Research into the effects of host genetics on HIV disease susceptibility and progression, and on the efficacy and toxicity of drug treatment, occupies a particular position in the landscape of HIV research. On the one hand, an increased understanding of the role played by host genetic factors in determining the response to HIV infection (for a review see ) will undoubtedly contribute to our understanding of the nature of the disease process, and will ultimately assist the development of therapeutic strategies – such as vaccines – that can augment the genetically determined host immune response to HIV infection. In a limited number of cases a favourable host genetic profile will provide protection from HIV infection, or will confer ‘long-term non-progressor’ status following infection, allowing durable control of HIV-associated disease progression without the requirement for drug therapy. On the other hand, the relevance of these genetic factors to the routine clinical management of HIV-infected patients is often perceived as being marginal compared with the cost and difficulty associated with undertaking genetic testing, so that the assessment of host genetic factors is not incorporated into standard guidelines for HIV management [2,3]. Moreover, whilst genetic factors may significantly alter the rate of disease progression at an individual level, clinical decisions are currently based on defined endpoints such as CD4 T-cell number, HIV viral load, rate of CD4 T-cell decline and the clinical expression of AIDS- defining illnesses, irrespective of the host factors that may determine these values [2,3].
Several reviews are available that enumerate those host genetic factors that have a demonstrable effect on the course of HIV infection, including a recent comprehensive assessment of this field of research . Here we will attempt to provide a broad conceptual framework for considering the impact of host genetic diversity on HIV/AIDS; one that argues that host genetic variation is an important factor in the response to HIV for every infected individual, and within every infected population; not just for those few individuals who carry genetic variants that have powerful protective (or deleterious) effects on HIV disease progression . This review incorporates an evolutionary perspective that recognizes the ongoing dynamic interplay between host and viral genetic diversity at the population level, providing the driving force for the selection of favourable host genetic profiles as well as for viral mutations that are best adapted to these host effects. We also present a clinical perspective that considers analogies between ‘endogenous’ antiviral effects conferred by a broad spectrum of host genetic factors, and the effects of drug therapy. This model provides for a broad conception of the role of host factors in determining the overall progression of HIV disease, both before and after the introduction of antiretroviral therapy (Fig. 1).
An evolutionary perspective: host–pathogen interactions at the genetic level
One interesting by-line in the story of the human genome project has been that our DNA is littered with the remnants of previous encounters with retroviruses. It is estimated that approximately 8% of human genetic sequence is derived directly from retroviral elements, and that subsequent transposition and recombination events have amplified this proportion to above 40% . Moreover, the more recent human endogenous retroviruses have been acquired in the period since human evolution diverged from our nearest primate ancestors . We have therefore encountered retroviral pathogens throughout our evolutionary history, and these infectious agents are likely to have shaped the evolution of critical aspects of our immunological response to viral infection. Recent evidence points to the purifying pressure that may be exerted by pathogenic viruses on host genetic diversity, suggesting that the selection of a limited number of major histocompatibility complex (MHC) alleles able to direct a strong protective immunological response against both SIV and the closely related human lentivirus HIV-1 has been a feature of the successful adaptation made by chimpanzees to SIV . Evolutionary history is punctuated by these bottleneck events in which diversity is sacrificed in order to ensure the survival of populations in the face of epidemic or endemic pathogens, and it is these events that are likely to have determined the non-random distribution of MHC variants in different ethnically and geographically separated groups [8–11]. It is also interesting to observe, however, that the incorporation of retroelements into the human genome creates sites of genetic instability that have contributed to large-scale genetic duplication and recombination events – including within the MHC region – thus producing quantum evolutionary changes and the development of new genetic loci critical for immune function .
If we consider populations both past and present with no access to effective treatment for HIV infection, the only ‘weapons’ available to combat the spread of HIV are host genetic diversity (at a given time) and host genetic adaptation (developing over generations under the selective pressure of endemic HIV infection). Given that HIV is capable of rapid genetic adaptation to the host immune response, producing multiple generations of virions every day, it would be anticipated that the pathogen has a marked advantage in this conflict. However, in the human host's favour, there is a remarkable degree of diversity in key regions of the genome that encode for proteins that shape the immune response, so that adaptation to one individual does not provide a particularly strong advantage when infection is passed on to the next host. It is this ‘strength in diversity’ that defines the host population's most significant natural advantage; one that needs to be exploited in the development of therapeutic strategies such as vaccines .
Can we extrapolate this evolutionary perspective to the present era in any useful way? After more than 20 years of epidemic HIV infection (i.e., approximately one human generation), it is probably too early to see if human HLA diversity is being affected by this selective pressure. However, this time scale is more than ample for the generation of viral diversity in response to the genetically encoded human immune system. In this context, the ability of autologous HIV to make the appropriate mutational adaptations to HLA-restricted immune response has been demonstrated at the population level, where it predicts pre-treatment viral load setpoint . This capacity for adaptation may be determined by: (i) the genetic barrier to escape (i.e., the number of mutational steps required to induce escape at a specific viral amino acid residue); (ii) costs to viral replicative fitness associated with escape mutations; (iii) the breadth of the HLA-restricted immune response to viral antigens (i.e., the number of epitopes recognized by a specific HLA allele); and (iv) the residual cytotoxic T lymphocyte (CTL) response present following escape mutation (see Fig. 2). We can therefore see that there is a dynamic relationship between the host and the infecting virus that is played out at the (host) individual level, as the virus seeks to evade the immune responses of the host in which it finds itself. This also translates to the population level, as HIV is passed from one individual to another through a population. It is therefore worth bearing in mind when considering the impact of specific host genetic factors that HIV represents a constantly shifting target for the host immune response.
Host genetic factors and the natural history of HIV disease progression
The host immune response to HIV infection is shaped to a large extent by an individual's repertoire of antigen recognition molecules encoded within the MHC on chromosome 6 [15,16]. This region of the human genome is characterized by intense polymorphism, with over 1600 individual alleles currently known at the major HLA loci (Class I, HLA-A, HLA-B, HLA-C; Class II, HLA-DR). Hence, the inheritance of HLA alleles as well as polymorphic immunoregulatory genes within the central MHC region that are in strong linkage disequilibrium with them (e.g., cytokines such as tumour necrosis factor-α, chaperone proteins such as heat shock proteins), profoundly influences the capacity to recognize and destroy pathogens that have managed to breach the defences provided by protective mucosal barriers and innate immune responses . The adaptive immune response also uses auxiliary systems of antigen recognition that are also highly polymorphic, such as the killer inhibitory receptor (KIR) gene cluster on chromosome 19 [18–21] which is involved in modulating immune responses through recognition of ‘missing self’ (identifying the absence of Class I MHC surface expression) as well as of specific ligand epitopes present on HLA-C and HLA-B alleles [18–21]. Polymorphic variation in chemokine receptor expression is also an important source of host defence against HIV , which is to some degree countered by the virus’ ability to utilize alternative coreceptors for cellular entry. Finally, there are a number of novel mechanisms used by the human host to neutralize the metabolic and transcriptional machinery employed by HIV for ongoing replication, which may be exemplified by the ability of the APOBEC3G gene product to induce hypermutation in the HIV gene sequence by interfering with pyrimidine nucleotide metabolism [22–24]. These non-antigen specific mechanisms are not subject to as much genetic polymorphism, and have in general provoked HIV to ‘solve’ the problems they pose (for example, the ability of the Vif regulatory protein to counter the antiviral effects of the APOBEC3G product [24–26]).
Impact of MHC alleles and haplotypes on HIV disease progression
Given that the immune response to viral antigens mediated by cytotoxic CD8 T cells is dependent on the presence of Class I MHC molecules (e.g., HLA-A and HLA-B), and that the recognition of peptide motifs by this system is highly specific for a given HLA allele, it is perhaps not surprising that the inheritance of certain Class I alleles has been associated with significantly more (or in some cases, less) effective immunological control of HIV infection compared with others [1,27]. A number of studies have identified effects of HLA alleles that are favourable in some cases (e.g., HLA-B57, HLA-B27) and unfavourable in others (e.g., HLA-B35 and HLA-B22 subtypes) [1,27–36], and have demonstrated that the combined effects of HLA alleles are predictive of long-term non-progressor status  and viral load set-point in the pre-treatment phase [30–32]. HLA-B18 has also been found to predict slower progression of HIV disease , and has also been linked to protection from acquiring HIV infection in two studies involving multiply exposed sex workers in Thailand  and Kenya . As previously mentioned, these dominant allelic associations represent extreme examples of the dynamic relationship between HLA-restricted antigen recognition and the capacity for HIV to evade immune surveillance through mutation . At one end of this spectrum are the powerful protective alleles such as HLA-B57 and HLA-B27, whilst at the other end of the spectrum are alleles that may recognize epitopes with few constraints to generating successful viral escape mutations. In each case, it is the effect on viral load setpoint that is primarily responsible for genetic associations with altered disease progression. As presented in Fig. 2, the factors outlined above that determine the antiviral efficacy of specific HLA alleles are analogous to those determining antiretroviral drug efficacy. Hence, concepts that are familiar to clinicians who manage HIV therapy may also be applied to the ‘endogenous drugs’ that are represented by inherited HLA alleles.
Modulating HIV disease progression at multiple levels
In certain cases, the influence of HLA alleles on disease progression appears to extend beyond a direct effect on HIV viral load (Fig. 1). For example, individuals who carry HLA-B8 as well as other genetic markers within the MHC region that are strongly linked to this allele (denoted the 8.1 ancestral haplotype) experience a more rapid CD4 T-cell decline , particularly early in the course of disease (from seroconversion to CD4 < 20%; Fig. 3) . Further genetic mapping of this association has shed some light on the CD4 T cell-depleting effect of this haplotype, indicating that this propensity is associated with unknown polymorphisms present within the central MHC region, rather than with HLA-B8 itself . Hence, it is plausible that immunoregulatory gene products encoded in this region determine the efficiency of immune-mediated CD4 T-cell destruction in response to a given HIV burden. This concept is supported by observations that a relative deficiency of type-1 cytokine production, characteristically seen with the HLA-B8/-DR3- associated MHC haplotype , is associated with increased susceptibility to activation-induced CD4 T-cell death .
Looking beyond the direct consequences of HIV infection (i.e., HIV viral load and CD4 T-cell decline), genetic factors also appear to independently modulate susceptibility to infections caused by opportunistic intracellular pathogens. For example, risk of developing HHV-8-associated Kaposi's sarcoma has been associated with HLA-DR5 in both ‘classical’ [43,44] forms of the disease as well as in HIV-associated Kaposi's sarcoma (along with HLA-DR1) [45–51] in Caucasian (but not African ) populations, whilst HLA-DR3 (a component of the HLA-B8-associated ancestral MHC haplotype) is protective [50,51]. In the case of the common Caucasian MHC haplotype that includes HLA-A1/ -B8/-DR3 alleles, these data indicate that individuals carrying this haplotype experience more rapid CD4 T-cell decline and are generally at increased risk of opportunistic infections; but at the same remain at low risk of developing Kaposi's sarcoma [50,51]. Susceptibility to disseminated Mycobacterium avium complex infection has also been linked to Class II MHC region, in this case to the closely linked HLA-DRB1*1501 and -DQ*0602 alleles previously associated with risk of tuberculosis and leprosy in populations where these diseases are prevalent [53,54]. Immune restoration disease (IRD) associated with aberrant inflammatory responses to pathogens following the introduction of antiretroviral therapy have also been associated with HLA alleles, with significant associations noted between the HLA-B44/-DR4 MHC haplotype and cytomegalovirus-related IRD .
These strong genetic risk factors indicate that susceptibility to specific opportunistic diseases is not simply a product of the severity of immunosuppresion, but is also modulated by the genetically determined immune response to the relevant pathogen; again suggesting that ‘progression to AIDS’ is a term that encompasses a broad range of pathological events. Additionally, HLA alleles expressed in the context of broader MHC haplotypes may have complex associations with HIV/AIDS progression, as outlined in Fig. 3.
Impact of chemokine receptor polymorphism
The disease-modifying effect of a 32-base pair deletion in the CCR5 receptor gene (CCR5Δ32) present in around 10% of Caucasians, and the significant protection against HIV-1 infection afforded by homozygosity at this allele, represents the prototypic association between a host genetic factor and altered HIV disease progression (reviewed in [1,56]). Interestingly, this genetic variant may have arisen in Northern European populations comparatively recently  under selective pressure provided by epidemic viral pathogens such as smallpox  or variola .
With increasing knowledge of the haplotype structure of the chemokine receptor genes, and the role of chemokine ligands such as MIP-1α, MIP-1β and RANTES in modulating chemokine receptor function, it has become apparent that numerous functional polymorphisms exist in these genetic systems [60,61]; extending the ‘breadth’ of effects of chemokine receptor variation far beyond a model with CCR5Δ32 as a single important loss-of-function variant. This topic has been elegantly reviewed elsewhere [1,56], and the issue of genetic variation in these interacting systems has been addressed in a large multinational study that also points out that effects of these host genetic factors on HIV/AIDS differ according to the population studied . Hence, the overall impact of chemokine receptor polymorphism and chemokine receptor ligand polymorphism may be considered in a similar manner to the MHC system, in that genetic variation is relevant to the response to HIV-1 infection in most if not all individuals, whilst dominant effects on disease progression (e.g., CCR5Δ32) are relatively uncommon.
The impact of chemokine receptor genotype may also provide some insights regarding the interdependent nature of host genetic effects on disease progression. First, the dominant genetic effect of the CCR5Δ32 receptor mutation can provide a significant barrier to successful HIV infection at an individual level, providing significant associations with delayed disease progression and long-term non-progressor status [1,56]. However, the predictive value of CCR5Δ32 on disease progression appears to be dependent on: (i) disease stage, with evidence for early effects that are subsequently lost as duration of HIV infection increases [62–64]; and (ii) presence of other host genetic factors, particularly HLA, that combine with CCR5Δ32 to determine ‘non-progressor’ or ‘progressor’ status [65,66]. This is not to downplay the impact of the CCR5Δ32 mutation or other protective chemokine receptor mutations that can certainly delay disease progression to an extent that is clinically relevant , but to place these genetic factors within an overall ‘landscape’ of selective pressure in untreated individuals (Fig. 4). For example, CCR5Δ32 heterozygosity is not in itself sufficient to confer non-progressor status [65,66], nor is carriage of the most potent protective HLA allele, HLA-B*5701 . However, each of these host genetic factors appears to contribute to a more broadly defined selective pressure provided by multiple genetically determined factors [29–31,34] (Fig. 4). In the case of chemokine receptor gene polymorphisms, by providing another source of selective pressure (in this case, against the emergence of CCR5-dependent M-tropic viral strains) , these host genetic effects contribute to the overall immunological and/or drug pressure against which HIV must adapt to optimize viral fitness. The CCR5Δ32 mutation may also augment the magnitude and durability of virological responses to HIV therapy [69–71] consistent with an ongoing contribution to overall virological control during treatment (Fig. 5), although this association has not been consistently observed [72,73].
Potential role of KIR genotypes and haplotypes
The KIR complex on chromosome 19 is a highly polymorphic region of the genome which encodes receptors that are widely expressed on natural killer cells. Knowledge of the genomic structure of this region is still incomplete, and the natural ligands for a number of KIR gene products remain unknown. However, cognate interactions between killer immunoglobulin-like receptors and their ligands may inhibit alloreactivity and cytotoxicity, but may also activate cell-mediated immune responses depending on the KIR gene involved [18–21].
The involvement of the KIR complex in modulating HIV disease progression has been a subject of increasing attention in recent times. For example, a known KIR recognition motif that is common to a number of HLA-B alleles (denoted Bw4) has been associated with slower HIV disease progression , with further data suggesting that the interaction of the Bw4 motif and a specific activating KIR (KIR3DS1) may explain this association . However, strong linkage disequilibrium within the KIR complex makes it difficult to assign effects to individual KIR genes within a haplotype. In recent studies we have identified associations between rapid CD4 T-cell decline and a KIR haplotype that contains KIR2SD2 and a predominance of activatory KIR alleles . These data suggest that the effect of KIR genotype on HIV disease progression may modify the susceptibility of CD4 T cells to undergo lysis, rather than affecting viral load set point, possibly reflecting the ability of immune cells expressing KIR to recognize and destroy HIV-infected CD4 T cells through recognition of both ‘positive’ signals (e.g., epitopes expressed on HLA-C and HLA-B alleles) and ‘negative’ signals (e.g., reduced Class I MHC expression – `missing self') induced by regulatory viral proteins such as nef . In this context, the genetically determined balance between inhibitory and activatory KIR alleles may play an important role in shaping the immunological response, along with the inheritance of HLA alleles with which KIR alleles interact.
Host genetic factors and the response to HIV therapy
Here the major focus of research has been on potential associations between drug hypersensitivity reactions and HLA alleles. This effort has borne fruit in the case of abacavir hypersensitivity, where two independent studies have demonstrated strong associations between HLA-B*5701 and susceptibility to this syndrome [78,79]. The predictive value of genetic testing may be further improved with the incorporation of a central MHC polymorphism (HSPA1L within the heat shock protein gene cluster) as well as HLA-B*5701, which in one study increased the positive predictive value of testing to > 90% and the negative predictive value to > 99% . This is certainly one area of research into host genetic effects that may have direct implications for clinical practice, as the avoidance of this hypersensitivity syndrome through prospective genetic testing may significantly reduce the burden of toxicity- associated morbidity (and mortality) associated with the use of abacavir .
It is also possible that susceptibility to nevirapine hypersensitivity – manifesting as potentially life-threatening hepatotoxicity with or without rash – is also conferred by genetic factors, as this syndrome is similar to abacavir hypersensitivity in that susceptible individuals develop symptoms after short-term exposure (including HIV-negative patients receiving nevirapine for post-exposure prophlaxis) [81–83]. The protective effect of lower CD4 T-cell counts in the case of nevirapine hypersensitivity , however, suggests that a genetic association is more likely to involve Class II MHC alleles such as HLA-DR, as indeed is the case for most of the described HLA-drug associations.
Another aspect of HLA–drug associations that has not yet received much attention is the potential for HLA alleles to influence the efficacy of drug therapy. This possibility arises from the notion that mutations selected by drug therapy may also be sites where selective pressure is provided by HLA alleles. Whilst the resistance mutations associated with specific antiretroviral drugs are generally distinct from ‘natural’ escape mutations described above, interactions may nevertheless exist, as the selective pressure of drug therapy provides a new impetus for site-specific mutations. This may result in: (i) the generation of novel epitopes for HLA-restricted immune recognition, as has been demonstrated for the M184V reverse transcriptase mutation which can act as a neoepitope for HLA-A2 ; and (ii) facilitation (or impairment) of the capacity for escape mutations to develop at the site of a drug resistance mutation, or at more distant sites through effects on conformational structure and/or charge of peptide sequences. For example, a protease inhibitor resistance mutation (V82A) that occurs within a high-avidity HLA-A2-restricted epitope (residues 76–84) leads to abrogation of immune recognition at this site, so that the protease inhibitor-selected V82A mutation acts as a protease inhibitor and a CTL escape mutant in HLA-A2-positive individuals . More work is required in this area, but it is conceivable that altered risk of developing drug resistance mutations associated with certain HLA alleles may prove to be sufficiently strong in some cases to influence the choice of antiretroviral regimen in the future.
Combining host and drug antiviral effects: clinical utility of host genetic factors?
At a fundamental level, it may be that drug therapy for HIV is more effective when there is also a contribution from the host immune response towards the suppression of viral load. Evidence supporting this proposition has been provided by studies demonstrating that CTL responses to HIV remains relevant during HIV treatment [87–92], particularly in the presence of incompletely suppressive treatment associated with detectable viraemia [89,90], and that this immune response contributes to the virological response to therapy [89,90]. Importantly, the effectiveness of CTL responses during therapy is predicted by those measured prior to commencing treatment [87,88], an observation that may explain why high viral load at baseline  and early in the course of treatment with HAART regimens [94,95] is associated with earlier virological failure  and higher rates of HIV-associated mortality .
It may therefore be possible to employ the same pragmatic approach to ‘managing’ host genetic effects that is already familiar to prescribers of antiretroviral therapy. That is, the level of viraemia in the pre-treatment stage provides a surrogate measure of the overall selective pressure provided by host genetic factors, and the degree to which the autologous virus has been able to adapt to this host immune response. For individuals with residual immunological control of viraemia, it may be argued that the viral load should be considered along with CD4 T-cell count when deciding when to initiate antiretroviral therapy, and which regimens to use. Delaying therapy until the viral load is very high (i.e., > 100 000 copies HIV RNA/ml) is likely to place a greater reliance on the efficacy of drug therapy to control viraemia, so that optimally effective first-line therapy is paramount in these individuals. On the other hand, initiating treatment while virological control is still present may allow for improved long-term outcomes by combining ‘endogenous drugs’ with antiretroviral therapy to effectively combat HIV (Fig. 4). Preserving the activity of endogenous antiviral factors for as long as possible may also have particular importance in compartments such as the central nervous system that may receive limited benefit from antiretroviral treatment .
It is argued here that our conception of host genetic factors as determinants of HIV disease progression needs to extend beyond those few examples where allelic variation at a single genetic locus confers a significant beneficial or harmful effect, to see that genetic variation operates at multiple levels to modulate disease progression for each individual and across populations. Recognizing that genetically determined factors operate in important ways in all infected individuals to modulate the immunological response to HIV infection, and that this variable host response then influences the evolution and diversity of the viral genome, allows for more powerful approaches to investigate both the immunological and virological aspects of HIV disease at the population level. Acknowledging the important contribution of host factors in controlling HIV infection throughout the course of the disease process – including the treatment phase – may also allow for increasingly optimized approaches to long-term HIV management.
This knowledge can then be utilized in a number of ways. From a research perspective, an understanding of the inherently complex and dynamic nature of host–pathogen interactions can shape the development of appropriate research methods. For example, utilizing ‘progression to AIDS’ as a study endpoint may encompass diverse effects including: susceptibility to HIV infection following exposure, HIV viral load setpoint, rate of CD4 T-cell decline, and susceptibility to specific AIDS-defining illnesses. Analysing these outcomes as independent and potentially interactive variables, however, may shed light on the underlying pathophysiology and help to define potential targets for therapeutics. Perhaps the most immediate and practical application of such knowledge is in vaccine development, a long sought after advance in HIV prevention, where a detailed knowledge of dynamic host–viral interactions, and how these interactions at the individual level then play out at the population level, is paramount for success. In this way, the advantages provided by the intensity of our host genetic diversity can be exploited to overcome the problems associated with HIV diversity; a concept that may be illustrated by a quotation attributed to the American president Abraham Lincoln:
`You can fool some of the people all of the time, and all of the people some of the time; but you can't fool all of the people all of the time.'
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