Research Area:	Immunology
Scientific Themes:	Immunology & Infectious Disease
Keywords:	HIV, AIDS, Immune response, HLA Class I, vaccine and viral fitness
Web Links:	Podcast 'Can we eradicate HIV?'

It is increasingly apparent that Highly Active Antiretroviral Therapy (HAART) may not be the long-term solution to the management of HIV infection. Despite major improvements in morbidity and mortality in HIV+ve individuals, lifespan on HAART is less than for the HIV uninfected, there is unexplained morbidity on HAART (cardiovascular, renal, hepatic complications plus osteoporosis, dementia, ‘frailty’ and ageing), not all of which can explained by drug toxicities. In addition, the practicalities of global drug provision are currently untenable – achieving the US target of 80% HAART coverage in developing regions would account for half of the US foreign aid budget by 2016. Achieving a ‘sterilising cure’ (infectious disease model) or ‘drug-free remission’ (tumour model) must therefore become a priority for global HIV management.

There are fundamental issues impacting eradication, related to a persistent proviral HIV reservoir. Stopping HAART results in rebound of viraemia to levels similar to those recorded pre-therapy, HIV DNA can be detected in PBMCs and lymphoid tissue at all stages of therapy, the cellular and anatomical HIV reservoirs are not defined, there is no ‘undetectable viral load’ on HAART (median value is 3.1 copies/ml) and we do not fully understand the processes by which latency is induced, or how transcription is activated.

The CHERUB co-operative (Collaborative HIV Eradication of Reservoirs: UK BRC) is a NIHR-funded platform funded to explore strategies for achieving HIV eradication in the UK. CHERUB comprises internationally recognised researchers from Oxford, Cambridge, Imperial College, UCL and King’s College, and the associated NHS Trusts. Through CHERUB, we are recruiting new patient cohorts to allow studies varying from basic laboratory research, to ex vivo analyses, to large-scale clinical trials of novel interventions.

The role of Oxford University within CHERUB is to lead the scientific strategy (John Frater is co-PI and Scientific Lead). Specifically, our work will focus on quantification of viral reservoirs, sequence analysis by standard and next generation models, immunology (predominantly looking at the role of CTL in remission strategies) and more fundamental research into new approaches to eradication such as nanotechnology. Working in collaboration with NHS Trusts and also with the pharmaceutical industry, we aim to push forward the boundaries in this new and exciting field.

Name	Department	Institution	Country
Jonathan Weber		Imperial College, London	UK
Sarah Fidler		Imperial College	UK
Angela McLean	Department of Zoology	University of Oxford	UK
Cloete van Vuuren		University of Free State	South Africa
The CHERUB Cooperative		NIHR	UK
Prof Rodney E Phillips	Experimental Medicine Division	Oxford University	UK

Fryer HR, Frater J, Duda A, Roberts MG, SPARTAC Trial Investigators, Phillips RE, McLean AR. 2010. Modelling the evolution and spread of HIV immune escape mutants. PLoS Pathog, 6 (11), pp. e1001196. Read abstract | Read more

During infection with human immunodeficiency virus (HIV), immune pressure from cytotoxic T-lymphocytes (CTLs) selects for viral mutants that confer escape from CTL recognition. These escape variants can be transmitted between individuals where, depending upon their cost to viral fitness and the CTL responses made by the recipient, they may revert. The rates of within-host evolution and their concordant impact upon the rate of spread of escape mutants at the population level are uncertain. Here we present a mathematical model of within-host evolution of escape mutants, transmission of these variants between hosts and subsequent reversion in new hosts. The model is an extension of the well-known SI model of disease transmission and includes three further parameters that describe host immunogenetic heterogeneity and rates of within host viral evolution. We use the model to explain why some escape mutants appear to have stable prevalence whilst others are spreading through the population. Further, we use it to compare diverse datasets on CTL escape, highlighting where different sources agree or disagree on within-host evolutionary rates. The several dozen CTL epitopes we survey from HIV-1 gag, RT and nef reveal a relatively sedate rate of evolution with average rates of escape measured in years and reversion in decades. For many epitopes in HIV, occasional rapid within-host evolution is not reflected in fast evolution at the population level. Hide abstract

Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A, Brumme Z, Brumme C, Allen T, Brander C, Kaslow R, Tang J, Hunter E, Allen S, Mulenga J, Branch S, Roach T, John M, Mallal S, Ogwu A, Shapiro R, Prado JG, Fidler S, Weber J, Pybus OG, Klenerman P, Ndung'u T, Phillips R, Heckerman D, Harrigan PR, Walker BD, Takiguchi M, Goulder P et al. 2009. Adaptation of HIV-1 to human leukocyte antigen class I. Nature, 458 (7238), pp. 641-645. Read abstract | Read more

The rapid and extensive spread of the human immunodeficiency virus (HIV) epidemic provides a rare opportunity to witness host-pathogen co-evolution involving humans. A focal point is the interaction between genes encoding human leukocyte antigen (HLA) and those encoding HIV proteins. HLA molecules present fragments (epitopes) of HIV proteins on the surface of infected cells to enable immune recognition and killing by CD8(+) T cells; particular HLA molecules, such as HLA-B*57, HLA-B*27 and HLA-B*51, are more likely to mediate successful control of HIV infection. Mutation within these epitopes can allow viral escape from CD8(+) T-cell recognition. Here we analysed viral sequences and HLA alleles from >2,800 subjects, drawn from 9 distinct study cohorts spanning 5 continents. Initial analysis of the HLA-B*51-restricted epitope, TAFTIPSI (reverse transcriptase residues 128-135), showed a strong correlation between the frequency of the escape mutation I135X and HLA-B*51 prevalence in the 9 study cohorts (P = 0.0001). Extending these analyses to incorporate other well-defined CD8(+) T-cell epitopes, including those restricted by HLA-B*57 and HLA-B*27, showed that the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P < 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level. This process of viral adaptation may dismantle the well-established HLA associations with control of HIV infection that are linked to the availability of key epitopes, and highlights the challenge for a vaccine to keep pace with the changing immunological landscape presented by HIV. Hide abstract

Frater AJ, Brown H, Oxenius A, Günthard HF, Hirschel B, Robinson N, Leslie AJ, Payne R, Crawford H, Prendergast A, Brander C, Kiepiela P, Walker BD, Goulder PJ, McLean A, Phillips RE et al. 2007. Effective T-cell responses select human immunodeficiency virus mutants and slow disease progression. J Virol, 81 (12), pp. 6742-6751. Read abstract | Read more

The possession of some HLA class I molecules is associated with delayed progression to AIDS. The mechanism behind this beneficial effect is unclear. We tested the idea that cytotoxic T-cell responses restricted by advantageous HLA class I molecules impose stronger selection pressures than those restricted by other HLA class I alleles. As a measure of the selection pressure imposed by HLA class I alleles, we determined the extent of HLA class I-associated epitope variation in a cohort of European human immunodeficiency virus (HIV)-positive individuals (n=84). We validated our findings in a second, distinct cohort of African patients (n=516). We found that key HIV epitopes restricted by advantageous HLA molecules (B27, B57, and B51 in European patients and B5703, B5801, and B8101 in African patients) were more frequently mutated in individuals bearing the restricting HLA than in those who lacked the restricting HLA class I molecule. HLA alleles associated with clinical benefit restricted certain epitopes for which the consensus peptides were frequently recognized by the immune response despite the circulating virus's being highly polymorphic. We found a significant inverse correlation between the HLA-associated hazard of disease progression and the mean HLA-associated prevalence of mutations within epitopes (P=0.028; R2=0.34). We conclude that beneficial HLA class I alleles impose strong selection at key epitopes. This is revealed by the frequent association between effective T-cell responses and circulating viral escape mutants and the rarity of these variants in patients who lack these favorable HLA class I molecules, suggesting a significant pressure to revert. Hide abstract

Zimbwa P, Milicic A, Frater J, Scriba TJ, Willis A, Goulder PJ, Pillay T, Gunthard H, Weber JN, Zhang HT, Phillips RE. 2007. Precise identification of a human immunodeficiency virus type 1 antigen processing mutant. J Virol, 81 (4), pp. 2031-2038. Read abstract | Read more

Human immunodeficiency virus type 1 (HIV-1) evokes a strong immune response, but the virus persists. Polymorphisms within known antigenic sites result in loss of immune recognition and can be positively selected. Amino acid variation outside known HLA class I restricted epitopes can also enable immune escape by interfering with the processing of the optimal peptide antigen. However, the lack of precise rules dictating epitope generation and the enormous genetic diversity of HIV make prediction of processing mutants very difficult. Polymorphism E169D in HIV-1 reverse transcriptase (RT) is significantly associated with HLA-B*0702 in HIV-1-infected individuals. This polymorphism does not map within a known HLA-B*0702 epitope; instead, it is located five residues downstream of a HLA-B*0702-restricted epitope SPAIFQSSM (SM9). Here we investigate the association between E169D and HLA-B*0702 for immune escape via the SM9 epitope. We show that this single amino acid variation prevents the immune recognition of the flanked SM9 epitope by cytotoxic T cells through lack of generation of the epitope, which is a result of aberrant proteasomal cleavage. The E169D polymorphism also maps within and abrogates the recognition of an HLA-A*03-restricted RT epitope MR9. This study highlights the potential for using known statistical associations as indicators for viral escape but also the complexity involved in interpreting the immunological consequences of amino acid changes in HIV sequences. Hide abstract

Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, de Pierres C, Mncube Z, Mkhwanazi N, Bishop K, van der Stok M, Nair K, Khan N, Crawford H, Payne R, Leslie A, Prado J, Prendergast A, Frater J, McCarthy N, Brander C, Learn GH, Nickle D, Rousseau C, Coovadia H, Mullins JI, Heckerman D, Walker BD, Goulder P et al. 2007. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med, 13 (1), pp. 46-53. Read abstract | Read more

Selection of T-cell vaccine antigens for chronic persistent viral infections has been largely empirical. To define the relationship, at the population level, between the specificity of the cellular immune response and viral control for a relevant human pathogen, we performed a comprehensive analysis of the 160 dominant CD8(+) T-cell responses in 578 untreated HIV-infected individuals from KwaZulu-Natal, South Africa. Of the HIV proteins targeted, only Gag-specific responses were associated with lowering viremia. Env-specific and Accessory/Regulatory protein-specific responses were associated with higher viremia. Increasing breadth of Gag-specific responses was associated with decreasing viremia and increasing Env breadth with increasing viremia. Association of the specific CD8(+) T-cell response with low viremia was independent of HLA type and unrelated to epitope sequence conservation. These population-based data, suggesting the existence of both effective immune responses and responses lacking demonstrable biological impact in chronic HIV infection, are of relevance to HIV vaccine design and evaluation. Hide abstract

Frater AJ, Edwards CT, McCarthy N, Fox J, Brown H, Milicic A, Mackie N, Pillay T, Drijfhout JW, Dustan S, Clarke JR, Holmes EC, Zhang HT, Pfafferott K, Goulder PJ, McClure MO, Weber J, Phillips RE, Fidler S et al. 2006. Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts. J Virol, 80 (14), pp. 7226-7234. Read abstract | Read more

Human immunodeficiency virus type 1 (HIV-1) genetic diversity is a major obstacle for the design of a successful vaccine. Certain viral polymorphisms encode human leukocyte antigen (HLA)-associated immune escape, potentially overcoming limited vaccine protection. Although transmission of immune escape variants has been reported, the overall extent to which this phenomenon occurs in populations and the degree to which it contributes to HIV-1 viral evolution are unknown. Selection on the HIV-1 env gene at transmission favors neutralization-sensitive variants, but it is not known to what degree selection acts on the internal HIV-1 proteins to restrict or enhance the transmission of immune escape variants. Studies have suggested that HLA class I may determine susceptibility to HIV-1 infection, but a definitive role for HLA at transmission remains unproven. Comparing populations of acute seroconverters and chronically infected patients, we found no evidence of selection acting to restrict transmission of HIV-1 variants. We found that statistical associations previously reported in chronic infection between viral polymorphisms and HLA class I alleles are not present in acute infection, suggesting that the majority of viral polymorphisms in these patients are the result of transmission rather than de novo adaptation. Using four episodes of HIV-1 transmission in which the donors and recipients were both sampled very close to the time of infection we found that, despite a transmission bottleneck, genetic variants of HIV-1 infection are transmitted in a frequency-dependent manner. As HIV-1 infections are seeded by unique donor-adapted viral variants, each episode is a highly individual antigenic challenge. Host-specific, idiosyncratic HIV-1 antigenic diversity will seriously tax the efficacy of immunization based on consensus sequences. Hide abstract

Scherer A, Frater J, Oxenius A, Agudelo J, Price DA, Günthard HF, Barnardo M, Perrin L, Hirschel B, Phillips RE, McLean AR, Swiss HIV Cohort Study et al. 2004. Quantifiable cytotoxic T lymphocyte responses and HLA-related risk of progression to AIDS. Proc Natl Acad Sci U S A, 101 (33), pp. 12266-12270. Read abstract | Read more

There are significant associations between possession of certain HLA class I alleles and rate of progression to AIDS. Immunological data provide an explanatory mechanism for this relationship. Patients with HLA types associated with rapid disease progression recognize a significantly smaller fraction of their known repertoire of viral epitopes than do patients with HLA types associated with slow progression. Population frequency of HLA types (or supertypes) and their capacity to elicit cytotoxic T lymphocyte responses are also negatively correlated. These data provide an immunological mechanism to explain HLA-related risk of progression to AIDS and emphasize the central role of viral evolution in the pathogenesis of HIV. Hide abstract

Frater AJ, Beardall A, Ariyoshi K, Churchill D, Galpin S, Clarke JR, Weber JN, McClure MO. 2001. Impact of baseline polymorphisms in RT and protease on outcome of highly active antiretroviral therapy in HIV-1-infected African patients. AIDS, 15 (12), pp. 1493-1502. Read abstract | Read more

To assess the therapeutic response and investigate the significance of polymorphic codons in African patients receiving highly-active antiretroviral therapy (HAART). Hide abstract

Frater AJ, Chaput CC, Beddows S, Weber JN, McClure MO. 2001. Simple detection of point mutations associated with HIV-1 drug resistance. J Virol Methods, 93 (1-2), pp. 145-156. Read abstract | Read more

A novel assay is described for the detection of HIV-1 drug resistance that is simple, cheap and sensitive. HIV-1 drug resistance in B and non-B HIV-1 subtypes was investigated using Mutagenically-Separated PCR (MS--PCR) --- a competitive semi-nested PCR which uses mutagenic primers. The assay was assessed for sensitivity, specificity and its ability to detect mutant virus within a mixed mutant--wild-type population. Gene sequencing was carried out simultaneously for comparison. MS--PCR detected five copies of HIV-1 RNA from laboratory isolates and 50 copies from patient samples. We demonstrate 100% specificity of detection for wild type or mutant virus for clades A, B, C, D and E. For mixed populations of virus, MS--PCR can detect at least a 10% mix of wild type:mutant, or vice-versa. When applied to African patient samples MS--PCR detected 91.6% of the codons tested. Concordance with sequencing data was 88.8% for protease and 97.2% for RT. MS--PCR is sensitive and specific for the detection of mutations in HIV-1, and can be adapted easily to test for resistance at any codon of interest. Hide abstract

HIV Eradication: exploring the molecular biology of the HIV reservoir

The candidate will undertake studies directed towards finding a cure for HIV infection, and will characterise the HIV reservoir using techniques such as qPCR, sequencing (Sanger and Next Generation approaches) and phylogenetics. The aim of the project is to explore further the cellular and anatomical characteristics of the HIV reservoir and the potential impact of novel interventions such as HDAC inhibitors within clinical trials. The work will be carried out as part of the CHERUB cooperative, ...

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