Investigating cross-clade immune responses in HIV-1 subtype C-infected individuals from South Africa: implications for HIV vaccine design

Background An effective HIV vaccine remains the main hope for controlling the HIV epidemic and is a global health priority. The genetic diversity of the virus across the globe is a major impediment to developing an effective vaccine. Whether a universal vaccine is possible still remain elusive. Therefore, there is need to fully characterise clusters of commonly targeted regions across the different HIV-1 clades. Centralized sequences have been suggested as vaccine immunogens and peptide reagents for assessing vaccine-induced responses, but their cross-reactivity has not been fully assessed in larger cohorts of subtype C-infection and in regions of differing HIV epidemics. In addition, the functional profile of HIV-specific T-cells recognizing variant epitopes has not been fully characterized. Whether cross-reactivity observed by IFN-γ production in an ELISpot assay can be observed at physiological concentrations of the peptides and for other functions of HIV-specific T-cells is an important question that remains to be answered. Methods The cross-reactivity of HIV-specific T-cells was assessed using clade-specific peptide reagents forming part of current candidate vaccine inserts based on the HIV-1 Gag protein from clades CDu422, CCH, A, B and D in 40 clade C-infected study participants using the IFN-γ ELISpot assay. To test the reactivity of group M consensus peptide reagents, 66 individuals, 44 of whom were ARV naïve, were assessed for HIV-specific T cell responses to group M Gag and Nef peptides. A selection of these individuals was screened for HIVspecific T-cell responses to clade CDu422 Gag peptides. Cross-reactivity of peptide variants was assessed at physiologically relevant peptide concentrations by functional avidity studies using peptide dilution IFN-γ ELISpot assays. Additionally, the cytokine profile, cytotoxic potential and proliferative capacity of cross-reactive peptide variants was characterised using multiparameter flow cytometry. Results The magnitude and breadth of HIV-specific T-cell responses were similar between the two clade-C peptide reagents in a clade C-infected population. However, the magnitude and breadth of responses to peptides based on clades A, B and D were significantly lower compared to the clade C peptides. Clusters of commonly targeted regions cross-reactive across the four clades investigated resided predominantly in conserved regions. Interestingly, there were Gag regions that were exclusively recognized in the different clades that had significantly lower entropy scores for the reactive variants than their nonreactive counterparts, suggesting that the variability in targeted regions could have been shaped by host immune pressure. For consensus group M peptides, the magnitude and breadth of Gag responses were significantly higher than that of Nef in clade C-infected individuals. In addition, consensus group M Gag peptides had significantly lower magnitude and breadth of HIV-specific T-cell responses compared to clade C peptide reagents, suggesting loss of responses by centralised reagents despite their central nature to group M viruses. On the contrary, the magnitude and breadth of responses to consensus group M Gag peptides were comparable to that of clade-mismatched peptides, namely clades A, B and D, suggesting that these reagents can be used interchangeably. Peptide dilution assays showed that amino acid mismatches have discordant effects on functional avidity and that some peptides are cross-reactive at physiological concentrations. Similarly, discordant effects (differences in functional avidity, cytokine and cytotoxic profiles and proliferative capacity) of amino acid mismatches on cytokine and cytotoxic potential profiles as well as proliferative capacity were observed. Conclusion People infected by a particular HIV clade can recognize HIV peptides based on other clades. However, the magnitude and breadth of responses are greater for the matched clades compared to mismatched clades, suggesting that there may be an advantage of using vaccines based on matched over unmatched clades. Group M based consensus sequences can be recognized in HIV-infected individuals, but with a lower frequency, magnitude and breadth of responses compared to clade-matched peptides, suggesting a limitation of these peptides both as reagents and vaccine immunogens. However, the frequency, magnitude and breadth T-cell reponses to consensus group M peptides were comparable to clademismatched responses, suggesting that these reagents may be used interchangeably. Furthermore, amino acid variations across corresponding viral regions have discordant effects on the functional avidity, cytokine profile, cytotoxic potential and proliferative capacity; implying that qualitative measures of cross-reactivity beyond IFN-γ frequencies need to be considered. These data may aid in the development of reagents for the assessment of vaccine-induced responses as well as in HIV vaccine immunogen design

Investigating cross-clade immune responses in HIV-1 subtype C-infected individuals from South Africa

Includes bibliographical references (leaves 114-147).The increasing diversity of HIV-1 in different geographic regions presents a challenge for the development of an HIV/AIDS vaccine. Even if proven effective, the ability of a vaccine to have cross-subtype and intra-subtype protection remains an important question. The aim of the study was to investigate cross- and intra-clade T cell immune responses in HIV-1 subtype C-infected individuals. The objectives were to genetically characterise full length gag gene sequences from individuals chronically infected with HIV-1 and then assess the degree of cross-reactive immune responses in an ELlS pot assay using peptide reagents based on vaccine candidates

Characterization of HIV-1 gag and nef in Cameroon: further evidence of extreme diversity at the origin of the HIV-1 group M epidemic

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

Strengthening HIV surveillance in the antiretroviral therapy era: rationale and design of a longitudinal study to monitor HIV prevalence and incidence in the uMgungundlovu District, KwaZulu-Natal, South Africa.

CAPRISA, 2015.Abstract available in pdf

Intra- and Inter-clade Cross-reactivity by HIV-1 Gag Specific T-Cells Reveals Exclusive and Commonly Targeted Regions: Implications for Current Vaccine Trials

The genetic diversity of HIV-1 across the globe is a major challenge for developing an HIV vaccine. To facilitate immunogen design, it is important to characterize clusters of commonly targeted T-cell epitopes across different HIV clades. To address this, we examined 39 HIV-1 clade C infected individuals for IFN-γ Gag-specific T-cell responses using five sets of overlapping peptides, two sets matching clade C vaccine candidates derived from strains from South Africa and China, and three peptide sets corresponding to consensus clades A, B, and D sequences. The magnitude and breadth of T-cell responses against the two clade C peptide sets did not differ, however clade C peptides were preferentially recognized compared to the other peptide sets. A total of 84 peptides were recognized, of which 19 were exclusively from clade C, 8 exclusively from clade B, one peptide each from A and D and 17 were commonly recognized by clade A, B, C and D. The entropy of the exclusively recognized peptides was significantly higher than that of commonly recognized peptides (p = 0.0128) and the median peptide processing scores were significantly higher for the peptide variants recognized versus those not recognized (p = 0.0001). Consistent with these results, the predicted Major Histocompatibility Complex Class I IC50 values were significantly lower for the recognized peptide variants compared to those not recognized in the ELISPOT assay (p<0.0001), suggesting that peptide variation between clades, resulting in lack of cross-clade recognition, has been shaped by host immune selection pressure. Overall, our study shows that clade C infected individuals recognize clade C peptides with greater frequency and higher magnitude than other clades, and that a selection of highly conserved epitope regions within Gag are commonly recognized and give rise to cross-clade reactivities

Characterization of HIV-1 <it>gag</it> and <it>nef</it> in Cameroon: further evidence of extreme diversity at the origin of the HIV-1 group M epidemic

Abstract 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.</p

Spatio-temporal estimates of HIV risk group proportions for adolescent girls and young women across 13 priority countries in sub-Saharan Africa

The Global AIDS Strategy 2021-2026 identifies adolescent girls and young women (AGYW) as a priority population for HIV prevention, and recommends differentiating intervention portfolios geographically based on local HIV incidence and individual risk behaviours. We estimated prevalence of HIV risk behaviours and associated HIV incidence at health district level among AGYW living in 13 countries in sub-Saharan Africa. We analysed 46 geospatially-referenced national household surveys conducted between 1999-2018 across 13 high HIV burden countries in sub-Saharan Africa. Female survey respondents aged 15-29 years were classified into four risk groups (not sexually active, cohabiting, non-regular or multiple partner[s] and female sex workers [FSW]) based on reported sexual behaviour. We used a Bayesian spatio-temporal multinomial regression model to estimate the proportion of AGYW in each risk group stratified by district, year, and five-year age group. Using subnational estimates of HIV prevalence and incidence produced by countries with support from UNAIDS, we estimated new HIV infections in each risk group by district and age group. We then assessed the efficiency of prioritising interventions according to risk group. Data consisted of 274,970 female survey respondents aged 15-29. Among women aged 20-29, cohabiting (63.1%) was more common in eastern Africa than non-regular or multiple partner(s) (21.3%), while in southern countries non-regular or multiple partner(s) (58.9%) were more common than cohabiting (23.4%). Risk group proportions varied substantially across age groups (65.9% of total variation explained), countries (20.9%), and between districts within each country (11.3%), but changed little over time (0.9%). Prioritisation based on behavioural risk, in combination with location- and age-based prioritisation, reduced the proportion of population required to be reached in order to find half of all expected new infections from 19.4% to 10.6%. FSW were 1.3% of the population but 10.6% of all expected new infections. Our risk group estimates provide data for HIV programmes to set targets and implement differentiated prevention strategies outlined in the Global AIDS Strategy. Successfully implementing this approach would result in more efficiently reaching substantially more of those at risk for infections

Spatio-temporal estimates of HIV risk group proportions for adolescent girls and young women across 13 priority countries in sub-Saharan Africa.

The Global AIDS Strategy 2021-2026 identifies adolescent girls and young women (AGYW) as a priority population for HIV prevention, and recommends differentiating intervention portfolios geographically based on local HIV incidence and individual risk behaviours. We estimated prevalence of HIV risk behaviours and associated HIV incidence at health district level among AGYW living in 13 countries in sub-Saharan Africa. We analysed 46 geospatially-referenced national household surveys conducted between 1999-2018 across 13 high HIV burden countries in sub-Saharan Africa. Female survey respondents aged 15-29 years were classified into four risk groups (not sexually active, cohabiting, non-regular or multiple partner[s] and female sex workers [FSW]) based on reported sexual behaviour. We used a Bayesian spatio-temporal multinomial regression model to estimate the proportion of AGYW in each risk group stratified by district, year, and five-year age group. Using subnational estimates of HIV prevalence and incidence produced by countries with support from UNAIDS, we estimated new HIV infections in each risk group by district and age group. We then assessed the efficiency of prioritising interventions according to risk group. Data consisted of 274,970 female survey respondents aged 15-29. Among women aged 20-29, cohabiting (63.1%) was more common in eastern Africa than non-regular or multiple partner(s) (21.3%), while in southern countries non-regular or multiple partner(s) (58.9%) were more common than cohabiting (23.4%). Risk group proportions varied substantially across age groups (65.9% of total variation explained), countries (20.9%), and between districts within each country (11.3%), but changed little over time (0.9%). Prioritisation based on behavioural risk, in combination with location- and age-based prioritisation, reduced the proportion of population required to be reached in order to find half of all expected new infections from 19.4% to 10.6%. FSW were 1.3% of the population but 10.6% of all expected new infections. Our risk group estimates provide data for HIV programmes to set targets and implement differentiated prevention strategies outlined in the Global AIDS Strategy. Successfully implementing this approach would result in more efficiently reaching substantially more of those at risk for infections