OpenUCT :: Browsing by Author "Williamson, Carolyn"

Browsing by Author "Williamson, Carolyn"

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Open Access
Adaptive changes in HIV-1 subtype c proteins during early infection and their effect on disease progression
(2010) Treurnicht, Florette Kathleen; Williamson, Carolyn
Open Access
Anaemia in acute HIV-1 subtype C infection
(Public Library of Science, 2008) Mlisana, Koleka; Auld, Sara C; Grobler, Anneke; Loggerenberg, Francois van; Williamson, Carolyn; Iriogbe, Itua; Sobieszczyk, Magdalena E; Karim, Salim S Abdool; Team, for the CAPRISA Acute Infection Study
BACKGROUND: The high prevalence of anaemia and the increased morbidity and mortality associated with anaemia during AIDS has been well described yet there has been little information about anaemia and changes in haemoglobin levels during acute and early HIV-1 infection. METHODS: HIV-negative women (n = 245) were enrolled into an observational cohort as part of the Centre for the AIDS Programme of Research in South Africa (CAPRISA) Acute Infection Study. Acute infection was diagnosed following a positive HIV RNA PCR in the absence of antibodies, or detection of HIV-1 antibodies within 3 months of a previously negative antibody test. Haemotologic parameters were assessed before infection and at regular intervals in the first twelve months of HIV infection. RESULTS: Fifty-seven participants with acute HIV infection were identified at a median of 14.5 days post-infection (range 10-81) and were enrolled in the CAPRISA Acute Infection cohort at a median of 41 days post-infection (range 15-104). Mean haemoglobin prior to HIV-1 infection was 12.7 g/dL, with a mean decline of 0.46 g/dL following infection. The prevalence of anaemia increased from 25.0% prior to HIV-1 infection to 52.6% at 3 months post-infection, 61.1% at 6 months post-infection, and 51.4% at 12 months post-infection. CONCLUSIONS: Haematologic derangements and anaemia with a trend towards iron deficiency are common with acute HIV-1 subtype C infection in this small cohort. The negative impact of anaemia concurrent with established HIV infection upon morbidity and mortality has been well documented but the prognostic potential and long-term effects of anaemia during acute HIV-1 infection remain unknown.
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.
Open Access
Challenges of diagnosing acute HIV-1 subtype C infection in African women: performance of a clinical algorithm and the need for point-of-care nucleic-acid based testing
(Public Library of Science, 2013) Mlisana, Koleka; Sobieszczyk, Magdalena; Werner, Lise; Feinstein, Addi; van Loggerenberg, Francois; Naicker, Nivashnee; Williamson, Carolyn; Garrett, Nigel
BACKGROUND: Prompt diagnosis of acute HIV infection (AHI) benefits the individual and provides opportunities for public health intervention. The aim of this study was to describe most common signs and symptoms of AHI, correlate these with early disease progression and develop a clinical algorithm to identify acute HIV cases in resource limited setting. METHODS: 245 South African women at high-risk of HIV-1 were assessed for AHI and received monthly HIV-1 antibody and RNA testing. Signs and symptoms at first HIV-positive visit were compared to HIV-negative visits. Logistic regression identified clinical predictors of AHI. A model-based score was assigned to each predictor to create a risk score for every woman. RESULTS: Twenty-eight women seroconverted after a total of 390 person-years of follow-up with an HIV incidence of 7.2/100 person-years (95%CI 4.5-9.8). Fifty-seven percent reported ≥1 sign or symptom at the AHI visit. Factors predictive of AHI included age <25 years (OR = 3.2; 1.4-7.1), rash (OR = 6.1; 2.4-15.4), sore throat (OR = 2.7; 1.0-7.6), weight loss (OR = 4.4; 1.5-13.4), genital ulcers (OR = 8.0; 1.6-39.5) and vaginal discharge (OR = 5.4; 1.6-18.4). A risk score of 2 correctly predicted AHI in 50.0% of cases. The number of signs and symptoms correlated with higher HIV-1 RNA at diagnosis (r = 0.63; p<0.001). CONCLUSIONS: Accurate recognition of signs and symptoms of AHI is critical for early diagnosis of HIV infection. Our algorithm may assist in risk-stratifying individuals for AHI, especially in resource-limited settings where there is no routine testing for AHI. Independent validation of the algorithm on another cohort is needed to assess its utility further. Point-of-care antigen or viral load technology is required, however, to detect asymptomatic, antibody negative cases enabling early interventions and prevention of transmission.
Open Access
Characterisation of functional properties of Envelopes of highly neutralisation resistant HIV-1 isolates
(2018) Guled, Fatuma Hassan; Dorfman, Jeffrey; Williamson, Carolyn
An effective antibody-based HIV-1 vaccine would ideally elicit potent antibodies capable of neutralising a wide range of HIV-1 isolates to better cover the human population. A primary concern is the virus’ ability to rapidly escape an antibody response. A strong neutralising response elicited by a vaccine may, in principle, select for viruses that are highly antibody resistant thereby significantly reducing the benefit of a vaccine. It is therefore important to study and better understand highly neutralisation resistant viruses. To this effect, we characterized sets of subtype C and CRF02_AG viruses whose neutralisation phenotype were well defined using within subtype neutralisation (neutralisation by subtype matched sera). Our main aim was to determine if there exists a relationship between neutralisation resistance and entry efficiency. Very highly neutralisation resistant viruses appear under-represented in the population. We hypothesised that this may be at least partially explained by decreased entry efficiency as changes to Envelope (Env) during escape could affect the entry process and provide opposing selective pressure that discourages the appearance of very highly neutralisation-resistant viruses. By comparing entry efficiencies of tier 3 viruses (highly resistant) to tier 2 (moderately resistant) and 1B (sensitive), we observed that the tier 3 viruses generally exhibited higher entry efficiency. This was the opposed of what we hypothesised at the outset of these experiments. We also measured characteristics of resistant HIV-1 Envs that can be inferred from the primary sequence such as the variable loop lengths, number of glycans and net charge. We found that the V2 net charge and the V5 loop length were associated with neutralisation resistance in subtype C viruses and the V2 loop length was associated with resistance in the CRF02_AG viruses. By analysing glycosylation patterns between the groups, we found that the presence of an N-linked glycan at position 413 and the lack of a glycan at N332 were predictors of neutralisation resistance in subtype C viruses. Tier 3 viruses were also more resistant than tier 2 and 1B viruses to the PGT121 (V3/glycan), 4E10 (MPER) and the CD4 binding site broadly neutralising antibodies VRC01 and 3BNC117; suggesting that the epitopes of these antibodies are important for driving resistance. Furthermore, we found no significant relationship between susceptibility to the entry inhibitors Maraviroc and PSC RANTES (CCR5 antagonists) and the fusion inhibitor T20 and resistance, indicating that neutralisation resistance did not alter inhibitor target sites. Based on our findings, it is clear that reduced entry efficiency does not explain why highly resistant viruses are not more common. We may speculate that the evolutionary steps needed to reach very high neutralisation resistance may be difficult to go through and/or that other countervailing selective pressures may be involved. In the context of an antibody based intervention, highly resistant viruses with increased entry efficiency circulating in the population could be a set back in the control of the HIV-1 epidemic. Therefore, for any long-term antibody-based intervention to be globally relevant it must elicit responses that limit occurrence of resistance and also increase chances that escape would lead to severely impaired viral fitness.
Open Access
Characterisation of HIV superinfection : genetic evolution and adaptive immune responses
(2011) Harvey, Hayley Janet; Williamson, Carolyn
In this thesis we aimed to determine the timing and frequency of intra-subtype C superinfection, and to determine if the reason for superinfection was a greater genetic distance within epitopes of the superinfecting virus compared to those of circulating strains from the same cohort.
Open Access
Characterisation of HIV-1 Envelope features of breakthrough infections from the CAPRISA 004 Microbicide Trial
(2016) Ismail, Sherazaan Dineo; Williamson, Carolyn; Selhorst, Philippe
The CAPRISA 004 trial demonstrated the safety and a 39% efficacy of a 1% tenofovir (TFV) gel for the prevention of HIV-1 acquisition in young African women. It was subsequently shown that women assigned to the TFV arm who became infected had higher viral loads, slower anti-HIV-1 antibody avidity maturation, and higher Gag-specific IFN-γ+ CD4+ T cell responses; although replication capacity, as measured by Gag-Pro recombinant viruses, did not differ between arms. We thus aimed to investigate if there were differences in Envelope function, or TFV susceptibility, which may be selected for during transmission in those who became infected despite being assigned to the TFV arm. Viruses from 39 out of 48 recently HIV-1 infected individuals from the trial (matched on time post-infection and the presence of protective HLAs) were isolated. Isolate env genes were sequenced using a single genome amplification approach and were compared to plasma sequences from the same time-point. To evaluate phenotypic characteristics of env, inhibition assays were performed using the following inhibitors: tenofovir, maraviroc, T20, PSC-RANTES and anti-CD4 antibody clone SK3. In addition, envs for 19 participants were cloned and used to generate pseudoviruses which were evaluated for entry efficiency. Viral isolates were identical or very similar to viruses in circulation in vivo; however had a lower diversity, indicating that they were representative of in vivo virus but did not reflect the entire quasispecies in plasma. The TFV arm viruses were not more resistant to TFV than those in the placebo arm. A comparison of variable loop characteristics, distance to a consensus representative of viruses circulating in the region, and sensitivity to inhibitors or entry efficiencies of the viruses, also found no difference in genotypic nor phenotypic properties between study arms. When assessing the impact of viral phenotype on markers of disease progression, it was found that sensitivity to inhibitors did not contribute to VL or CD4+ count in this cohort. To evaluate envelope in isolation of the rest of the genome, pseudoviruses were generated from 11 participants. We found that PSV entry efficiency did not correlate with VL at isolation, 3 months post-infection and set-point, or with CD4+ counts at set-point. However, pseudovirus inhibitor sensitivities were significantly different to those of isolates for the inhibitors T20, anti-CD4 antibody SK3 and PSC-RANTES. Overall, the isolate env genotypic and phenotypic characteristics investigated in this study did not differ between trial arms. Interestingly, pseudoviruses showed significant differences in their sensitivity to entry inhibitors when compared to their corresponding isolate, highlighting the importance of caution when interpreting data from in vitro studies, and motivates for further evaluation of in vitro models.
Open Access
Characterisation of two aphid picorna-like viruses
(1988) Williamson, Carolyn; Rybicki, Edward P; Von Wechmar, M Barbara
A new aphid virus, aphid lethal paralysis virus (ALPV), was isolated from laboratory-propagated Rhopalosiphum padi aphids co-infected with R. padi virus (RhPV). ALPV and RhPV were separated and ALPV was characterised in detail. Virions are isometric with a diameter of 26 nm, a sedimentation coefficient of 164 Sand a density in CsCl of 1.34 g/ml. Virions contain a 9.7 kb polyadenylated, singlestranded RNA and three major proteins with molecular weights of approximately 30 kilodaltons. By characterising RhPV further, two additional putative capsid proteins were found, an RNA poly(A) tract was detected and an RNA size of 10 kb was determined. A South African isolate of RhPV (RhPVoFs) was found to be serologically identical but physically distinct from a USA isolate. Complementary DNA was synthesized from RhPVOFS RNA and cloned into the plasmid vector, pBR322. This clone was used for the detettion of virus in aphids. ALPV and RhPV are serologically unrelated. ALPV is serologically distantly related to two insect picornaviruses, cricket paralysis virus (CrPV) and Drosophila C virus. No nucleic acid homology was detected between ALPV cDNA and CrPV by dot-blot hybridization. ALPV is serologically unrelated to seven other insect picornalike viruses. RhPV is serologically unrelated to any of the above mentioned viruses. ALPV and RhPV RNAs were efficiently translated in rabbit reticulocyte lysate into high molecular weight polypeptides, the sum of which exceeded the coding capacity of the genomes. Putative capsid precursor proteins of ALPV and RhPV were identified by immunoprecipitation. ALPV translation products were post-translationally cleaved as demonstrated in pulse-chase experiments and in experiments using a translation inhibitor. The efficiency of cleavage was concentration-dependent indicating the action of a protease. In parallel experiments with RhPV RNA, no evidence of post-translational cleavage was observed. In a survey of aphids collected in South Africa, ALPV and RhPV were detected in aphids from two major small-grain producing areas. Both viruses were found to naturally infect most of the cereal aphid species found in this country. ALPV and RhPV infections of R. padi resulted in a marked reduction in longevity and fecundity relative to uninfected aphids. Both viruses were found to be horizontally and vertically transmitted through aphid populations, and aphid host plants and aphid predators could be implicated in virus dissemination. ALPV and RhPV have many properties in common with each other as well as with insect and mammalian picornaviruses. Based on this data, it is proposed that ALPV and RhPV be classified into the picornavirus group (family Picornaviridae).
Open Access
Characterization of genotypic and phenotypic properties of transmitted Human Immunodeficiency virus type 1 variants circulating in Mbeya Tanzania
(2013) Nofemela, Andile; Williamson, Carolyn; Woodman, Zenda
Includes abstract. Includes bibliographical references.
Open Access
Characterization of HIV-1 gag and nef in Cameroon: further evidence of extreme diversity at the origin of the HIV-1 group M epidemic
(BioMed Central Ltd, 2013) Tongo, Marcel; Martin, Darren; Zembe, Lycias; Mpoudi-Ngole, Eitel; Williamson, Carolyn; Burgers, Wendy
BACKGROUND: Cameroon, in west central Africa, has an extraordinary degree of HIV diversity, presenting a major challenge for the development of an effective HIV vaccine. Given the continuing need to closely monitor the emergence of new HIV variants in the country, we analyzed HIV-1 genetic diversity in 59 plasma samples from HIV-infected Cameroonian blood donors. Full length HIV gag and nef sequences were generated and phylogenetic analyses were performed. FINDINGS: All gag and nef sequences clustered within HIV-1M. Circulating recombinant form CRF02_AG predominated, accounting for 50% of the studied infections, followed by clade G (11%), clade D and CRF37_cpx (4% each), and clades A, F, CRF01_AE and CRF36_cpx (2% each). In addition, 22% of the studied viruses apparently had nef and gag genes from viruses belonging to different clades, with the majority (8/10) having either a nef or gag gene derived from CRF02_AG. Interestingly, five gag sequences (10%) and three (5%) nef sequences were neither obviously recombinant nor easily classifiable into any of the known HIV-1M clades. CONCLUSION: This suggests the widespread existence of highly divergent HIV lineages in Cameroon. While the genetic complexity of the Cameroonian HIV-1 epidemic has potentially serious implications for the design of biomedical interventions, detailed analyses of divergent Cameroonian HIV-1M lineages could be crucial for dissecting the earliest evolutionary steps in the emergence of HIV-1M.
Open Access
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.
Open Access
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection
(BioMed Central Ltd, 2008) Bandawe, Gama; Martin, Darren; Treurnicht, Florette; Mlisana, Koleka; Karim, Salim; Williamson, Carolyn
BACKGROUND:The high diversity of HIV variants driving the global AIDS epidemic has caused many to doubt whether an effective vaccine against the virus is possible. However, by identifying the selective forces that are driving the ongoing diversification of HIV and characterising their genetic consequences, it may be possible to design vaccines that pre-empt some of the virus' more common evasion tactics. One component of such vaccines might be the envelope protein, gp41. Besides being targeted by both the humoral and cellular arms of the immune system this protein mediates fusion between viral and target cell membranes and is likely to be a primary determinant of HIV transmissibility. RESULTS: Using recombination aware analysis tools we compared site specific signals of selection in gp41 sequences from different HIV-1 M subtypes and circulating recombinant forms and identified twelve sites evolving under positive selection across multiple major HIV-1 lineages. To identify evidence of selection operating during transmission our analysis included two matched datasets sampled from patients with acute or chronic subtype C infections. We identified six gp41 sites apparently evolving under different selection pressures during acute and chronic HIV-1 infections. These sites mostly fell within functional gp41 domains, with one site located within the epitope recognised by the broadly neutralizing antibody, 4E10. CONCLUSION: Whereas these six sites are potentially determinants of fitness and are therefore good candidate targets for subtype-C specific vaccines, the twelve sites evolving under diversifying selection across multiple subtypes might make good candidate targets for broadly protective vaccines.
Open Access
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection
(2008-11-24) Bandawe, Gama P; Martin, Darren P; Treurnicht, Florette; Mlisana, Koleka; Karim, Salim S A; Williamson, Carolyn
Background: The high diversity of HIV variants driving the global AIDS epidemic has caused many to doubt whether an effective vaccine against the virus is possible. However, by identifying the selective forces that are driving the ongoing diversification of HIV and characterising their genetic consequences, it may be possible to design vaccines that pre-empt some of the virus' more common evasion tactics. One component of such vaccines might be the envelope protein, gp41. Besides being targeted by both the humoral and cellular arms of the immune system this protein mediates fusion between viral and target cell membranes and is likely to be a primary determinant of HIV transmissibility. Results: Using recombination aware analysis tools we compared site specific signals of selection in gp41 sequences from different HIV-1 M subtypes and circulating recombinant forms and identified twelve sites evolving under positive selection across multiple major HIV-1 lineages. To identify evidence of selection operating during transmission our analysis included two matched datasets sampled from patients with acute or chronic subtype C infections. We identified six gp41 sites apparently evolving under different selection pressures during acute and chronic HIV-1 infections. These sites mostly fell within functional gp41 domains, with one site located within the epitope recognised by the broadly neutralizing antibody, 4E10. Conclusion: Whereas these six sites are potentially determinants of fitness and are therefore good candidate targets for subtype-C specific vaccines, the twelve sites evolving under diversifying selection across multiple subtypes might make good candidate targets for broadly protective vaccines.
Open Access
Detectable HIV-1 in semen in individuals with very low blood viral loads
(2020-03-05) Kariuki, Samuel M; Selhorst, Philippe; Norman, Jennifer; Cohen, Karen; Rebe, Kevin; Williamson, Carolyn; Dorfman, Jeffrey R
Abstract Background Several reports indicate that a portion (5–10%) of men living with HIV-1 intermittently shed HIV-1 RNA into seminal plasma while on long term effective antiretroviral therapy (ART). This is highly suggestive of an HIV-1 reservoir in the male genital tract. However, the status of this reservoir in men living with HIV-1 who are not under treatment is underexplored and has implications for understanding the origins and evolution of the reservoir. Finding Forty-three HIV-1 positive, antiretroviral therapy naïve study participants attending a men’s health clinic were studied. Semen viral loads and blood viral loads were generally correlated, with semen viral loads generally detected in individuals with blood viral loads > 10,000 cp/ml. However, we found 1 individual with undetectable viral loads (<20cp/ml) and 2 individuals with very low blood viral load (97 and 333cp/ml), but with detectable HIV-1 in semen (485–1157 copies/semen sample). Blood viral loads in the first individual were undetectable when tested three times over the prior 5 years. Conclusions Semen HIV-1 viral loads are usually related to blood viral loads, as we confirm. Nonetheless, this was not true in a substantial minority of individuals suggesting unexpectedly high levels of replication in the male genital tract in a few individuals, despite otherwise effective immune control. This may reflect establishment of a local reservoir of HIV-1 populations.
Open Access
Establishing a cohort at high risk of HIV infection in South Africa: challenges and experiences of the CAPRISA 002 acute infection study
(Public Library of Science, 2008) van Loggerenberg, Francois; Mlisana, Koleka; Williamson, Carolyn; Auld, Sara C; Morris, Lynn; Gray, Clive M; Karim, Quarraisha Abdool; Grobler, Anneke; Barnabas, Nomampondo; Iriogbe, Itua
Objectives To describe the baseline demographic data, clinical characteristics and HIV-incidence rates of a cohort at high risk for HIV infection in South Africa as well as the challenges experienced in establishing and maintaining the cohort. Methodology/Principle FINDINGS: Between August 2004 and May 2005 a cohort of HIV-uninfected women was established for the CAPRISA 002 Acute Infection Study, a natural history study of HIV-1 subtype C infection. Volunteers were identified through peer-outreach. The cohort was followed monthly to determine HIV infection rates and clinical presentation of early HIV infection. Risk reduction counselling and male and female condoms were provided. After screening 775 individuals, a cohort of 245 uninfected high-risk women was established. HIV-prevalence at screening was 59.6% (95% CI: 55.9% to 62.8%) posing a challenge in accruing HIV-uninfected women. The majority of women (78.8%) were self-identified as sex-workers with a median of 2 clients per day. Most women (95%) reported more than one casual sexual partner in the previous 3 months (excluding clients) and 58.8% reported condom use in their last sexual encounter. Based on laboratory testing, 62.0% had a sexually transmitted infection at baseline. During 390 person-years of follow-up, 28 infections occurred yielding seroincidence rate of 7.2 (95% CI: 4.5 to 9.8) per 100 person-years. Despite the high mobility of this sex worker cohort retention rate after 2 years was 86.1%. High co-morbidity created challenges for ancillary care provision, both in terms of human and financial resources. Conclusions/Significance Challenges experienced were high baseline HIV-prevalence, lower than anticipated HIV-incidence and difficulties retaining participants. Despite challenges, we have successfully accrued this cohort of HIV-uninfected women with favourable retention, enabling us to study the natural history of HIV-1 during acute HIV-infection. Our experiences provide lessons for others establishing similar cohorts, which will be key for advancing the vaccine and prevention research agenda in resource-constrained settings.
Open Access
Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition: implications for active and passive immunization
(Public Library of Science, 2016) Rademeyer, Cecilia; Korber, Bette; Seaman, Michael S; Giorgi, Elena E; Thebus, Ruwayhida; Robles, Alexander; Sheward, Daniel J; Wagh, Kshitij; Garrity, Jetta; Carey, Brittany R; Gao, Hongmei; Greene, Kelli M; Tang, Haili; Bandawe, Gama P; Marais, Jinny C; Diphoko, Thabo E; Hraber, Peter; Tumba, Nancy; Moore, Penny L; Gray, Glenda E; Kublin, James; McElrath, M Juliana; Vermeulen, Marion; Middelkoop, Keren; Bekker, Linda-Gail; Hoelscher, Michael; Maboko, Leonard; Makhema, Joseph; Robb, Merlin L; Karim, Salim Abdool; Karim, Quarraisha Abdool; Kim, Jerome H; Hahn, Beatrice H; Gao, Feng; Swanstrom, Ronald; Morris, Lynn; Montefiori, David C; Williamson, Carolyn
Author Summary: Vaccine and passive immunization prophylactic trials that rely on antibody-mediated protection are planned for HIV-1 clade C epidemic regions of southern Africa, which have amongst the highest HIV-1 incidences globally. This includes a phase 2b trial of passively administered monoclonal antibody, VRC01; as well as a phase 3 trial using the clade C modified version of the partially efficacious RV144 vaccine. The extraordinary diversity of HIV-1 poses a major obstacle to these interventions, and our study aimed to determine the implications of viral diversity on antibody recognition. Investigations using our panel of very early viruses augment current knowledge of vulnerable targets on transmitted viruses for vaccine design and passive immunization studies. Evidence of antigenic drift with viruses becoming more resistant over time suggests that these prevention modalities will need to be updated over time and that combinations of antibodies will be necessary to achieve coverage in passive immunization studies. We further show that it may be more difficult to obtain protection in the genetically diverse clade C epidemic compared to RV144 where the epidemic is less diverse, although it should be noted that the correlates of infection risk are yet to be defined in the clade C setting.
Open Access
HIV-1 strain-specific neutralizing antibody responses and the dynamics of viral evolution
(2016) Majara, Lerato Charlotte; Williamson, Carolyn; Anthony, Colin Scott
It is widely held that for an HIV-1 vaccine to provide sterilizing immunity, it would need to elicit broadly neutralizing antibodies (bnAbs). However, factors underlying the development of these antibodies are not clear. There is evidence to suggest that in some individuals who develop bnAbs, the development of breadth is influenced by the co-evolution of the transmitted/founder (t/f) virus and earlier strain-specific neutralizing antibody (ssnAb) responses. Here we characterized the viral evolution, ssnAb and bnAbs responses in CAP292, an HIV-1 infected woman who developed bnAb responses from one year post infection. We used single genome amplification (SGA) to characterize viral evolution at four time points: at acute infection; after the development of strain-specific neutralizing responses; at the first detection of the broadly neutralizing antibody response; and lastly, at the peak of the broad response. We identified the t/f virus, and generated chimeric viruses from this to determine the targets of the ssnAb responses. A panel of site-directed mutant viruses were used to map the specificity of the bnAb responses. Our data indicated that infection was most likely founded by a single virus and that the first wave of ssnAbs emerged at 14 weeks post infection (w.p.i), targeting the V1V2 loop of Envelope (Env). A second wave of ssnAbs, possibly targeting the C3V4 region, emerged by 30 w.p.i. Two distinct viral clusters were detected by the time the bnAb response peaked, suggesting the presence of distinct escape pathways. Mapping of the bnAb specificities indicated that CAP292 produced PGT128-like bnAb responses targeted toward the 332 glycan.
Open Access
Human immunodeficiency virus type-1 distribution in South Africa and the relevance of genetic diversity on vaccine design
(1999) Van Harmelen, Joanne Heidi; Williamson, Carolyn
The overall aim of this project was to investigate HIV-1 genetic diversity in South Afri ca and to characterise the immune response in mice to a South African subtype C gp120. To investigate the relationship between subtype and mode of transmission, samples were collected from individuals infected by heterosexual and male homosexual transmission from patients attending local HIV/AIDS clinics in Cape Town (n=49) and Bloemfontein (n=4). Isolates were subtyped using heteroduplex mobility assay (HMA) based on the V3-V5 region of the env geneusing reference plasmids (2 B, 2 C and 1 D) representative of local subtypes. HMA identified four env subtypes: A, B, C and D. Subtype B viruses were found in 92.9% (26/28) of the male homosexual/bisexual group and subtype C viruses in 77.2% (17 /22) of the heterosexual group. Subtype B viruses were also identified in two heterosexual patients, one patient infected by blood transfusion and in two patients with. unknown mode of transmission. Subtype D viruses were found in one male homosexual patient and one heterosexual patient and a husband and wife couple were infected with subtype A viruses. A significant association between subtype and mode of transmission (p=<0.0001) was identified, confirming two independent epidemics. To determine the subtype distribution of HIV within urban heterosexual populations throughout South Africa, samples were collected from women attending antenatal clinics in Johannesburg (n=34), Pretoria (n=S) and Durban (n=20). Samples from Bloemfontein (n=24) were taken from individuals attending an HIV/AIDS clinic. All eighty-three samples were subtyped by HMA in the env region as before. The predominant subtype circulating within the urban heterosexual population throughout South Africa was identified as subtype C (92.8%) although subtype B was also detected (7.2%). It may thus be beneficial if a HIV vaccine for South Africa is based on a subtype C model. In addition, a rapid method for identification of HIV-1 gag subtypes was developed based on restriction fragment length polymorphism (RFLP) analysis of 400bp (p17) or 650bp (p17 and 5' p24) long PCR fragments. This strategy was appl i ed to eighty-six samples (Cape Town n=47, Johannesburg n=20, Bloemfontein n=17 and Durban n=2) previously subtyped by either sequence analysis of the gag p17 region (n=31), heteroduplex mobility assay (HMA) based on the env gene (n=76), or both (n=21). RFLP analysis identified two subtype A, twenty-five subtype B, fifty-eight subtype C and one subtype D isolates. There were no discrepancies between RFLP and sequence gag subtypes, demonstrating the reliability of this method and no discordance between gag RFLP subtypes and env HMA subtypes, indicating no recombinant viruses in the genomic regions analysed.
Open Access
Human Immunodeficiency Virus? One of nature's greatest evolutionary machines
(2004) Martin, Darren; Williamson, Carolyn
Transmission of an HIV-like virus from chimpanzees to humans approximately 80 years ago triggered the worldwide AIDS pandemic. Possessing very high mutation and recombination rates, the descendants of this ancestral virus have evolved greatly. Most of this evolution has been in response to selective pressures imposed by human immune responses and has not provided HIV with any significant new biological characteristics. The continuing diversification of HIV variants is a principal obstruction to controlling the virus with drugs and vaccines.
Open Access
Impact of Cytotoxic T Lymphocyte (CTL) escape mutations in acute/Early HIV-1 Subtype C Infection on Disease Progression
(2009) Chopera, Denis Rutendo; Williamson, Carolyn
Most HIV vaccines currently in development aim to protect people from infection or disease by eliciting strong anti-HIV cytotoxic T lymphocyte (CTL) responses. Evolved evasion mutations that undermine host immune responses pose a major challenge to the development of such vaccines. Understanding the mechanisms that selectively favour the emergence of CTL evasion mutations in vivo and the impact of these mutations on both disease progression and long-term HIV evolution will not only contribute to our understanding of HIV pathogenesis, but will also inform vaccine design strategies. This study aimed at investigating CTL escape mutations in HIV-1 Gag and Nef, during the acute and early phases of infection and the impact of these mutations on subsequent disease progression in a cohort of recently HIV-1 subtype C infected females. Of 36 women recruited into the study within 12 weeks of infection (median 6 weeks) and followed for six months, 32 were infected with single viruses. Two participants were infected with epidemiologically unlinked viruses (dual infection), and in a further two individuals the viruses were highly divergent suggestive of dual infection and/or recombination. These individuals were excluded from further analysis as it was difficult to predict CTL escape due to high degrees of diversity between sequences. In the remaining 32 study participants, there was a high frequency of CTL escape with putative escape mutations identified in 21 of 32 individuals (66%). Twelve of these 21 (33%) harboured viruses which developed escape mutations in Gag, and 17 (53%) developed escape mutations in Nef. In the conserved structural protein, p24, potential reversion mutations were more frequent than potential escape mutations. During the first six months of infection whereas potential reversion mutations occurred at low entropy sites, potential escape mutations occurred at high entropy sites. Although there was no detectable association between the timing of escape mutations and disease progression, there was an association between the degree of deviation of the p24 sequence from the subtype-C population consensus (a measure of escape mutation load) and CD4+ counts. Analysis of the earliest sampled viruses from HLA-B*57/B*5801 negative study participants for viral genetic markers associated with disease progression identified two iv polymorphisms, A146X (n = 9) and T242N (n =6), that were associated with improved viral control. The polymorphisms are well-known escape mutations in HLAB* 57/B*5801 restricted epitopes. This suggested transmission of these variants from individuals carrying these alleles. Further evidence that viruses carrying the T242N and/or A146X mutations had been previously passaged through B*57/B*5801 positive individuals came from the fact that the observed T242N mutations reverted to wild type during follow-up. There was no significant change in viral load and CD4+ counts upon reversion of the T242N mutations. In vitro replication assays using chimeric viruses containing gag sequences from one of participants showed that the virus harbouring the T242N mutation was fitter than that carrying the reversion mutation. These viruses harboured other T242N associated compensatory mutations suggesting that these compensatory mutations may themselves carry a fitness cost in the absence of the T242N mutation. This suggests that there possibly exist networks of B*57/B*5801 associated mutations and that reversion of some of these mutations in isolation does not necessarily restore viral fitness. Lastly, the kinetics of CTL escape in HLA-B*5801 positive participants (n = 6) and the impact of escape on disease progression was investigated. CTL escape within B *5801 positive individuals was found to predominantly occur within the TW10 in Gag (n = 4) and KAF9 in Nef (n = 6) epitopes. The emergence of the T242N mutation in TW10 was always preceded by mutations elsewhere in the epitope and was associated with the occurrence of previously described compensatory mutation upstream of the epitope. The targeting of TW10 and the emergence of T242N escape mutations were associated with higher CD4+ counts at 12 months postinfection in the B*5801 positive individuals (p = 0.0231 and p = 0.0282, respectively). Independent of host HLA genotypes, the presence of the A146X and T242X mutations was associated with higher CD4+ counts (p = 0.0495). This study provides some useful insights into HIV-1 subtype C pathogenesis. The notion that CTL escape mutations do not invariably result in less fit viruses is evidenced by the observation that escape was not obviously associated with disease progression in this cohort, while escape mutations in the Gag p24 region within B*5801 positive individuals v in particular, was associated with improved viral control. There is therefore evidently a complex interaction between escape and compensatory mutations and further work is required to identify the impact of compensatory mutations on viral fitness. Overall, this study provides further evidence that vaccines need to elicit responses that specifically target the functionally constrained regions of the HIV proteome.