Browsing by Author "Abrahams, Melissa-Rose"

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    Open Access
    Case report: mechanisms of HIV elite control in two African women
    (BioMed Central, 2018-01-25) Moosa, Yumna; Tanko, Ramla F; Ramsuran, Veron; Singh, Ravesh; Madzivhandila, Mashudu; Yende-Zuma, Nonhlanhla; Abrahams, Melissa-Rose; Selhorst, Philippe; Gounder, Kamini; Moore, Penny L; Williamson, Carolyn; Abdool Karim, Salim S; Garrett, Nigel J; Burgers, Wendy A
    Background: The majority of people living with HIV require antiretroviral therapy (ART) for controlling viral replication, however there are rare HIV controllers who spontaneously and durably control HIV in the absence of treatment. Understanding what mediates viral control in these individuals has provided us with insights into the immune mechanisms that may be important to induce for a vaccine or functional cure for HIV. To date, few African elite controllers from high incidence settings have been described. We identified virological controllers from the CAPRISA 002 cohort of HIV-1 subtype C infected women in KwaZulu Natal, South Africa, two (1%) of whom were elite controllers. We examined the genetic, clinical, immunological and virological characteristics of these two elite HIV controllers in detail, to determine whether they exhibit features of putative viral control similar to those described for elite controllers reported in the literature. Case presentation: In this case report, we present clinical features, CD4+ T cell and viral load trajectories for two African women over 7 years of HIV infection. Viral load became undetectable 10 months after HIV infection in Elite Controller 1 (EC1), and after 6 weeks in Elite Controller 2 (EC2), and remained undetectable for the duration of follow-up, in the absence of ART. Both elite controllers expressed multiple HLA Class I and II haplotypes previously associated with slower disease progression (HLA-A*74:01, HLA-B*44:03, HLA-B*81:01, HLA-B*57:03, HLA-DRB1*13). Fitness assays revealed that both women were infected with replication competent viruses, and both expressed higher mRNA levels of p21, a host restriction factor associated with viral control. HIV-specific T cell responses were examined using flow cytometry. EC1 mounted high frequency HIV-specific CD8+ T cell responses, including a B*81: 01-restricted Gag TL9 response. Unusually, EC2 had evidence of pre-infection HIV-specific CD4+ T cell responses. Conclusion: We identified some features typical of elite controllers, including high magnitude HIV-specific responses and beneficial HLA. In addition, we made the atypical finding of pre-infection HIV-specific immunity in one elite controller, that may have contributed to very early viral control. This report highlights the importance of studying HIV controllers in high incidence settings.
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    Characterizing the cellular latent reservoir of HIV-1 and the effect of immune activation on characteristics of the reservoir
    (2022) Ismail, Sherazaan Dineo; Burgers, Wendy A; Williamson, Carolyn; Riou, Catherine; Abrahams, Melissa-Rose
    Since the advent of antiretroviral therapy (ART) and the resultant suppression of viraemia in the majority of people living with HIV-1 (PLWH) on ART, HIV-1 infection has become manageable and PLWH have similar life expectancies as uninfected persons. However, ART is not curative, is needed lifelong, and its cessation leads to the recrudescence of viraemia. This is due to the formation of a latent reservoir that is long-lived and stable over time, precluding HIV-1 cure. The factors affecting reservoir formation, establishment, and kinetics are not fully understood. Furthermore, differences exist at the population level in disease progression in PLWH depending on ethnicity, biological sex, and infecting viral subtype. Similarly, differences in the latent reservoir of HIV-1 have been described, although less extensively. Understanding what shapes the latent HIV-1 reservoir is critical for developing strategies for cure. Furthermore, it is imperative that cure research is undertaken in diverse populations to ensure coverage of knowledge across different demographics. The latter will ensure that a cure strategy can be developed that will be globally implementable. In the Introductory chapter of this thesis, I provide a detailed review of the current literature and address the need for cure research in low-and middle- income countries. If a global cure is to be achieved, the burden of HIV-1 will need to be addressed in many different populations, most notably African women, as women bear the burden of HIV-1 globally. In South Africa, the country in the sub-Saharan African region with the highest prevalence of HIV-1, women are roughly twice as likely to be living with HIV than men (aged 15 to 49), with a prevalence rate 6% higher than the national average of 19%. Since women are underrepresented in HIV-1 research in general and more specifically in cure studies due to the paucity of research in countries outside of the global North, reservoirs and cure strategies ii need to be characterized in this context. Furthermore, while early treatment is the WHO standard of care for people diagnosed with HIV, a large majority of PLWH only initiated treatment in chronic infection. Since early ART is known to restrict formation of the latent reservoir of HIV-1, research in both early and late ART initiators is necessary. This research focused on characterising the viral reservoir in South African women in a well-established cohort of women who were recruited during acute HIV infection and followed until treatment initiation (which occurred during chronic infection) and beyond. Overall, this thesis focuses on characterising immune activation and inflammation during the course of both untreated and treated HIV-1 infection in a cohort of South African women and subsequently determining whether clinical or immune measures influence characteristics of the latent reservoir of HIV-1. T cell activation and the levels of soluble inflammatory cytokines in plasma were determined in forty-six women in the CAPRISA 002 Acute infection cohort. Chapter 2 describes the cellular immune activation and inflammation profiles of these participants throughout the course of infection at the following timepoints: acute infection, oneyear post-infection, and within a year preceding ART initiation, and two- and four- years postART initiation. T cell activation peaked in chronic infection and reduced dramatically after ART initiation. CD4+ and CD8+ T cell activation reached a post-treatment nadir by two years after ART initiation. Cytokine measures were within the ranges reported in the literature for PLWH. Notably CXCL-10 levels in plasma decreased significantly between two- and four years post-ART, indicating that it may be a sensitive marker of ongoing systemic inflammation in people on ART. In short, the T cell activation and inflammation profiles of the women in this study reflected what has been observed in other cohorts. iii The size of the replication-competent HIV-1 reservoir, measured by quantitative viral outgrowth assay after 5 years of suppressive antiretroviral therapy (ART), was quantified in twenty women of the cohort. In Chapter 3, the clinical and immunological correlates of reservoir size were investigated. Predictive modelling showed that the size of the replicationcompetent reservoir is directly related to viral load and CD4+ T-cell counts over the course of infection, although these measures do not fully predict reservoir size. We found that, in addition to viral load and CD4+ T-cell count, CD8+ T-cell activation within the year preceding ART, nadir CD4+ T-cell count, and baseline as well as on-treatment CD4:CD8 ratio at the time of sizing was associated with replication-competent reservoir size. We provide evidence that the late CD8+ T-cell activation level before treatment, together with viral loads and CD4+ T-cell counts, are directly related to the size of the replication-competent reservoir of HIV-1. Our results are consistent with the hypothesis that the host immune milieu near the time of ART initiation plays an important role in shaping the durable reservoir of HIV infection that persists on ART. Another characteristic of the HIV-1 reservoir is persistence: the presence of all forms of HIV1 within cells and tissues that contribute to pathogenesis, including defective, non-induced, and non-integrated forms of HIV-1. In Chapter 4, total HIV-1 DNA levels were measured as a proxy for viral persistence in thirty-one participants, and the correlates thereof investigated. The HIV-1 DNA levels in this cohort were similar to those reported in the literature for other cohorts where participants initiated therapy in late chronic infection. HIV-1 DNA levels did not differ significantly between two- and four years post-ART, but there was a trend to lower HIV-1 DNA when measuring pol versus gag gene frequencies in peripheral blood mononuclear cells (PBMC). These findings indicate that HIV-1 DNA decay rates may differ depending on the gene being measured, even when using the same assay. A weak significant correlation was iv found between CD4+ T cell counts at ART initiation and the change in HIV-DNA levels between two-and four years on ART. There was a significant correlation between residual CD4+ T cell activation at four years post-ART initiation and gag copies per million PBMC. A trend towards a correlation was found between CD4+ T cell activation and pol copies per million PBMC at the same timepoint. Finally, we found significant correlations between several cytokines at one-year post-infection and within one year pre-ART. These findings further solidify the hypothesis that the immune milieu around the time of ART initiation and after may play a complex role in formation of the viral reservoir of HIV-1. Our studies show a significant link between chronic immune activation and replication competent reservoir size, and also ongoing immune activation and viral persistence on ART. Further studies into whether these immune measures affect the timing of establishment and clonality of the reservoir in this cohort are ongoing and will inform the field about whether differences in cure strategies will need to be explored for those PLWH who had high levels of chronic immune activation before treatment initiation and subsequent shaping for the long-lived viral reservoir.
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    Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection
    (Public Library of Science, 2009) Moore, Penny L; Ranchobe, Nthabeleng; Lambson, Bronwen E; Gray, Elin S; Cave, Eleanor; Abrahams, Melissa-Rose; Bandawe, Gama; Mlisana, Koleka; Karim, Salim S Abdool; Williamson, Carolyn
    Author Summary Most HIV-1 infected individuals develop neutralizing antibodies against their own virus, termed an autologous neutralizing response. It is known that this response exerts pressure on the envelope of HIV, the target of such antibodies, resulting in neutralization escape. Here we have identified the targets of these antibodies and the precise genetic basis of neutralization escape in 4 individuals infected with HIV-1 subtype C. We show that V1V2 is commonly involved in escape, and that the C3 region is also a target in some cases. The latter observation confirms this region is exposed in subtype C, unlike subtype B. We show that neutralization escape is conferred by a few amino acid mutations, some of which are outside the antibody target site. Moreover, escape from these limited specificities even within a single individual occurs via a variety of different pathways involving substitutions, indels and glycan shifts. The finding in 2 individuals that an anti-C3 response developed first, followed by an anti-V1V2 response, suggests there may be specific regions of envelope particularly vulnerable to antibody neutralization. Overall, we propose a mechanistic explanation for how HIV-1 epitopes drive sequential waves of neutralization escape in early subtype C infection.
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    The Influence of HIV-1 Subtype C LTR Genotype on Latency Potential
    (2018) Doolabh, Deelan Sudhir; Abrahams, Melissa-Rose; Williamson, Carolyn
    The persistence of latent viral reservoirs, that are insensitive to antiretroviral therapy (ART), remains the greatest barrier to HIV-1 eradication. The role that viral factors play in HIV-1 latency establishment and maintenance is poorly understood, and characterisation of these factors is imperative for the development of curative strategies or interventions that could lead to HIV-1 remission in infected individuals. Subtype level genotypic variation within regulatory elements of the HIV-1 promoter, the long terminal repeat (LTR), has been shown to influence latency establishment in in vitro models. We investigated the influence of inter-participant subtype C LTR genotypic variation on the establishment of latency in a dual reporter HIV-1 plasmid model and evaluated potential correlates of this latency potential. Long terminal repeats from 11 ART-naïve, acutely subtype-C infected women in the CAPRISA 004 cohort from Durban, South Africa were cloned into an HIV-1-expressing vector (pRGH) used to generate pseudovirions following HEK293T transfection. Pseudoviruses harboured a gag-eGFP gene under the control of the participant LTR, allowing measurement of active replication, and an mCherry gene under the control of a constitutive CMV promoter allowing measurement of viral integration. Latency potential was expressed as the ratio of mCherry only (latent) to eGFP and mCherry (active replication), as measured by flow cytometry after infection of Jurkat E6-1 and CEM.NKR CCR5+ cell lines before and after T cell activation with PMA/Ionomycin. A panel of LTRs cloned into a pGL4.10 luciferase expression vector were used to measure basal LTR expression and Tat-induced LTR expression. All LTR sequences were classified as subtype C, with an average inter-participant pairwise DNA distance of 7.6%. The median basal LTR activity was approximately two times higher than that of the BaL isolate (interquartile range: 1.38-2.14), and Tatinduced activity approximately nine times higher than that of BaL (interquartile range: 6.16-10.33). We observed consistently greater proportions of latently infected cells than actively infected cells. In Jurkat E6-1 cells, the median latent:active infection ratio was 1.97 (range 0.86-2.83; three experiments). Latency was reversible in a proportion of cells as the median latent:active infection ratio decreased to 0.55 (range 0.46-0.78). The latent:active ratio was unchanged, post-stimulation, in CEM.NKR CCR5+ cells and was therefore found not to be a suitable cell-line for the model. Latency potential did not correlate with basal or Tat-induced activity (Spearman correlation tests, basal p=0.25, r=-0.38, Tat-induced p=0.42, r=-0.27). The DNA distance in characterised functional sites from consensus did not correlate with latency potential (Spearman correlation test p=0.67, r=0.14). Our data suggest that HIV-1 LTRs have intrinsic properties which influence latency potential and the proportion of latently infected cells early post-infection. However, since differences were independent of basal and Tat-induced LTR activity, other factors such as regulatory element interaction and the efficiency of recruitment of molecules responsible for establishing latency, such as histone modifiers, may play a role.