Introduction Standard immunogenicity assays, such as ELISpot and intracellular cytokine staining, fail to correlate HIV-1-specific CD8+T-cells responses with HIV-1 replication in-vivo. Therefore, it is essential to develop assays that can determine antiviral potential of vaccine elicited CD8+T-cells. The current ELISA-VIA measures HIV-1-p24 production overtime in autologous CD4+T-cells. However, it is not designed to identify the class-I-HLA-allele involved in mediating the response. We developed a new FACS based VIA that can investigate CD8+T-cells antiviral potential in the context of restricting class-I-HLA alleles. The assay measures the ability of CD8+T-cells to kill HIV-1 infected GXR-cells over-expressing class-I-HLA allele of interest. The assay utilises a GXR-cell engineered to express GFP upon HIV-1 infection. Methods CD8+T-cells were co-cultured with HIV-1 infected GXR-cells for 3 days. Reduction in the infected GXR-cells expressing GFP measured by FACS was used to evaluate the CD8+T-cells killing activity. The assay was validated using a panel of 9 HIV-infected samples and were concurrently assayed with the ELISA-VIA. The tested results on each assay were categorised into four groups namely: true-inhibition (TI ≥50%), doubtful-inhibition (DI ≥20% to ≤49.99%), false-inhibition (FI ≥10% to ≤19.99%) and non-inhibition (NI≤ 9.99%). These results were used in a 2 by 2 table to compute sensitivity (TI/TI+DI) and specificity (FI/FI+NI). Results True inhibition was observed in 44% of samples analysed using GXR-VIA compared to 33% with ELISA-VIA. 11% with GXR-VIA had doubtful result compared to 33% with ELISA-VIA. 22% with GXR-VIA were categorised as false inhibition compared to 33% with ELISA-VIA. Interestingly, no sample showed non-inhibition with GXR-VIA whereas 22% showed no inhibition by ELISA-VIA. Collectively, GXR-VIA is very specific (100%) but less sensitive (57%) at detecting virus inhibition activity. Conclusion The specificity of GXR-VIA and its marginal sensitivity indicates that the assay is capable of identifying CD8+T-cells-mediated inhibition of HIV-1 replication. Overall, the GXR-VIA provides a platform to assess the influence of different restricting class-I-HLA alleles on HIV-1-specific CD8+T-cells antiviral function.

Background Increasing data suggest an important role of KIR+ NK cells in the control of HIV-1, however the precise mechanisms on how NK cells recognize HIV-1-infected cells remain poorly understood. KIRs can bind to HLA class I molecules, but the binding affinity of these interactions is dependent on the HLA class I presented epitope. Recent reports have suggested that sequence variations within HIV-1 epitopes presented by HLA class I can affect the binding of inhibitory KIRs expressed on NK cells, potentially modulating NK cell responses to infected cells. Here we investigated whether HIV-1 might adapt to the combined KIR/HLA genotypes on a population level to identify areas within HIV-1 that might be targeted by KIR+ NK cells.

ABSTRACT HIV-1 attenuation resulting from immune escape mutations selected in Gag may contribute to slower disease progression in HIV-1-infected individuals expressing certain HLA class I alleles. We previously showed that the protective allele HLA-B*81 and the HLA-B*81-selected Gag T186S mutation are strongly associated with a lower viral replication capacity of recombinant viruses encoding Gag-protease derived from individuals chronically infected with HIV-1 subtype C. In the present study, we directly tested the effect of this mutation on viral replication capacity. In addition, we investigated potential compensatory effects of various polymorphisms, including other HLA-B*81-associated mutations that significantly covary with the T186S mutation. Mutations were introduced into a reference subtype B backbone and into patient-derived subtype C sequences in subtype B and C backbones by site-directed mutagenesis. The exponential-phase growth of mutant and wild-type viruses was assayed by flow cytometry of a green fluorescent protein reporter T cell line or by measurement of HIV-1 reverse transcriptase activity in culture supernatants. Engineering of the T186S mutation alone into all patient-derived subtype C sequences failed to yield replication-competent viruses, while in the subtype B sequence, the T186S mutation resulted in impaired replication capacity. Only the T186S mutation in combination with the T190I mutation yielded replication-competent viruses for all virus backbones tested; however, these constructs replicated slower than the wild type, suggesting that only partial compensation is mediated by the T190I mutation. Constructs encoding the T186S mutation in combination with other putative compensatory mutations were attenuated or defective. These results suggest that the T186S mutation is deleterious to HIV-1 subtype C replication and likely requires complex compensatory pathways, which may contribute to the clinical benefit associated with HLA-B*81.

Immune escape mutations selected by human leukocyte antigen class I-restricted CD8(+) cytotoxic T lymphocytes (CTLs) can result in biologically and clinically relevant costs to HIV-1 replicative fitness. This phenomenon may be exploited to design an HIV-1 vaccine capable of stimulating effective CTL responses against highly conserved, mutationally constrained viral regions, where immune escape could occur only at substantial functional costs. Such a vaccine might 'channel' HIV-1 evolution towards a less-fit state, thus lowering viral load set points, attenuating the infection course and potentially reducing the risk of transmission. A major barrier to this approach, however, is the accumulation of immune escape variants at the population level, possibly leading to the loss of immunogenic CTL epitopes and diminished vaccine-induced cellular immune responses as the epidemic progresses. Here, we review the evidence supporting CTL-driven replicative defects in HIV-1 and consider the implications of this work for CTL-based vaccines designed to attenuate the infection course.

BACKGROUND:Human immunodeficiency virus type 1 (HIV-1)-specific CD8(+) responses contribute to the decline in acute peak viremia following infection. However, data on the relative immunogenicity of CD8(+) T-cell epitopes during and after acute viremia are lacking.METHODS:We characterized CD8(+) T-cell responses in 20 acutely infected, antiretroviral-naive individuals with HIV-1 subtype C infection using the interferon-γ enzyme-linked immunosorbent spot assay. Eleven of these had not fully seroconverted at the time of analysis. Viruses from plasma were sequenced within defined cytotoxic T-lymphocyte (CTL) cell epitopes for selected subjects.RESULTS:At approximately 28 days after estimated initial infection, CD8(+) T-cell responses were directed against an average of 3 of the 410 peptides tested (range, 0-6); 2 individuals had no detectable responses at this time. At 18 weeks, the average number of peptides targeted had increased to 5 (range 0-11). Of the 56 optimal Gag CTL epitopes sequenced, 31 were wild-type in the infecting viruses, but only 11 of 31 elicited measurable CD8(+) T-cell responses.CONCLUSIONS:These data demonstrate that the majority of CD8(+) responses are not elicited during acute HIV infection despite the presence of the cognate epitope in the infecting strain. There is a need to define factors that influence lack of induction of effective immune responses and the parameters that dictate immunodominance in acute infection.

ABSTRACT HLA class I-mediated selection of immune escape mutations in functionally important Gag epitopes may partly explain slower disease progression in HIV-1-infected individuals with protective HLA alleles. To investigate the impact of Gag function on disease progression, the replication capacities of viruses encoding Gag-protease from 60 individuals in early HIV-1 subtype C infection were assayed in an HIV-1-inducible green fluorescent protein reporter cell line and were correlated with subsequent disease progression. Replication capacities did not correlate with viral load set points (P = 0.37) but were significantly lower in individuals with below-median viral load set points (P = 0.03), and there was a trend of correlation between lower replication capacities and lower rates of CD4 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 load set points (P = 0.01). Further, polymorphisms associated with host-specific protective HLA alleles were linked with higher viral load set points (P = 0.03). These data suggest that transmission or early HLA-driven selection of Gag polymorphisms results in reduced early cytotoxic T-lymphocyte (CTL) responses and higher viral load set points. In support of the former, 46% of individuals with nonprotective alleles harbored a Gag polymorphism exclusively associated with a protective HLA allele, indicating a high rate of their transmission in sub-Saharan Africa. Overall, HIV disease progression is likely to be affected by the ability to mount effective Gag CTL responses as well as the replication capacity of the transmitted virus.

ABSTRACT It is unknown whether favorable HLA class II alleles may attenuate HIV-1 through selection pressure in a manner similar to that of protective HLA class I alleles. We investigated the relationship between HLA class II alleles and in vitro replication capacities of recombinant viruses encoding HIV-1 subtype C Gag-protease from chronically infected individuals. No associations were found between individual alleles and lower replication capacity, suggesting no significant HIV-1 attenuation by HLA class II-restricted Gag-specific CD4 + T cell immune pressure.

ABSTRACT The mechanisms underlying HIV-1 control by protective HLA class I alleles are not fully understood and could involve selection of escape mutations in functionally important Gag epitopes resulting in fitness costs. This study was undertaken to investigate, at the population level, the impact of HLA-mediated immune pressure in Gag on viral fitness and its influence on HIV-1 pathogenesis. Replication capacities of 406 recombinant viruses encoding plasma-derived Gag-protease from patients chronically infected with HIV-1 subtype C were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. Viral replication capacities varied significantly with respect to the specific HLA-B alleles expressed by the patient, and protective HLA-B alleles, most notably HLA-B*81, were associated with lower replication capacities. HLA-associated mutations at low-entropy sites, especially the HLA-B*81-associated 186S mutation in the TL9 epitope, were associated with lower replication capacities. Most mutations linked to alterations in replication capacity in the conserved p24 region decreased replication capacity, while most in the highly variable p17 region increased replication capacity. Replication capacity also correlated positively with baseline viral load and negatively with baseline CD4 count but did not correlate with the subsequent rate of CD4 decline. In conclusion, there is evidence that protective HLA alleles, in particular HLA-B*81, significantly influence Gag-protease function by driving sequence changes in Gag and that conserved regions of Gag should be included in a vaccine aiming to drive HIV-1 toward a less fit state. However, the long-term clinical benefit of immune-driven fitness costs is uncertain given the lack of correlation with longitudinal markers of disease progression.

Background Control of HIV replication is determined by a complex interaction of viral genetic, host genetic and immune factors, the understanding of which is crucial to developing an effective vaccine. In some studies, HIV Gag immune responses correlate with low viral loads and it is hypothesised that some HLA alleles select for escape mutations in conserved Gag epitopes, resulting in a fitness cost. We are investigating the impact of HLA-driven variation in Gag on fitness and disease progression in a population of 451 HIV-1 subtype C infected individuals.