changing.
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    HIV‐1 DNA decay is faster in children who initiate ART shortly after birth than later
    (International AIDS Society, 2019-08) Veldsman, Kirsten A.; Janse van Rensburg, Anita; Isaacs, Shahieda; Naidoo, Shalena; Laughton, Barbara; Lombard, Carl; Cotton, Mark F.; Mellors, John W.; van Zyl, Gert U.
    Introduction: There is limited data in children on whether persistence of HIV‐1 infected cells is affected by age at initiating antiretroviral therapy (ART), its duration or any subsequent ART interruption. We therefore investigated the effects of both age of ART initiation and duration of ART interruption on HIV‐1 DNA decay in children. Methods: We investigated HIV‐1 DNA decay in three groups of children on ART: Group‐1 (n = 7) started uninterrupted ART within eight days of life; Group‐2 (n = 8) started uninterrupted ART at a median of five months of age; and Group‐3 (n = 23) started ART at a median age of 1.8 months for either 40 or 96 weeks, then interrupted ART (median of seven months), and restarted ART based on CD4 count and clinical criteria. Total HIV‐1 DNA was assayed using a sensitive HIV‐1 subtype C‐adapted quantitative PCR for integrase. The duration of ART was square root transformed to fit the observed slowing of HIV‐1 DNA decay rate. For each group, point estimates for decay rates were determined after six months of continuous suppressive ART in groups 1 and 2 or six months after restarting ART in Group‐3. Groups‐2 and 3 were combined using a mixed effect regression model to investigate covariates of HIV‐1 DNA decay rate. Results and Discussion: At six months of continuous suppressive ART, the HIV‐1 DNA t½ (95% CI) was shorter in Group‐1 (n = 7): 2.7 months (2.1 to 3.8), than 9.2 months (7.4 to 12.1) in Group‐2 (n = 8); and 9.6 months (7.6 to 12.6) in Group‐3 (n = 23) (p < 0.01). In multivariable analyses, HIV‐1 DNA before treatment (p < 0.001) and the change in HIV‐1 DNA during interruption (p < 0.01) were independent predictors of slower HIV‐1 DNA decay. Conclusions: These data suggest that ART initiation within the first week of life can reduce the persistence of long‐lived infected cells. Delaying ART is associated with slower decay of infected cells.