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Doctoral Degrees (Virology)

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    Pandemic genomic surveillance: SARS-CoV-2 real-time genomic epidemiology to identify and track variants in South Africa and Africa.
    (2022) Tegally, Houriiyah.; De Oliveira, Tulio Paivan N Andrade.
    The SARS-CoV-2 pandemic has both been one of the largest public health emergencies of modern times and an unprecedented opportunity to track the epidemic progression of an evolving virus. Globally, more than 13 million genomic sequences have been generated, over 140,000 of which was from surveillance in African countries. The work presented in this thesis employs methods of real-time genomic surveillance and epidemiology, genome assembly, phylogenetic analysis and phylodynamic modelling to characterise the evolution of SARS-CoV-2 in South Africa and Africa with immediate public health impact globally. Chapter 2 describes the setting up and results of genomic surveillance in all provinces during the first wave of infections in South Africa. Insights included the description of three local lineages that caused over half of infections in the first wave and the establishment of surveillance baselines that enabled rapid characterization of variants of concern in upcoming waves. Chapter 3 provides a description of, for the first time in the world, the emergence of a SARS-CoV-2 variant of concern. The study gives an overview of the detection of the Beta variant, its association with an accelerating epidemic in the Eastern Cape province and the inferred phylogeography of how the variant spread to coastal provinces during summer holidays in South Africa. Chapter 4 describes the characterisation and phylodynamics of the Omicron variant of concern in record time at the start of the 4th wave of infections in southern Africa. Chapter 5 provides insights into the continued evolution of Omicron into sublineages BA.4 and BA.5, which went on to dominate the epidemic in other parts of the world in mid-2022. Finally, Chapter 6 and 7 are comprehensive studies of continental genomic surveillance in Africa, giving insights into establishment of epidemics from introductions from external sources, cross-border viral movements and the expansion of genomic surveillance on the continent to cover blindspots. This thesis also contributed to a number of other studies where genomic sequencing of SARSCoV- 2 helped to answer critical questions during pandemic response, which is described in the last chapter. In conclusion, this thesis exemplifies how genomic epidemiology can be utilised in real-time to track the evolution of a pandemic pathogen as well as rapidly raise alarms of detected global health threats.
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    HIV-1 integrase inhibitor mutations: analysis of structural and biochemical effects.
    (2021) Mbhele, Nokuzola Brightness.; Gordon, Michelle Lucille.; Khan, Rene Bernadette.
    Introduction. Combination antiretroviral therapy (cART), composed of drugs from different drug classes, is an effective HIV-1 treatment strategy. As part of cART, integrase strand transfer inhibitors (INSTIs) have become essential drugs and are now recommended for use in first-line, second-line, and subsequent HIV-1 treatment regimens. Though highly potent, the use of first-generation INSTIs Raltegravir and Elvitegravir still resulted in the development of integrase drug resistance mutations. Second-generation INSTIs Dolutegravir, Bictegravir, and Cabotegravir were developed to combat the emerging resistant virus strains to first-generation INSTIs and are considered some of the best antiretroviral drugs in HIV-1 treatment. Despite the fundamental changes and improved performance in second-generation INSTIs, they are not immune to drug resistance. This highlights the need to understand the molecular mechanisms of resistance to INSTIs. This thesis, through a combination of structural and biochemical methods, seeks to understand resistance development in South African HIV-1 subtype C (HIV-1C) viruses and the effect of resistance mutations on enzyme-substrate binding, DNA binding, and 3’ processing. Methods. A total of 48 HIV-1C sequences were analyzed in this study, of which 7 had a virologic failure (i.e. plasma viral loads >1000 copies/mL) and 41 were INSTI naïve isolates (32 treatment-naïve South African HIV-1C integrase sequences downloaded from GenBank and 9 INSTI-naïve isolates amplified in our laboratory). Virologic failures were receiving at least 6 months of INSTI-based cART and presented at the King Edward VIII hospital, a 3rd line regimen referral hospital in Durban, South Africa. Viral RNA was extracted, and the integrase region was amplified and sequenced using Sanger sequencing. To investigate the effect of mutations on the integrase structure, wild-type and representative mutant isolates were modeled on the SWISS model online server and visualized in Chimera v1.13.1. Raltegravir, Elvitegravir, and Dolutegravir were docked into each of the structures using the AutoDock-Vina Plugin available on Chimera, and molecular dynamics simulations were conducted using the AMBER 18 package. Integrase biochemical assays were carried out using a wild-type protein and the 3 mutant recombinant proteins that were expressed and purified. Integrase - LTR binding and 3’ processing assays were then performed. Results. Only one of the 7 (14,28%) INSTI-treated isolates had major mutations (i.e., G140A and Q148R). In addition, this isolate harboured the E157Q minor mutation and previously identified polymorphisms. Interestingly, S119T & V151I, located near the integrase active site, were only found in INSTI failures. Structural analysis results showed a reduced binding affinity for the mutants, which was supported by their weaker hydrogen-bond interaction compared to the wild-type. Our findings showed that the G140A+Q148R double mutant had the strongest effect on the HIV-1C protein structure and binding of EVG and RAL with binding free energies of -12.49 and -11.45 kcal/mol for EVG and RAL, respectively, which are approximately three times lower than the wild-type binding energy. Biochemical assays performed with purified integrase showed a decrease in integrase-LTR binding for all mutants. The 3’ processing activity was slightly decreased in the mutants compared to the wild-type protein; however, no appreciable differences were observed across the mutant isolates. Conclusions Changes near the highly conserved active site residues in HIV-1C integrase core domain and mutations in the 140’s loop have a negative effect on in vitro integrase activity, suggesting that these changes impact viral integration. While they are still few reports of INSTI resistance-associated mutations (RAMs) in South Africa , identification of the G140A+Q148R double mutant for the first time in South African HIV-1 clinical samples, and the identification of S119T and V151I in INSTI-treated patients warrants further investigation. This data broadens the understanding of HIV-1C resistance against INSTIs and adds to the available knowledge of drug resistance mutations that guide therapeutic decisions.
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    Biochemical characterization of highly mutated South African HIV-1 subtype C protease.
    (2021) Eche, Simeon.; Gordon, Michelle Lucille.
    Understanding the underlying molecular mechanism of HIV-1 protease (PR) inhibition by HIV-1 protease inhibitors (PIs) is essential to gain mechanistic insight into the evolution of resistance to HIV-1 PIs. HIV-1 PIs have improved patient care management, but the accumulation of drug resistance mutations in the HIV-1 PR gene diminishes their inhibitory capacity. The current study investigated the kinetic and structural characteristics of highly mutated South African HIV-1 subtype C PR from clinical isolates obtained from individuals failing a lopinavir (LPV) inclusive regimen at the point of switch to darunavir (DRV) based therapy. In this study, enzyme activity and inhibition assays were used to determine the biochemical fitness of HIV-1 PR variants and the inhibitory constants of HIV-1 PIs for drug-resistant HIV-1 subtype C proteases. The mechanistic insight into the impact of the accumulated drug resistance mutations on the HIV-1 PR structure and its interaction with LPV and DRV was obtained using fluorescence spectroscopy and molecular dynamic simulation. The study showed that the unfavorable binding landscape caused by the accumulation of drug-resistance mutations resulting from LPV associated drug pressure would shape the outcome of DRV-based therapy after a switch in the treatment regimen. This is related to the distortion of the HIV-1 PR structure associated with increased solvent exposure and instability of the HIV-1 PR dimer caused by these mutations leading to a shorter lifetime of the enzyme-inhibitor complex. Analysis of the binding kinetics of LPV and DRV with the HIV-1 PR variants showed that the drug resistance mutations caused an imbalance between the association and dissociation rate constants favoring a fast dissociation rate. The latter resulted in a reduced inhibitor residence time. Our findings showed that LPV had a longer residence time than DRV when bound to the HIV-1 PR variants; this shows LPV can be a suitable platform for developing newer HIV-1 PIs with a longer residence time. However, the enzyme inhibition mechanism shows both LPV and DRV act via a two-step tight-binding mixed inhibition mechanism, suggesting the existence of a second binding site on HIV-1 PR for these inhibitors. The information provided in this thesis adds to existing knowledge about HIV-1 PI drug resistance and for the design of novel HIV-1 PIs with the potential to evade drug resistance mutations.
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    Prevention of HIV-1 acquisition and determinants of disease progression.
    (2021) Moyano De Las Muelas, Ana.; Mann, Jaclyn Kelly.; Sigal, Alexander.; Ndung'u, Peter Thumbi.
    Introduction HIV-1 infection can be managed using multiple strategies, including preventative approaches and therapeutic approaches. Current preventative and treatment strategies are suboptimal and there is a need to develop an effective prophylactic or therapeutic vaccine and to improve the public health approaches against the virus. This requires more detailed understanding of the infection, from prevention to natural disease progression. We performed several studies that cover a range of infection attributes, from understanding the mechanism of action of pre-exposure prophylaxis (PrEP) and determining the effectiveness of different compounds in blocking initial infection, to gaining further insight into potential mechanisms of natural control of HIV-1 disease progression in viraemic controllers (VC) with (VC+) and without (VC-) protective class I human leukocyte antigen (HLA-I) alleles. In order to cover this range of infection attributes we investigated two hypotheses: (i) initial low dose infection can be cleared with suboptimal drug inhibition, which allows ongoing viral replication, as long as the drug mechanism acts before the first cell is infected; and (ii) individuals without protective HLA-I alleles have CD8+ T cell-independent mechanisms of control. Methods To understand the mechanism of action of PrEP, the probability of extinction of new infections in the presence of two drug mechanisms (interference of initial infection with tenofovir (TFV), or reduction of burst size with atazanavir (ATV)), or with no drug, was modelled as a function of initial infected cells and viral replication ratio. The fraction of extinguished infections was experimentally determined with low viral input in the presence of either drug, or with no drug, in an in vitro model of PrEP. To gain insight into potential mechanisms of control, we studied immune cells in 12 VC+ and 9 VC- and, compared these 21 controllers with 5 rapid progressors (RP). Measurements included the magnitude and breadth of CTL responses using the ELISpot assay, as well as flow cytometry-based characterization of NK cell and T cell populations, which included the measurement of surface markers for activation, maturation, and exhaustion on these populations. Further, NK cell function was measured by intracellular cytokine staining following stimulation of these cells. Results Our study showed that TFV dramatically increased clearance while ATV did not, both for our mathematical model and our experimental study. We observed that both VC, in particular VC-, had a higher contribution of Gag CTL responses to the total CTL response than RP (p=0.04), however there was no significant difference in the magnitude and breadth of CTL responses between VC+ and VC-. In addition, VC- NK cells had higher levels of the activation markers HLA-DR (p=0.007) and co-expression of CD38 and HLA-DR (p=0.03) when compared to VC+ and uninfected individuals (UI), and lower cytokine expression (MIP-1β and TNF-α) than VC+ NK cells (p=0.05 and p=0.04, respectively). We found a negative correlation between the expression of MIP-1β and the co-expression of CD38 and HLA-DR (r =-0.45, p=0.05). Furthermore, VC- T cells had higher levels of CD38 and HLA-DR co-expression (p=0.05), and a trend of higher HLA-DR (p=0.07) as well as CD57 expression (p=0.09) when compared to VC+. Conclusions The ability of drugs to clear initial but not established infection depends only on the ability to target initial infection. This implies that in diseases which involve transmission of low pathogen numbers upon exposure, but have robust replication when established, such as HIV-1, a possibility to clear infection should exist even with relatively weak inhibition as long as the drug has the mechanism of targeting the initial infection. This finding is particularly relevant in scenarios of variable adherence that result in sub-optimal drug levels or possible future PrEP strategies with drugs that have long half-lives yet do not completely suppress viral replication. VC have a more Gag focused CTL response than RP, however this feature did not distinguish VC+ from VC-. NK and T cell profiles differ between VC+ and VC-. VC- have a more activated NK cell profile with lower cytokine expression, and a more active and terminally differentiated T cell profile than VC+. A possible explanation for our results is that the increased CD38+HLA-DR+ NK cells in VC- may represent NK cells acting as antigen presenting cells (APCs), which may then directly interact with a more activated and terminally differentiated population of T cells observed in VC-. Further work to test this hypothesis is necessary to better understand the mechanisms underlying control in these two groups of VC patients. It is also suggested that transcriptomic studies may contribute further to understanding the distinct NK and T cell profiles observed between VC+ and VC- and how these may result in differing mechanisms of control.
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    The impact of antiretroviral therapy and Immunological factors on preterm and small for gestational age deliveries in HIV infected pregnant women.
    (2020) Mdletshe, Nontlantla Cecilia.; Ndung'u, Peter Thumbi.; Tshabalala, Christina Thobakgale.
    Introduction Antiretroviral therapy (ART) during pregnancy may be associated with an increased risk of adverse pregnancy outcomes, including preterm delivery (PTD) and small-for-gestational-age (SGA) but the underlying biological mechanisms remain unclear. Immune activation as well as the use of ART have been associated with adverse outcomes during pregnancy. We explored the association between adaptive and innate immune cell activation markers ex vivo in HIV-infected women initiating ART during or before pregnancy with PTD or SGA. Materials and methods Study participants were women living with HIV drawn from the PIMS cohort, based in Cape Town South Africa and initiated ART during pregnancy or conceived while on ART. Participants were enrolled at median 15 week’s gestation; and were analyzed for immune markers, matched on ART initiation timing (15 women initiated pre- and 15 during pregnancy). There were 30 PTD (delivery <37 weeks), 30 SGA (weight for age ≤10th centile) cases and 30 controls (term, weight for gestational age >25th centile) as outcomes. Immunological parameters were compared T cell activation, antigen presenting cell subsets, activation and function, regulatory T cell phenotypes and functions and plasma cytokine profiles. Results We found that CD8+ T cell, monocyte and dendritic cell activation were lower in PTD women initiating ART in pregnancy when compared to SGA cases and AGA controls over time. Classical (CD14+CD16-) and intermediate (CD14+CD16+) monocyte frequencies were higher in PTD than in SGA cases and AGA women initiating ART in pregnancy compared to those stable on ART. There was lower inflammatory monocyte (CD14dimCD16+) frequencies over time. Monocytes and mDCs but not pDCs showed higher levels of activation in patients initiating ART compared to those stable on ART. A lower activation of APCs (monocytes, mDCs and pDCs) was associated with the PTD outcome. When APCs were stimulated with TLR ligands, a lower IFN-α production by monocytes following TLR4 was associated with PTD. A similar trend was also observed for TLR9 and TLR7/8 stimulation at some time points. Some plasma cytokine levels were higher in participants initiating treatment in pregnancy compared to those stable on ART but there was no link of cytokine levels with birth outcomes. Regulatory T cell frequencies did not differ between ART initiators and those stable on ART, did not change over the course of pregnancy and were not associated with pregnancy outcomes. Conclusion Overall, we noted that lower levels of monocyte activation and reduced functionality (IFN-α production) of monocytes in response to TLR stimulation were associated with PTD. A similar trend of reduced production of MIP-1β and TNF-α by monocytes was noted for PTD cases. This suggests that reduced responsiveness to antigen stimulation may be an underlying factor for PTD, especially for women initiating ART in pregnancy. The markers of immune activation described here may be potential biomarkers to identify women at risk for PTD. Our results also suggest that PTD and SGA have distinct underlying immunological determinants that warrant further investigation.
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    HIV cell-to-cell spread leads to a differential transcriptional response and slows evolution of drug resistance relative to cell-free infection.
    (2020) Hunter, Jessica Rose.; Sigal, Alexander.
    HIV transmits between hosts but also transmits between cells in the same host. How this latter, cellular transmission occurs has been the subject of extensive study. Yet why HIV transmits between cells using two different infection modes: cell-to-cell spread and cell-free infection, is not clearly understood. This is because cell-to-cell spread is a more efficient mode of infection, where the virus is able to be successfully transmitted between cells despite natural inhibitors such as antibodies. Here, using in vitro experimentation, I have determined some of the implications of cell-to-cell spread of HIV for cell death, evolution, and inflammation. I have discovered potential costs to this infection mode, such as increased cell death, slowed evolution of resistance, and an increased interferon response which may interfere with viral replication. Hence, costs associated with cell-to-cell spread may prevent it being the dominant infection mode in cellular transmission.
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    Mucosal-associated invariant T (MAIT) cell heterogeneity in peripheral blood and bronchoalveolar compartment: implications for TB and HIV immunity.
    (2020) Khuzwayo, Sharon Jabu.; Ndung'u, Peter Thumbi.; Wong, Emily.
    Tuberculosis (TB) is the leading cause of infectious mortality globally and the leading cause of death in people living with human immunodeficiency virus (HIV). Understanding the mechanisms leading to impaired anti-TB immunity at mucosal sites and how this is altered during HIV infection, may assist in the development of more effective TB vaccines or immune-based therapies. Mucosalassociated invariant T (MAIT) cells are depleted and dysfunctional in the peripheral blood during HIV infection, but little is known about HIV’s impact on their quantity and quality at the lung’s mucosal surface, the site of TB infection. We aimed to characterise phenotypic, functional and transcriptomic features of MAIT cells in the peripheral blood and lung mucosa of people with latent Mycobacterium tuberculosis (Mtb) infection and HIV co-infection. Matched peripheral blood and bronchoalveolar lavage fluid were collected from consenting participants with confirmed latent TB infection, either with or without HIV. Characterisation of MHC class I-related protein 1 (MR1) 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU) tetramer-positive T cells from the lung was performed by cloning, immunophenotyping, functional assays and T cell receptor sequencing. The phenotype, function and transcriptome of MAIT cells from both compartments were characterised by surface marker staining, intracellular cytokine staining, as well as single-cell and bulk RNA-sequencing of MR1 5-OP-RU tetramer-positive T cells from HIVnegative and HIV-positive individuals. Peripheral blood MAIT cells were characterised by the CD161++CD26++ phenotype and produced more interferon (IFN)-γ (P = 0.016) than bronchoalveolar MAIT cells in HIV-negative individuals. Bronchoalveolar MR1 5-OP-RU tetramer-positive cells, included subpopulations with the atypical CD161-CD26++ and CD161-CD26- phenotypes. T cell cloning demonstrated that cells from the typical and atypical CD161/CD26 phenotypic subpopulations all had MR1-restricted function and MAIT cell consistent T cell receptors. In HIV infection, the frequency of both peripheral blood and bronchoalveolar MAIT cells was reduced (P = 0.035 and P = 0.047 respectively), with peripheral blood MAIT cells producing less interleukin (IL)-17 (P = 0.025) and expressing higher levels of the inhibitory co-stimulatory molecule T cell immunoglobulin and mucin domain-containing protein (TIM)-3. Interestingly, the phenotype and function of bronchoalveolar MAIT cells remained relatively unchanged by HIV. Single-cell transcriptional analysis confirmed MAIT cell heterogeneity in the bronchoalveolar compartment which contained two distinct transcriptional subsets, one associated with typical MAIT cell features and effector functions and the other associated with alternative MAIT cell functions including tissue-repair. We report previously undocumented phenotypic and transcriptional heterogeneity in bronchoalveolar MAIT cells, which were also less pro-inflammatory than those in peripheral blood. HIV infection led to depletion of MAIT cells in both compartments, but phenotypic and functional alterations were more pronounced in the peripheral blood compartment. The preservation of function and heterogeneity in bronchoalveolar MAIT cells may represent a potential avenue for therapeutic targeting to restore normal MAIT cell function in people living with HIV. This data suggests that understanding immune responses requires compartment-specific analyses, which may lead to the development of more effective vaccines and immunotherapies targeted at inducing immune responses at the site of infection.
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    Pharmacokinetic influences of selected phytochemical compounds from herbal medicine used by HIV- positive patients on drugs-metabolising proteins of HIV-1 protease inhibitor drugs.
    (2020) Idowu, Kehinde Ademola.; Gordon, Michelle Lucille.; Nlooto, Manimbulu.
    Introduction: Sub-Saharan Africa has the highest incidence of HIV/AIDS and AIDS-related deaths in the world. Although there is currently no cure for the disease, significant progress has been made in developing antiretroviral drugs (ARVs) that can inhibit disease progression. However, despite the availability of these ARVs, HIV-positive patients use traditional herbal medicines (THMs) either alone or simultaneously with conventional ARVs. This simultaneous usage may cause serious adverse effects due to herb-drug interactions, although there are also possible positive effects such as the enhanced bioavailability of the ARVs or possible antiviral activity. Aim: These potential interactions prompted this study which examined the pharmacokinetic properties and influences of selected phytochemical compounds (PCs) commonly found in THMs on drug-metabolising proteins involved in the metabolism of protease inhibitor drugs (PIs) as well as their potential as inhibitors of HIV-1 protease. Method: The potential inhibitory activities of fifteen PCs (Epigallocatechin gallate (EGCG), Fisetin (FST), Ellagic acid (EGA), Cholesta-4,6-dien-3-ol (CHD), Lanosteol (LNT), Benzyl Isothiocyanate (BIT), Gallic acid, (GA), Isosteviol (IST), Stigmasterol (STG), Phthalic acid (PTA), Naringenin (NGN), Kaempferol-7-glucoside (K7G), Luteolin (LUT), Geranin (GER), Apigenin (APG)) against the South African sub-type C HIV-1 protease enzyme and PIs’ drug-metabolizing proteins were investigated, using molecular dynamic (in-silico) techniques. Furthermore, an in vitro evaluation of the cytotoxicity assays, cell viability profiles and modulatory influences of the most promising antiviral PCs on the mRNA and protein expressions of the drug-metabolising proteins in two human cell lines (liver (HepG2) and kidney (HEK293)) was carried out. Result: Four of the fifteen PCs (EGCG, K7G, LUT and EGA) were predicted to be potential inhibitors of HIV-1 protease, as well as inhibitors of cytochrome P450 3A4 (CYP3A4) and Pglycoprotein P-gp/ABCB1. Results from the in vitro study showed that these four PCs were not toxic to HepG2 cells at their IC50 (50% cell viability) and IC20 (80% cell viability). ATP (adenosine triphosphate) levels increased at IC20, with no significant change at IC50. In addition, no significant change in LDH (lactate dehydrogenase) was seen (with the exception of LUT).In the HepG2 cells, ABCB1 protein expression (western blot) decreased overall. While all PCs decreased CYP3A4 protein expression at IC20, (with the exception of LUT) xxv protein expression increased at IC50. mRNA levels were decreased for EGCG and K7G at IC20. InHEK293 cells, all PCs were non-toxic. ATP concentrations were similar to the control except for EGCG which decreased at IC20, and K7G which increased at IC50. LDH concentration decreased when exposed to the PCs at IC20, but a significant (p < 0.05) increase was recorded in LUT IC50. ABCB1 protein expression increased at both IC20 and IC50 concentrations, although LUT and EGA mRNA expression decreased at IC50. The decreased protein activities of CYP3A4 in K7G IC50 and LUT IC20 correlates with increased intracellular ATP. Conclusion: The study therefore suggests that EGCG, K7G, LUT and EGA could decrease the biotransformation of drugs, and eventually increase drug plasma concentrations in the systemic circulation. These natural compounds that can serve as inhibitors of drugmetabolizing proteins and the HIV-1 protease enzymecould be useful in the treatment of HIV-1.
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    In vitro modelling of the impact of anti-inflammatory drugs on cellular cytotoxicity, activation and inflammation.
    (2020) Cromarty, Ross Thomas.; Archary, Derseree.
    The relationship between inflammation and HIV has been a major focus of HIV research. In people living with HIV (PLWH), HIV-associated immune activation drives HIV disease progression. While genital inflammation has been significantly associated with increased risk for HIV acquisition and transmission, immune correlates for reduced HIV risk remain less well defined. In HIV-exposed seronegative individuals, the immune quiescent phenotype, characterised by regulated immune activation and inflammation, has been implicated in reducing HIV acquisition risk. Targeted management of inflammation, therefore, is a plausible strategy to mitigate the risk of HIV infection, and to slow HIV disease progression. Therefore, we sought to investigate how anti-inflammatory drugs affect TLR-mediated inflammation and impact HIV infection of CD4+ T cells. This study utilized an in vitro peripheral blood mononuclear cell (PBMC) model. PBMCs were either treated with the anti12 inflammatory drugs ibuprofen (IBF) or betamethasone (BMS) or were left untreated. Thereafter they were either left unstimulated or were stimulated with phytohaemagglutinin (PHA) or Toll-like receptor (TLR) agonists Pam3CSK4 (TLR1/2), LPS (TLR4) or R848 (TLR7/8) before exposure to HIV NL4-3 AD8. To assess inflammation, multiplexed ELISA was used to measure 28 proinflammatory, chemotactic, growth-related, adaptive response-related or regulatory cytokines. Flow cytometry was used to measure activation (CD38, HLA-DR and CCR5) and HIV infection (p24 production) of CD4+ T cells. Despite minimal immune activation, TLR stimulation elicited significant cytokine responses (p<0.05). TLR4 stimulation significantly reduced HIV infection of CD4+ T cells (p<0.01). With the addition of IBF, minimal immunosuppressive effects were observed. In contrast, BMS significantly dampened inflammation (p<0.05) and immune activation (p<0.05) regardless of the stimulation condition. Regardless of global immunosuppression, only with TLR4 stimulation did BMS significantly reduce HIV infection of CD4+ T cells (p=0.02). The finding that TLR4 stimulation reduces rather than increases susceptibility of CD4+ T cells to HIV infection, while BMS only affected HIV infection in the TLR4 condition, strongly suggests that additional factors, and not only inflammation play a powerful, although complex, role in determining HIV infection risk. Together, these data emphasize the importance of understanding signalling pathways induced during inflammation to identify novel targets to mitigate HIV infection.
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    Gag-protease driven viral replication capacity among HIV-1 subtypes: Implications for disease progression, epidemic spread and vaccine design.
    (2020) Farinre, Omotayo Oluwaremilekun.; Ndung'u, Peter Thumbi.; Mann, Jaclyn Kelly.
    The HIV-1 epidemic in sub-Saharan Africa is heterogeneous with diverse unevenly distributed subtypes and regional differences in prevalence. Subtype-specific differences in disease progression rate and transmission efficiency have been reported, but the underlying biological mechanisms have not been fully characterized. In this study, I tested the hypothesis that the subtypes prevalent in the East African epidemic, where adult prevalence rate is higher, have lower viral replication capacity (VRC) than their West African counterparts where adult prevalence rates are lower. Materials and methods: Gag-protease sequencing was performed on plasma samples from 213 and 160 antiretroviralnaïve participants from West and East Africa, respectively. Online bioinformatic tools were used to infer HIV-1 subtypes and recombination patterns. Replication capacities of patientderived gag-protease chimeric viruses from West (n=178) and East (n=114) Africa were determined using a green fluorescent protein reporter-based cell assay. Subtype and regional differences in viral replication capacity and amino acid variants impacting replication capacity were identified using appropriate statistical methods. Results: Subtypes identified in West Africa were CRF02_AG (65%, n=139), G (7%, n=15), A3 (5%, n=10), other CRFs (12%, n=26), various pure subtypes (9%, n=19) and A1G recombinants (2%, n=4). Subtypes A1 (64%, n=103), D (22%, n=35), AD (11%, n=17) and AC (3%, n=5) were identified in East Africa. Chimeric viruses from West Africa had significantly higher VRC compared to those from East Africa (p < 0.0001), with subtype-specific differences found among strains within West and East Africa (p < 0.0001). Recombination patterns showed a preference for subtypes D, G or J rather than subtype A in the p6 region of gag, with evidence that subtype-specific differences in this region impact viral replication capacity. Furthermore, the Gag A83V polymorphism was associated with reduced viral replication capacity in CRF02_AG (median < 0.86). HLA-A*23:01 (p = 0.0014) and HLA-C*07:01 (p = 0.002) were associated with significantly lower viral replication capacity in subtype A infected individuals from East Africa. Conclusion: Overall, the data showed that viruses from West Africa displayed higher replication capacity than those from East Africa, which is consistent with the hypothesis that lower viral replication capacity is associated with higher population prevalence.
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    The HIV-1 gag and protease: exploring the coevolving nature and structural implications of complex drug resistance mutational patterns in subtype C.
    (2019) Marie, Veronna.; Gordon, Michelle Lucille.
    Due to the high prevalence of HIV-1 subtype C infection coupled with increasing antiretroviral (ARV) drug treatment failure, the elucidation of complex resistance mutational patterns arsing through protein coevolution is required. Despite the inclusion of LPV and DRV in second- and third-line, many patients still fail treatment. In this study, protease (PR) inhibitor resistance mutations were identified by comparing treatment versus naïve sequences datasets in Gag and PR. Thereafter, to investigate Gag-PR coevolution and pathways to LPV resistance, phylogenetic analyses and Bayesian networks were constructed. Following this, structural analyses combining homology modelling, molecular docking and molecular dynamic simulations were carried out on specific patterns of protease resistance mutations (PRMs). To complement these analyses, the structural impact of a mutated Gag cleavage site on PR resistance dynamics was also evaluated. Accordingly, this study identified 12 major PRMs and several resistance combinations. Of these, the M46I+I54V+V82A pattern frequently occurred. The second most frequently recurring pattern included L76V as a fourth mutation to the above triplet. Coevolution analyses revealed correlations between positions 10, 46, 54 and 82 in PR. Of these, minor PRM L10F occurred in 6.4% of the dataset and was involved in pathways to LPV resistance. Additionally, Gag cleavage site (CS) mutation A431V was also correlated with L10F and the major PRMs. Distinct changes in PR’s active site, flap and elbow regions due to the PRMs (L10F, M46I, I54V, L76V, V82A) were found to alter LPV and DRV drug binding. When the PRMs were combined with the mutant Gag CS binding was greatly exacerbated. While the A431V Gag CS mutation coordinated several amino acid residues in PR, the L76V mutation was found to have a significant role in substrate recognition rather than directly inhibiting the drugs. These data show that the co-selection of mutations in Gag-PR greatly contributes to resistance outcomes and that our understanding on drug resistance is largely lacking, particularly where structure is concerned.
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    Phenotypic effects and predictions of HIV-1 subtype C reverse transcriptase C-terminal domain mutations on reverse transcriptase inhibitors.
    (2018) Mkhwanazi, Nompumelelo Prudence.; Gordon, Michelle Lucille.
    Antiretroviral drug therapy has been shown to reduce the death of HIV-1 infected individuals. However, the emergence of HIV-1 drug resistance has hindered the success of HIV-1 treatment. Genotyping tests mainly concentrate on the polymerase domain of HIV-1 RT leaving the rest understudied. Recently, data from HIV-1 C suggested that drug resistance could be caused by mutations in the connection and RNase H domains either alone or in combination with mutations in the polymerase region. Here, the phenotypic effects of the specific RNase H domain mutations in HIV-1 subtype C on RTIs were investigated. The predictions of HIV-1 subtype C reverse transcriptase C-terminal domain mutations on reverse transcriptase inhibitors were also investigated. Material and methods Viral RNA was extracted from 500μl of plasma using the Viral RNA extraction kit (Qiagen,Germany) according to the manafacturer’s instructions, and stored at -80oC until utilisation. The RNA was amplified using the Superscript III One-step RT-PCR system with Platinum Taq DNA polymerase (Invitrogen, Life Technologies Corporation, Carlsbad, CA, California). The HIV-1 RT amplicon was cloned into a TOPO vector using the TOPO TA cloning kit (Invitrogen, Life Technologies). Viral mutants were constructed using site-directed mutagenesis, introducing D67N in the polymerase domain and E529D, L517I, T470S, and T470P mutations in the RNase H domain. Viral replication capacity and drug susceptibilities were determined using the single cycle luciferase assay in TZM-bl cells. To identify the HIV-1 connection domain (CN) mutations associated with drug resistance, HIV-1 subtype C sequences were downloaded from the Los Alamos and Stanford HIV- drug resistance xvi databases from drug naïve and treated-experienced patients. The presence of connection domain (CN) mutations were identified using REGA HIV-1 subtyping tools (Universiteit Leuven, Belgium). Bayesian Network (BN) analysis (B-course) was used to determine the association of connection domain (CN) mutations (condon 320-440) with other TAMS. The effect of RNase H domain mutations on the structure of reverse transcriptase was determined using Swiss Model and viewed in Chimera. Results The replication capacities of T470S, T470P, L517I, E529D RNase H domain mutations were lower than the HIV-1 subtype C wild type in the absence of drugs. The D67N mutation alone had a lower replication capacity compared with the wild-type. Combination of L517I and D67N showed a further decrease in replication capacity compared to the wild type in the absence of drugs. E529D mutation replication capacity was assessed in TZM-bl cell line in both HIV-1 subtype B and C. Although not statistically significant, both competent subtype B and C E529D mutant had a decreased growth and infectivity rate compared to their respective wildtypes. The RNase H domain mutation T470S showed a moderate level of resistance to NVP (10.2X), ETR (8.75X), d4T (5X) and no resistance to AZT and EFV. Interestingly, T470P showed a moderate level of resistance to NVP (6X) and no resistance to ETR and d4T, as well as EFV. It did however show a 5-fold change to AZT when compared to the wild-type virus. As expected, the thymidine analog mutation, D67N, showed a high level of resistance to AZT (103.3X), moderate level of resistance to d4T (6.2X) and low level of resistance to ETR (3.2X) and no resistance to NVP and EFV. The RNase H domain L517I mutation showed moderate level of resistance to AZT (5.2X), d4T (6.0X) and NVP (10.79X), and low level of resistance to ETR (3.50X). L517I mutation caused hypersusceptibility to EFV. The combination of RNase H and TAM (L517I+D67N) showed high xvii level of resistance to AZT (157.3X), moderate level of resistance to NVP (11.3X), low level of resistance to d4T (3.9X) and no resistance to ETR and EFV. Subtype C E529D mutation conferred up to 2-fold stavudine (d4T), 3-fold zidovudine (AZT) and nevirapine (NVP) resistance, respectively. These findings demonstrate that RNase H mutation E529D can confer mild resistance to nucleotide (AZT and d4T) and non-nucleotide (NVP) reverse transcriptase inhibitors. New connection domain mutations identified were: D324G/N/P, T338S, I341F/L/V, M357R, E370D, M377T/L, A376S, I434M/L, A437V/I. E370D and A437V/I were directly associated with treatment in the BN, while N348I was only indirectly associated with treatment. Discussion and Conclusions Overall, the RNase H domain mutations impaired replication capacity in the absence of drugs, suggesting that they are acquired at a fitness cost (as withmost drug resistance mutations). While T470S decreased drug susceptibility to ETR, it was shown to be hypersusceptible to EFV. Interestingly, T470S is very common in subtype C RTI treated patients and could indicate that a switch to the newer NNRTI might not be as beneficial as expected. The phenotypic data also suggests that the resistance pathways for T470S and T470P could be different; however further studies are required to investigate their mechanism of resistance. The L517I mutation alone only minimally decreased drug susceptibility to both NRTI and NNRTIs. However it futher decreased drug susceptibility to the NRTIs when in combination with D67N, compared to D67N alone. D67N is known to affect the NRTIs, and the combined effect of D67N and L517I on NVP, a NNRTI, was surprising. The decreased replication capacity in the L517I indicated that it has additive effect in fitness loss of the viral. Further site-directed mutagenesis studies are needed to understand the effect of these RNase H mutations alone and in xviii combination with other polymerase domain mutations or with connection domain mutations on nucleoside reverse transcriptase inhibitors. Structural analysis showed that the T470S/P mutations cause an inward movement of the RNase H active site amino acids residues, which may have an affect on RNase H activity. There was no interaction between L517I and E529D with the RNase H active site amino acid residues observed. The observed interaction was between the amino acids that form part of the RNase H primer grip and these RNase H mutations. New HIV-1 subtype C connection domain mutations were identified and phenotypic studies are required to investigate their role in HIV-1 drug resistance. In conclusion, this is the first study to show that T470S/P, L517I and E529D in HIV-1 subtype C affect NNRTI drug susceptibility. This provides further support for the monitoring of C-terminal domain mutations in relation to NNRTI, as well as NRTI drug resistance. In addition, these mutations need to be taken into account when designing newer NNRTI with the ability to retain activity against these mutants.
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    Genotypic and phenotypic characterization of HIV-1 from cerebrospinal fluid and blood compartments in patients with cryptococcal meningitis.
    (2017) Sojane, Katlego.; Ndung'u, Peter Thumbi.
    The combination of HIV and cryptococcal meningitis (CM) is a major cause of morbidity and mortality in sub-Saharan Africa. The phylogenetic relatedness of HIV-1 subtype C (HIV-1C) variants in peripheral blood and the central nervous system (CNS) compartments of individuals with CM is unknown. Additionally, the major and alternative coreceptor usage of HIV-1C in those compartments are not clear and these have implications for the pathogenesis of the virus, and the use of coreceptor blocking therapies. For genotypic studies, 16 antiretroviral therapy naïve individuals with CM were randomly selected. We conducted single-genome, or bulk PCR amplification and sequencing of full-length HIV-1 env genes from plasma and/or cerebrospinal fluid (CSF) of the participants. Additionally, we estimated the prevalence of CXCR4-using variants in our cohort using coreceptor usage prediction algorithms (CPAs). Next, we evaluated the usage of CCR3, CCR5 and CXCR4 expressed on NP2/U87-CD4 cells by HIV-1C Envs derived from the plasma and/or CSF of 14 of the 16 participants. CCR3 alone, or in combination with the other receptors. Overall, our results have improved the understanding of HIV-1C pathogenesis in the peripheral blood and CNS compartments of individuals with end-stage infection and CM, and provides clinically relevant information for therapies including coreceptor antagonists in this setting.
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    Acquired and transmitted drug resistance in HIV-1 subtype C : implications of novel mutations on replication capacity, cleavage and drug susceptibility.
    (2015) Singh, Urisha.; Gordon, Michelle Lucille.
    Introduction Large scale roll-out of combination antiretroviral therapy (cART) has been successful in improving the quality of life of HIV-1 infected individuals in South Africa (SA). However the development and transmission of drug resistance threatens the future success and longevity of cART in the country. Studies have shown that resistance to Protease inhibitors (PI’s), in the absence of mutations in Protease (PR), is increasing in SA. Whilst some studies attribute this to poor treatment adherence, others have shown that mutations in Gag contribute to PI resistance. The majority of these studies however have been conducted on HIV-1 subtype B, despite HIV-1 subtype C being the most prevalent subtype globally. Given that Gag is highly polymorphic between subtypes, studies focusing on HIV-1 subtype C are required. Despite the high rate of virologic failure of patients on PI inclusive treatment regimens, no transmitted drug resistance (TDR) studies have identified PI associated TDR mutations. This could be due to the high fitness cost associated with PR mutations which would result in rapid reversion or low frequency of mutations within the viral quasispecies. Most TDR studies in SA, as in other resource limited settings, have used recently infected cohorts to measure TDR. It is however unlikely that rapidly reverting mutations would be detected in recent infection. Furthermore, these studies have all used Sanger sequencing which only detects mutations at frequencies >15-20%. With recent studies showing that low frequency mutations present at frequencies as low as 1% impact treatment outcomes, the elucidation of these mutations using deep-sequencing techniques is necessary. For a true measure of TDR, studies employing acute infection cohorts and deep-sequencing techniques are required. The current study aimed to identify mutations in Gag-Protease associated with PI resistance/exposure, and to determine their impact on replication capacity and drug susceptibility. The prevalence of low frequency TDR mutations in an HIV-1 subtype C acute infection cohort was also investigated. Methods A cohort of 80 HIV-1 subtype C infected participants failing a PI inclusive treatment regimen (i.e. PCS cohort) from 2009–2013 in Durban, South Africa was used to assess the role of Gag in PI resistance. Gag mutations were divided into three groups: PI exposure associated Gag mutations; resistance associated Gag mutations (rGag) and novel Gag mutations (nGag). Frequencies of each of these mutations were compared amongst: 80 PCS cohort sequences, 2,481 HIV-1 subtype B treatment naïve sequences, 954 HIV-1 subtype C treatment naïve sequences and 54 HIV-1 subtype C sequences from acutely infected individuals, in order to identify PI associated mutations and natural polymorphisms. Next, recombinant viruses for all 80 participants were generated by co-transfection of a CEM derived T-cell line (i.e. GXR cells) with an NL43-deleted-gag-protease (NL43Δgag-protease) backbone and patient derived Gag-Protease amplicons. Thereafter, the replication capacity of each virus was assessed using a replication assay that employed a green fluorescent protein reporter cell line and flow cytometry. Associations between replication capacity and Gag-Protease mutations were established. Eighteen viruses with mutations of interest were then selected for use in drug susceptibility assays, where the impact of mutations on susceptibility to lopinavir (LPV) and darunavir (DRV) was assessed in a luciferase based assay. Lastly, the impact of novel Gag mutations on replication capacity and drug susceptibility was validated by generating site-directed mutant viruses with mutations of interest and using these mutant viruses in replication capacity and drug susceptibility assays. Furthermore the cleavage profile of each site-directed mutant virus was established by western blotting. Samples available from 47 HIV-1 subtype C acutely infected individuals collected from 2007-2014 in Durban, South Africa, was used to assess low frequency TDR mutations in HIV-1 subtype C acute infection. Firstly the RT and PR region of each virus was genotyped using the Viroseq HIV-1 genotyping system in order to identify the prevalence of TDR in the cohort. Thereafter 14 participant samples were selected, based on the availability of plasma at one week after onset of plasma viremia (OPV), for sequencing by ultra-deep pyrosequencing (UDPS). This served to identify low frequency mutations. Comparisons in TDR prevalence was made between Sanger sequencing and UDPS. Thereafter, the impact of low frequency TDR mutations on treatment outcomes was assessed by comparing time to virologic suppression for two participants with low frequency mutations to that of four participants without low frequency mutations. Results Protease resistance associated mutations (RAMs) occurred in 34/80 (42.5%) participants, whilst Gag mutations associated with PI resistance in subtype B were detected in 67/80 (84%) participants. Overall, 12 Gag mutations associated with PI exposure (i.e. E12K, V35I, G62R, V370A/M, S373P/Q/T, A374P, T375N, I376V, G381S, I389T, I401T and H219Q), eight rGag mutations (i.e. R76K, Y79F, V128I, A431V, K436R, L449F, R452K and P453L) and four nGag mutations (i.e. Q69K, S111C/I, T239A/S and I256V) were identified in the PCS cohort. The E12K, V370A/M, T375N, G381S, R76K and Y79F mutations all occurred as natural polymorphism in HIV-1 subtype C. The A431V, K436R, L449F, R452K, P453L, Q69K, S111C/I, T239A/S and I256V mutations were all associated with PI resistance/exposure. Interestingly all viruses with PR RAMs harboured rGag and nGag mutations, however rGag and nGag mutations were also found to occur without PR RAMs. Protease RAMs were associated with significantly reduced replication capacity. The K335R and A431V mutations were the only Gag mutations associated with significantly reduced replication capacity. Viruses with PR RAMs were associated with significantly reduced susceptibility to LPV (>15 FC in IC50) and DRV (>6 FC in IC50). Furthermore, the following combinations of rGag and nGag mutations were found to confer reduced susceptibility to LPV and DRV in the absence of PR RAMs: R76K+Y79F+K436R+L449P+I256V (5.2 fold increase in IC50 for DRV), R76K+R453L (23.88 fold increase in IC50 for LPV and a 6.73 fold increase in IC50 for DRV) and R76K+K436R+Q69K+S111C (7.40 fold increase in IC50 for LPV). Analysis of recombinant viruses showed that the Q69K nGag mutation rescued replication capacity of all viruses harbouring A431V+PR RAMs. This was validated by SDM, where Q69K rescued the replication capacity of site-directed mutant viruses harbouring A431V+V82A. The Q69K mutation was also associated with increasing polyprotein cleavage when found in conjunction with A431V+V82A. With regards to TDR, we demonstrated a prevalence of 57% of TDR mutations with UDPS and 2.2% with Sanger sequencing. Sanger sequencing identified the K103N non-nucleoside reverse transcriptase inhibitor (NNRTI)-associated TDR mutation. In addition to K103N (frequency: >99%), the following low frequency mutations were detected by UDPS: the K65R (1-1.5%) and D67N (3.88%) nucleotide reverse transcriptase inhibitor (NRTI)-associated TDR mutations, the F53L (17.6%) and M46L (6.3%) Protease inhibitor (PI)-associated TDR mutations, and the T97A (2.90%) integrase strand transfer inhibitor (InSTI)-associated TDR mutations. Participants with low frequency TDR mutations took 40 days longer to achieve viral suppression than participants without low frequency TDR mutations, when placed on fixed dose combination antiretroviral therapy.
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    Impact of injectable hormonal contraceptives on innate immune environment in the genital tract in women at high risk for HIV-1 infection.
    (2015) Ngcapu, Sinaye.; Abdool Karim, Quarraisha.; Passmore, Jo-Ann Shelley.
    Abstract available in PDF file.
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    Functional and clinical consequences of immune-driven sequence variation of gag-protease in HIV-1 subtypes A, C, D and recombinants.
    (2016) Kiguoya, Marion Wangui.; Ndung'u, Peter Thumbi.; Mann, Jaclyn Kelly.
    Abstract available in PDF file.
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    The role of natural killer cells in preventing HIV-1 acquisition and controlling disease progression.
    (2013) Naranbhai, Vivek.; Abdool Karim, Salim Safurdeen.; Carr, William Henry.
    In sub-Saharan Africa, women carry a disproportionate burden of the Human Immunodeficiency Virus Type 1 (HIV-1) pandemic. The high risk of HIV acquisition in these women and the variability in their disease progression is not fully understood. Natural Killer (NK) cells, which are innate immune antiviral lymphocytes, present systemically and at mucosal surfaces, may play a role in preventing HIV acquisition and/or altering disease progression, as they are key early mediators of the response to viral infections and are equipped to kill infected cells. The purpose of this study was to evaluate the role of NK cells in HIV-1 acquisition and following acquisition, in disease progression. The study participants were selected women who were participating in a randomized controlled trial assessing the effectiveness of 1% Tenofovir gel in preventing HIV-1 (CAPRISA 004 trial). The study design was a case-control study nested within the cohorts followed up in the CAPRISA 004 trial. In this trial, 889 sexually-active women aged 18-40 years were randomized to receive Tenofovir or placebo gel and prospectively followed. Assessment of HIV infection was performed monthly by rapid HIV-1 antibody tests, supplemented by HIV-1 RNA polymerase chain reaction (PCR), p24 Western blotting and/or ELISA. Samples obtained prior to the first positive rapid antibody test were retrospectively tested by HIV specific PCR to identify window period infections. The date of infection in this study was estimated as the midpoint between the last negative and first positive antibody test, or 14 days prior to the first HIV-1 RNA-PCR positive result. Multi-parametric flow cytometry techniques developed and validated in healthy blood donors were used to asses the bidirectional relationship between NK cells and HIV-1. To simulate in vivo interaction between NK cells and autologous HIV infected cells, an in vitro infection and coculture assay was used in addition to conventional assays of NK cell recognition of HLA-deficient cell lines. These were supplemented with measurement of plasma cytokines by Luminex and microbial products by ELISA. In this study, 44 cases who acquired HIV-1 were sampled prior to infection and 39 controls who remained HIV-1 negative despite high behavioural exposure at the timepoint when their preceding sexual activity was highest. To understand how HIV infection affected NK cells during early HIV-1 infection, the first sample obtained after acquisition was studied and compared to preinfection samples from the same participant. The case and control groups were broadly similar in the proportions using tenofovir gel, proportions infected with HSV-2 and number of sexual partners but tended to be marginally older than cases (27.6 vs 23.3 years). By design control women had higher sexual activity than cases (mean 11 vs. 5.7 sex acts per month). The frequency of IFN-γ secreting NK cells from women who acquired HIV infection were significantly lower than from women who remained uninfected in response to 721 cells-an EBV transformed B cell line (background-adjusted median 13.7% vs. 21.6%; p=0.03) and to autologous HIV infected T-cells (background-adjusted median 0.53% vs. 2.09%; p=0.007). NK cells from HIV acquirers displayed impaired proliferation but enhanced spontaneous degranulation compared with non-acquirers after co-culture with HIV uninfected or infected autologous T-cell blasts. Adjusting for age, gel arm, HSV-2 infection status and levels of NK cell activation, IFN-γ+ NK cell responses to autologous HIV infected cells were associated with reduced odds of HIV acquisition (OR 0.582; 95% CI 0.35-0.98; p=0.04). In addition, even in the absence of ex vivo stimulation, HIV acquirers had higher levels of generalised innate immune activation measured by systemic cytokine concentrations (TNF-α, IL2, IL-7 and IL12p40), peripheral blood platelet concentrations (p=0.038), and non-specific ex vivo NK cell activation (p<0.001). Generalised NK cell activation measured directly ex vivo without stimulation was associated with acquisition. Further, if innate immune activation was assembled as a principal component in an unsupervised fashion but taking into account all the measures made, it was significantly associated with HIV acquisition (OR adjusted for age, tenofovir gel use, and HSV-2 status for PC with innate immune factor loadings 11.27; 95% CI 1.84- 69.09; p=0.009). The causes of preinfection innate immune activation could not be established in this study but the degree of activation could not be explained by microbial translocation as both HIV acquirers and non-acquirers had similar levels of plasma lipopolysaccharide (LPS), soluble CD14 (sCD14) and intestinal fatty-acid binding protein (I-FABP). Similarly, both HIV acquirers and non-acquirers had similar NK cell and cytokine responses to Toll-like Receptor (TLR)-2, 3 or 7/8 agonists 11. During early HIV-infection, NK cells demonstrated significantly higher activation (p=0.03), expression of Killer-cell immunoglobulin-like Receptors (KIR) (p=0.006) and expression of chemokine receptor 7 (CCR7, p<0.0001) compared with prior to acquisition. Although NK cells had reduced cytolytic potential following HIV acquisition, antiviral IFN-γ secretion appeared to be preserved. NK cell responses were not different between tenofovir and placebo gel recipients, but women who acquired HIV whilst using tenofovir gel had higher gag-specific IFN-γ CD4+ T-cell responses during early infection. Overall, the findings suggest that the frequency of NK cells producing IFN-γ specifically after co-culture with HIV-1 infected target cells was associated with protection from HIV-1 acquisition but, generalised, non-specific activation of NK cells and other innate immune components enhanced HIV acquisition. Since neither microbial translocation nor TLR responsiveness were associated with pre-existing immune activation further studies will be required to identify the drivers of generalised innate immune activation. Methods to dampen generalised innate immune activation and/or augment specific NK cell antiviral responses in women at risk for HIV-1 may reduce HIV-1 acquisition. During primary HIV-1 infection, NK cells underwent impairment of cytolytic function but not IFN-γ secretory function; this may affect their ability to affect disease progression. Although Tenofovir gel did not alter innate immune responses in women with breakthrough infection, it preserved HIV-specific Tcell immune responses, the consequences of which need further exploration. Understanding how Tenofovir gel mediated preservation of adaptive immune responses may lead to interventions that will reinforce protective host responses. In conclusion, innate immune responses by NK cells have been shown to impact HIV acquisition; HIV-specific IFN-γ responses by NK cells were protective while generalised NK activation was detrimental. The causes of innate immune activation are not known but these effects were independent of the impact of Tenofovir gel. Future prevention strategies targeting mucosal transmission of HIV should assess their impact on NK cell responses, to avoid general innate immune activation and enhance their ability to protect against HIV acquisition.
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    Impact of immune-driven sequence variation in HIV-1 subtype C Gagprotease on viral fitness and disease progression.
    (2011) Wright, Jaclyn.; Ndung'u, Peter Thumbi.
    Understanding of the viral and host factors that determine time for progression to acquired immunodeficiency syndrome (AIDS) in individuals infected with human immunodeficiency virus type 1 (HIV-1) could aid in the design of an effective HIV-1 vaccine. Human leukocyte antigen (HLA) class I profile is strongly and consistently associated with differential rates of HIV-1 disease progression, however the mechanisms explaining this are not well understood. It has been hypothesised that “protective” HLA alleles select escape mutations in functionally important epitopes in the conserved group specific antigen (Gag) protein resulting in HIV-1 attenuation, which may result in slower disease progression. Many of the studies investigating the fitness cost of Gag escape mutations have concentrated on a few pre-selected mutations and have not assessed fitness consequences in the natural sequence background. Furthermore, the majority of studies have focussed on HIV-1 subtype B, while HIV-1 subtype C is the most prevalent subtype worldwide. Therefore, in the present study, a large population-based approach and clinically-derived Gag-protease sequences were used to comprehensively investigate the relationship between immunedriven sequence variation in Gag, viral replication capacity and markers of disease progression in HIV-1 subtype C chronic infection. The influence of Gag function on HIV-1 disease progression was further investigated in early HIV-1 subtype C infection. It was also hypothesised that Gag may contribute significantly to overall HIV-1 fitness and towards fitness differences between HIV-1 subtypes. Materials and Methods Recombinant viruses encoding Gag-protease, derived from antiretroviral naïve HIV-1 subtype C chronically (n=406) and recently (n=60) infected patients as well as a small subset of HIV-1 subtype B chronically infected patients (n=25), were generated by electroporation of an HIV-inducible green fluorescent protein (GFP)-reporter T cell line with plasmaderived gag-protease PCR products and linearised gag-protease-deleted NL4-3 plasmid. The replication capacities of recombinant viruses, as well as intact HIV-1 isolates from peripheral blood mononuclear cells of patients chronically infected with HIV-1 subtype C (n=16), were assayed in the GFP-reporter T cell line by flow cytometry. Replication capacity was defined as the slope of increase in percentage infected cells from days 3-6 following infection, normalised to the growth of a wild-type NL4-3 control. Replication capacities were related to patient HLA alleles and markers of disease progression (viral load, CD4+ T cell count, and rate of CD4+ T cell decline in chronically infected patients, and viral set point and rate of CD4+ T cell decline in recently infected patients). Replication capacities were compared between isolates and recombinant viruses encoding Gag-protease from the same isolates, as well as between HIV-1 subtype B and C recombinant viruses matched for viral load and CD4+ T cell count. Bulk sequencing of patient -derived gagprotease amplicons was performed and mutations were identified that were significantly associated with altered viral replication capacity. The fitness effect of some of these mutations was directly tested by site-directed mutagenesis followed by assay of the mutant viruses. Results In HIV-1 subtype C chronic infection, protective HLA-B alleles, most notably HLA-B*81 (p<0.0001), were associated with lower replication capacities. HLA-associated mutations at low entropy sites (i.e. conserved sites) in or adjacent to Gag epitopes were associated with lower replication capacities (p=0.02), especially the HLA-B*81-associated 186S mutation in the TL9 epitope (p=0.0001). The fitness cost of this mutation was confirmed in site-directed mutagenesis experiments (p<0.001), and the co-varying mutations tested did not significantly compensate for this fitness cost. Replication capacity also correlated positively of an HIV-inducible green fluorescent protein (GFP)-reporter T cell line with plasmaderived gag-protease PCR products and linearised gag-protease-deleted NL4-3 plasmid. The replication capacities of recombinant viruses, as well as intact HIV-1 isolates from peripheral blood mononuclear cells of patients chronically infected with HIV-1 subtype C (n=16), were assayed in the GFP-reporter T cell line by flow cytometry. Replication capacity was defined as the slope of increase in percentage infected cells from days 3-6 following infection, normalised to the growth of a wild-type NL4-3 control. Replication capacities were related to patient HLA alleles and markers of disease progression (viral load, CD4+ T cell count, and rate of CD4+ T cell decline in chronically infected patients, and viral set point and rate of CD4+ T cell decline in recently infected patients). Replication capacities were compared between isolates and recombinant viruses encoding Gag-protease from the same isolates, as well as between HIV-1 subtype B and C recombinant viruses matched for viral load and CD4+ T cell count. Bulk sequencing of patient -derived gagprotease amplicons was performed and mutations were identified that were significantly associated with altered viral replication capacity. The fitness effect of some of these mutations was directly tested by site-directed mutagenesis followed by assay of the mutant viruses. Results In HIV-1 subtype C chronic infection, protective HLA-B alleles, most notably HLA-B*81 (p<0.0001), were associated with lower replication capacities. HLA-associated mutations at low entropy sites (i.e. conserved sites) in or adjacent to Gag epitopes were associated with lower replication capacities (p=0.02), especially the HLA-B*81-associated 186S mutation in the TL9 epitope (p=0.0001). The fitness cost of this mutation was confirmed in site-directed mutagenesis experiments (p<0.001), and the co-varying mutations tested did not significantly compensate for this fitness cost. Replication capacity also correlated positivelyof an HIV-inducible green fluorescent protein (GFP)-reporter T cell line with plasmaderived gag-protease PCR products and linearised gag-protease-deleted NL4-3 plasmid. The replication capacities of recombinant viruses, as well as intact HIV-1 isolates from peripheral blood mononuclear cells of patients chronically infected with HIV-1 subtype C (n=16), were assayed in the GFP-reporter T cell line by flow cytometry. Replication capacity was defined as the slope of increase in percentage infected cells from days 3-6 following infection, normalised to the growth of a wild-type NL4-3 control. Replication capacities were related to patient HLA alleles and markers of disease progression (viral load, CD4+ T cell count, and rate of CD4+ T cell decline in chronically infected patients, and viral set point and rate of CD4+ T cell decline in recently infected patients). Replication capacities were compared between isolates and recombinant viruses encoding Gag-protease from the same isolates, as well as between HIV-1 subtype B and C recombinant viruses matched for viral load and CD4+ T cell count. Bulk sequencing of patient -derived gagprotease amplicons was performed and mutations were identified that were significantly associated with altered viral replication capacity. The fitness effect of some of these mutations was directly tested by site-directed mutagenesis followed by assay of the mutant viruses. Results In HIV-1 subtype C chronic infection, protective HLA-B alleles, most notably HLA-B*81 (p<0.0001), were associated with lower replication capacities. HLA-associated mutations at low entropy sites (i.e. conserved sites) in or adjacent to Gag epitopes were associated with lower replication capacities (p=0.02), especially the HLA-B*81-associated 186S mutation in the TL9 epitope (p=0.0001). The fitness cost of this mutation was confirmed in site-directed mutagenesis experiments (p<0.001), and the co-varying mutations tested did not significantly compensate for this fitness cost. Replication capacity also correlated positively with baseline viral load (p<0.0001) and negatively with baseline CD4+ T cell count (p=0.0004), but not with subsequent rate of CD4+ T cell decline (p=0.73). In HIV-1 subtype C recent infection, replication capacities of the early viruses did not correlate with subsequent viral set points (p=0.37) but were significantly lower in individuals with below median viral set points (p=0.03), and there was a trend of correlation between lower replication capacities and slower rates of CD4+ T cell decline (p=0.09). Overall, the proportion of host HLA-specific Gag polymorphisms in or adjacent to epitopes was negatively associated with replication capacities (p=0.04) but host HLA-B-specific polymorphisms were associated with higher viral set points (p=0.01), suggesting a balance between effective Gag CD8+ T cell responses and viral replication capacity in influencing viral set point. A moderate statistically significant correlation was found between the replication capacities of whole isolates and their corresponding Gag-protease recombinant viruses (p=0.04) and the replication capacities of the subtype C recombinant viruses were significantly lower than that of the subtype B recombinant viruses (p<0.0001). The subtype-specific difference in the consensus amino acids at Gag codons 483 and 484 was found in site-directed mutagenesis experiments to largely contribute to the fitness difference between subtypes, possibly by influencing budding efficiency. Discussion The data support that protective HLA alleles, in particular HLA-B*81, attenuate HIV-1 through HLA-restricted CD8+ T cell-mediated selection pressure on Gag. Results suggest that viral replication capacity determined by sequence variability in Gag-protease has an impact on HIV-1 disease progression, but also indicate that a balance between HLA-driven fitness costs and maintenance of effective CD8+ T cell responses is important in determining clinical outcome. Gag-protease was observed to significantly contribute to overall HIV-1 replication capacity and variability in this region between HIV-1 subtypes B and C is suggested to partly explain the difference in viral fitness between these subtypes. Specific mutations in Gag-protease associated with viral attenuation were identified and it was also observed that mutations in conserved Gag regions carried the greatest cost to HIV-1 replication capacity. Overall, the data support the concept of, and may assist in the rational design of, an HIV-1 vaccine in which immune responses are directed towards several conserved epitopes, particularly in Gag, with the aim to constrain immune escape (thereby maintaining effective CD8+ T cell responses) and attenuate HIV-1 (in the event of partial escape), resulting in slower disease course and reduced HIV-1 transmission at the population level.
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    Regulation of TRIM E3 Ligases and Cyclophilin A and the impact on HIV-1 replication and pathogenesis.
    (2011) Singh, Ravesh.; Ndung'u, Peter Thumbi.
    No abstract available.
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    Molecular characterisation of endogenous loci related to jaagsiekte sheep retrovirus.
    (2007) Hallwirth, Claus Volker.; York, Denis Francis.; Fan, Hung Y.
    The study of retroviruses has been of pivotal significance to the field of biomedical science, where it has provided fundamental insights into the processes underlying both viral and non-viral carcinogenesis. Ovine pulmonary adenocarcinoma (OP A), a contagious lung cancer of sheep and goats, has emerged over the past three decades as an invaluable model of human epithelial cancers. It is one of the very few animal models of retrovirus induced neoplasia of epithelial tissues, whereas most other such animal models of human cancers pertain to the haematopoietic system. OP A represents a unique, naturally occurring, inducible, outbred animal model of peripheral lung carcinomas, and is caused by a betaretrovirus - jaagsiekte sheep retrovirus (JSRV) - that is receiving increasing attention in the fields of retrovirology and lung cancer research. JSRV exists in two highly homologous, yet molecularly distinct forms. The first is an exogenous form of the virus that is transmitted horizontally from one animal to another. This form is infectious and the direct cause of OP A. The other is an endogenous form, 15 to 20 proviral copies of which reside benignly in the genome of sheep and are transmitted vertically from one generation to the next. At the time this study commenced, no knowledge existed regarding the underlying pathogenic mechanism by which JSRV causes OPA. Even though the nucleotide sequence of exogenous JSRV had been elucidated seven years earlier, only limited sequence information was available on endogenous JSRVs. With a view towards identifying genetic regions or elements within exogenous JSRV that could potentially be implicated in its pathogenic function, this study began with the cloning of the first three full-length endogenous JSRV loci ever isolated from sheep. The DNA sequences of these full-length endogenous JSRV loci were determined and comprehensively analysed. Comparison with exogenous JSRV isolates revealed that the two forms of the virus are highly homologous, yet can be consistently distinguished in three short regions within the coding genes. Two of these reside in the gag gene, and one at the end of the env gene. These regions were named the variable regions (VRs) of sheep betaretroviruses. The JSRV VR3 in env was linked by our collaborators to the virus's ability to transform cells in tissue culture. The effects and biological significance of VRI and VR2 in gag are subtler and more difficult to determine. After identifying these regions, it became the objective of this study to develop relevant molecular tools that could be used to discern the significance of these variable regions in vivo, and to characterise these tools in vitro to assess their suitability for in vivo studies. The development of these tools entailed the design of a novel strategy that was implemented to precisely substitute the endogenous VRI and VR2 (individually and in combination) into an infectious molecular clone of exogenous JSRV. These chimeric constructs were shown to support retroviral particle release into the supernatant of transiently transfected cells in tissue culture. These particles were confirmed by independent experiments to have arisen specifically from transfection with the chimeric clones. Finally, the particles were shown to be capable of infecting cultured cells and of productively integrating their genomes into those of their host cells, rendering these particles fully competent retroviruses that can be used in the context of in vivo studies to determine the biological significance of VRI and VR2. This study has made a significant contribution to the further development of the OP A / JSRV model system of human epithelial lung cancers. It has also led to the design of a molecular substitution strategy that can be adapted to introduce any genetic region into a cloned DNA construct, regardless of the degree - or lack of interrelation - of the two DNA sequences, thereby creating a highly versatile molecular biological tool.