Origins of HIV and the Evolution of Resistance to AIDS

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Science  28 Jul 2006:
Vol. 313, Issue 5786, pp. 462-466
DOI: 10.1126/science.1123016


The cross-species transmission of lentiviruses from African primates to humans has selected viral adaptations which have subsequently facilitated human-to-human transmission. HIV adapts not only by positive selection through mutation but also by recombination of segments of its genome in individuals who become multiply infected. Naturally infected nonhuman primates are relatively resistant to AIDS-like disease despite high plasma viral loads and sustained viral evolution. Further understanding of host resistance factors and the mechanisms of disease in natural primate hosts may provide insight into unexplored therapeutic avenues for the prevention of AIDS.

Human immunodeficiency viruses HIV-1 and HIV-2, the causes of AIDS, were introduced to humans during the 20th century and as such are relatively new pathogens. In Africa, many species of indigenous nonhuman primates are naturally infected with related lentiviruses, yet curiously, AIDS is not observed in these hosts. Molecular phylogeny studies reveal that HIV-1 evolved from a strain of simian immunodeficiency virus, SIVcpz, within a particular subspecies of the chimpanzee (Pan troglodytes troglodytes) on at least three separate occasions (1). HIV-2 originated in SIVsm of sooty mangabeys (Cercocebus atys), and its even more numerous cross-species transmission events have yielded HIV-2 groups A to H (2, 3). The relatively few successful transfers, in contrast to the estimated >35 different species of African nonhuman primates that harbor lentivirus infections, indicate that humans must have been physically exposed to SIV from other primate species, such as African green monkeys. However, these SIV strains have not been able to establish themselves sufficiently to adapt and be readily transmitted between humans. Thus, it is important to understand the specific properties required for successful cross-species transmission and subsequent adaptation necessary for efficient spread within the new host population. Notably, among the three SIVcpz ancestors of HIV-1 that have successfully crossed to humans, only one has given rise to the global AIDS pandemic: HIV-1 group M with subtypes A to K. Here, we survey genetically determined barriers to primate lentivirus transmission and disease and how this has influenced the evolution of disease and disease resistance in humans.

Origins and Missing Links

A new study of SIVcpz not only confirms that HIV-1 arose from a particular subspecies of chimpanzee, P. t. troglodytes, but also suggests that HIV-1 groups M and N arose from geographically distinct chimpanzee populations in Cameroon. Keele et al. (1) combined pain-staking field work collecting feces and urine from wild chimpanzee troupes with equally meticulous phylogenetic studies of individual animals and the SIV genotypes that some of them carry. These data have enabled a more precise origin of HIV-1 M and N to be determined. The origin of group O remains to be identified, but given the location of human cases, cross-species transmission may have occurred in neighboring Gabon.

Although HIV-1 has clearly come from SIVcpz, only some of the extant chimpanzee populations harbor SIVcpz. SIVcpz itself appears to be a recombinant virus derived from lentiviruses of the red capped mangabey (SIVrcm) and one or more of the greater spot-nosed monkey (SIVgsn) lineage or a closely related species (4). Independent data reveal that chimpanzees can readily become infected with a second, distantly related lentivirus (5), suggesting that recombination of monkey lentiviruses occurred within infected chimpanzees, giving rise to a common ancestor of today's variants of SIVcpz, which were subsequently transmitted to humans (Fig. 1A).

Fig. 1.

Possible cross-species transmission events giving rise to SIVcpz as a recombinant of different monkey-derived SIVs. Three different scenarios are considered. (A) P. t. troglodytes as the intermediate host. Recombination of two or more monkey-derived SIVs [likely SIVs from red capped mangabeys (rcm), and the greater spot-nosed (gsn) or related SIVs, and possibly a third lineage]. Recombination requires coinfection of an individual with one or more SIVs. Chimpanzees have not been found to be infected by these viruses. (B) Unidentified intermediate host. The SIVcpz recombinant develops and is maintained in a primate host that has yet to be identified, giving rise to the ancestor of the SIVcpz/HIV-1 lineage. P. t. troglodytes functions as a reservoir for human infection. (C) An intermediate host that has yet to be identified, which is the current reservoir of introductions of SIVcpz into current communities of P. t. troglodytes and P. t. schweinfurthii, as a potential source of limited foci of diverse SIVcpz variants.

It is tempting to speculate that the chimeric origin of SIVcpz occurred in chimpanzees before subspeciation of P. t. troglodytes and P. t. schweinfurthii. However, this proposed scenario raises several questions: Why is SIVcpz not more widely distributed in all four of the proposed chimpanzee subspecies? Why is it so focal in the two subspecies in which it is currently found? These issues raise further questions regarding the chimpanzee's anthropology, its natural history, the modes of transmission of SIVcpz among chimpanzees, and the reasons that it is not a severe pathogen (5). These questions lead to other hypotheses that speculate about the intermediate hosts that might have given rise to SIVcpz and ultimately to HIV-1 (Fig. 1, B and C).


Although the interspersal of SIVcpz and SIVsm in the molecular phylogeny of HIV-1 and HIV-2, respectively, reveals successful cross-species transmission events, there are a surprisingly limited number of documented cases, and direct evidence of a simian-to-human transmission is still missing. This suggests that, in contrast to a fulminant zoonotic (a pathogen regularly transmitted from animals to humans), a complex series of events (for instance, adaptations and acquisition of viral regulatory genes such as vpu, vif, nef, and tat and structural genes gag and env) was required for these SIVs to infect a human and to sustain infection at levels sufficient to become transmissible within the local human population. Closer examination of HIV-1 and HIV-2 groups and subgroups reveals differences in variants and genetic groups and rates of transmission in different populations even after infection is well established. This complex picture is beginning to merge with our understanding of the dynamics of evolving lentiviral variants that infect the natural nonhuman primate hosts. For instance, within the eight HIV-2 groups, A and B are endemic, whereas the others represent single infected persons clustering closely to SIVsm strains (2, 6). These observations reinforce the notion that important adaptations have been necessary for the virus to acquire the ability to be efficiently transmitted.

Since its emergence, HIV-1 group M has diverged into numerous clades or subtypes (A to K) as well as circulating recombinant forms (CRFs) (7). There appears to have been an early “starburst” of HIV-1 variants leading to the different subtypes. CRFs have segments of the genome derived from more than one subtype, and two of these—CRF01_AE in Southeast Asia and CRF02_AG in West Africa—have relatively recently emerged as fast-spreading epidemic strains. Currently, subtype C and subtype A + CRF02_AG account for approximately 75% of the 14,000 estimated new infections that occur daily worldwide.

Regarding HIV in the Americas, subtype B was the first to appear in the United States and the Caribbean, heralding the epidemic when AIDS was first recognized in 1981. Subtype B remains the most prevalent (>80%) throughout the Americas, followed by undetermined CRFs (9%), F (8%), and C (1.5%) (7). There is a particularly high degree of genetic diversity of HIV-1 in Cuba, unparalleled in the Americas and similar to Central Africa (8), perhaps becausex Cuban troops served there for the United Nations. Less than 50% of Cuban infections are subtype B, and sequences of all subtypes are represented either as subtypes or in CRFs. The incidence of subtype C appears to be increasing rapidly in Brazil, just as it has in Africa and in East Asia.

Host-Pathogen Evolution

Upon adaptation of the virus to a new host, Darwinian selection would not only apply to the virus and host, but also to the modes of transmission between individuals in the new species, as well as to efficient replication within the infected individual (9). The modes of transmission of SIV likely differ from species to species. For example, parenteral transmission from bites and wounds as a consequence of aggression may be the main route of transmission in many nonhuman primates (5), whereas the major current mode of HIV transmission among humans is sexual. Nevertheless, parenteral transmission may well have played a more important role early in the emergence of the African epidemic (10), and it remains a risk today when nonsterile injecting equipment is used. Thus, efficient HIV transmission across mucosal surfaces may be a strongly selected secondary adaptation by the virus, given that humans tend to inflict minor parenteral injuries on each other less frequently then simians.

Whether genetic properties of the virus determine the rapid spread of HIV-1 subtypes such as C and CRF02_AG is not clear, although relative to other subtypes, subtype C appears to be present at higher load in the vaginas of infected women (11). It is not yet apparent whether certain subtypes are more virulent than others for progression to AIDS, although some indications of differences do exist (12).

SIVs do not appear to cause AIDS in their natural African hosts (Table 1). Similar to humans, however, several species of Asian macaques (Macaca spp.) develop AIDS when infected with a common nonpathogenic lentivirus of African sooty mangabeys (SIVsm became SIVmac). This observation demonstrates the pathogenic potential of such viruses after cross-species transmission from an asymptomatic infected species to a relatively unexposed naïve host species. Furthermore, SIV infection of macaques has provided a powerful experimental model system in which specific host as well as viral factors can be controlled and independently studied (13).

Table 1.

Natural lentivirus infections without immunopathology in African nonhuman primates.

Naturally resistant species and features of resistance
    Chimpanzees (P. troglodytes), SIVcpz (HIV-1 in humans)
    Sooty mangabeys (C. atys), SIVsm (HIV-2 in humans)
    African green monkeys (AGMs) (Chlorocebus sp.), SIVagm
Common features of asymptomatic lifelong infection
    Persistent plasma viremia
    Maintenance of peripheral CD4 T cell levels
    Sustained lymph node morphology
    High mutation rate in vivo
    Marginal increase in apoptosis returning to normal range
    Transient low-level T cell activation and proliferation, returning to normal range
    Less rigorous T cell responses than those in disease-susceptible species
Observed in one of these species, awaiting confirmation in others
    High replication of virus in gastrointestinal tract, transient loss of CD4 T cells
    CTL responses to conserved viral epitopes
    Maintenance of dendritic cell function
    Early induction of transforming growth factor—β1 and FoxP3 expression in AGMs with renewal of CD4 and increase in IL-10

During the AIDS pandemic, it has become clear that host genetic differences between individuals as well as between species affect the susceptibility or resistance of disease progression, revealing a clinical spectrum of rapid, intermediate, or slow progression or, more rarely, nonprogression to AIDS within infected populations. A range of distinct genetic host factors, linked to the relative susceptibility or resistance to AIDS, influence disease progression. In addition to those genes that affect innate and adaptive immune responses, recently identified genes block or restrict retroviral infections in primates (including the human primate). These discoveries provide a new basis for detailed study of the evolutionary selection and species specificity of lentiviral pathogens.

Among the most important antiviral innate and adaptive immune responses of the host post-infection are those regulated by specific molecules of the major histocompatibility complex (MHC) (13). It is conceivable that in the absence of a vaccine or antiviral drugs, the human population will evolve and ultimately adapt to HIV infection, in much the same way that HIV is evolving and adapting to selective pressures within its host. Indeed, examples of similar host-viral adaptation and coevolution are evident in lentivirus infections of domestic animals. Nevertheless, greater insight into CD4 tropic lentiviruses and acquired resistance to AIDS has come from African nonhuman primates, which are not only reservoirs giving rise to the current human lentivirus epidemic but also possible reservoirs of past and future retroviral plagues.

Host Resistance Factors Influencing HIV Infection and Progression to AIDS

In humans, a spectrum of disease progression has emerged. Within the infected population, there are individuals with increased susceptibility as well as increased resistance to infection, who display rapid or slow progression to AIDS, respectively. Analyses of several large AIDS cohorts have revealed polymorphic variants in loci that affect virus entry and critical processes for the intracellular replication of lentivirions as well as subsequent early innate and especially highly specific adaptive host responses (14). To date, there is a growing list of more than 10 genes and more than 14 alleles that have a positive or negative effect on infection and disease progression (Table 2).

Table 2.

Human genes identified that influence HIV infection and disease.

Gene productsAllele(s)Effect
Barriers to retroviral infection
TRIM5α SPRY species specific Infection resistance, capsid specific
ABOBEC3G Polymorphisms Infection resistance, hypermutation
Influence on HIV-1 infection
    CCR5 Δ32 homozygous ↓ Infection
    CCL2, CCL-7, CCL11 ↑ Infection
    (MCP1, MCP3, eotaxin), H7
    IL-10 5′A dominant ↓ Infection
Influence on development of AIDS
    CCR5 Δ32 heterozygous ↓ Disease progression
    CCR2 164 dominant ↓ Disease progression
    CCL5 (RANTES) ln1.1c dominant ↑ Disease progression
    CCL3L1 (MIP1α) Copy number ↓ Disease progression
    DC-SIGN Promoter variant ↓ Parenteral infection
    IL-10 5′A dominant ↑ Disease progression
    IFN-γ 179T dominant ↑ Disease progression
    KIR3DS1 (with HLA-Bw4) 3DS1 epistatic ↓ Disease progression
    HLA-A, HLA-B, HLA-C Homozygous ↑ Disease progression
    HLA-B*5802, HLA-B*18 Codominant ↑ Disease progression
    HLA-B*35-Px Codominant ↑ Disease progression
    HLA-B*27 Codominant ↓ Disease progression
    HLA-B*57, HLA-B*5801 Codominant ↓ Disease progression

Polymorphic loci that limit HIV infection include the well-described CCR5Δ32 variants (15, 16). The chemokine ligands for these receptors also influence disease progression: One example is Regulated on Activation Normal T Cell Expressed and Secreted (RANTES) (encoded by CCL5), with which elevated circulating levels have been associated with resistance to infections and disease. Moreover, it is the combination of polymorphisms controlling levels of expression of ligands and their specific receptors that exerts the most profound effect on HIV susceptibility and progression to AIDS; for example, gene dosage of CCL3L1 acts together with CCR5 promoter variants in human populations (17).

After retrovirus entry into target cells, intracellular “restriction factors” provide an additional barrier to viral replication. To date, three distinct antiviral defense mechanisms effective against lentiviruses have been identified: TRIM5α, a tripartite motif (TRIM) family protein (18); apolipoprotein B editing catalytic polypeptide (APOBEC3G), a member of the family of cytidine deaminases (19); and Lv-2 (20). TRIM5α restricts post-entry activities of the retroviral capsids in a dose-dependent manner (18, 21), and the human form of this protein has apparently undergone multiple episodes of positive selection that predate the estimated origin of primate lentiviruses (22). The species-specific restriction of retroviruses is due to a specific SPRY domain in this host factor, which appears to have been selected by previous ancestral retroviral epidemics and their descendant endogenous retroviral vestiges. TRIM5α proteins from human and nonhuman primates are able to restrict further species of lentiviruses and gamma-retroviruses, revealing a host-specific effect on recently emerged lentiviruses.

The cytidine deaminase enzymes APOBEC3G and APOBEC3F also represent post-entry restriction factors that act at a later stage of reverse transcription than TRIM5α and are packaged into nascent virions. The APOBEC family in primates consists of nine cytosine deaminases (cystosine and uracil) and two others that possess in vivo editing functions (19, 23). In the absence of the lentivirus accessory gene “virion infectivity factor” (vif), APOBEC3G becomes incorporated into nascent virions and inhibits HIV activity by causing hypermutations that are incompatible with further replication. At the same time, this represents a potentially risky strategy for the host, given that in some circumstances it might provide an opportunity for viral diversification (24). As with the primate TRIM5α family, APOBEC3G activity shows species-specific adaptations (25) emphasizing that coevolution of lentiviruses was a prerequisite for adaptation to a new host after cross-species transmission (26). Thus, although APOBEC3G clearly possessed an ancient role in defense against RNA viruses, a function that predates estimates of the emergence of today's primate lentiviruses, APOBEC3G appears to remain under strong positive selection by exposure to current RNA viral infections (27).

Evolving Host Resistance in the Face of New Lentiviral Pathogens

Failing the establishment of productive infection by the earliest innate defenses, natural killer (NK) cells of the immune system sense and destroy virus-infected cells and modulate the subsequent adaptive immune response. At the same time, the potentially harmful cytotoxic response of NK cells means that they are under tight regulation (28), which is centrally controlled by a raft of activating and inhibitory NK receptors and molecules encoded by genes of the MHC. Viruses have a long coevolutionary history with molecules of the immune system and a classical strategy for evading the cytotoxic T cell response of the adaptive immune system is by altering antigen presentation by MHC class I-A, I-B, or I-C molecules (29). In turn, the NK response has evolved to sense and detect viral infection by activities such as the down-regulation of class I MHC proteins.

Human lymphoid cells protect themselves from NK lysis by expression of the human MHC proteins human lymphocyte antigen (HLA)–C and HLA-E as well as by HLA-A and HLA-B. HIV-1, however, carries accessory genes, including nef, that act to differentially decrease the cell surface expression of HLA-A and HLA-B but not HLA-C or HLA-E (30). Such selective down-regulation may not only facilitate escape from cytotoxic T lymphocytes (CTLs) that detect antigens presented in the context of these MHC proteins but also escape from NK surveillance that might be activated by their loss of expression. However, within human MHC diversity, there may be an answer to the deception of NK cells by HIV. Certain alleles of HLA (HLA-Bw4) have been found to act as ligands for the NK inhibitory receptor (KIR) KIR3DSI and correlations with slower rates of progression to AIDS in individuals with the HLA-Bw4 ligand have been made with the corresponding expression of KIR3DSI expression on NK cells (31). The strength of this association between increased NK cell killing and HIV progression will have to bear the test of time as well as the test of the epidemic.

In the event that rapidly evolving pathogens such as HIV are able to evade innate defenses, adaptive defenses such as CTLs provide mechanisms for the recognition and lysis of new virus-infected targets within the host. This recognition depends on the highly polymorphic MHC class I molecules to bind and present viral peptides. However, a long-term CTL response will only be successful if the virus does not escape it through mutation. Additionally, it is advantageous to maintain MHC variability for controlling HIV replication and slowing disease progression (32), given that a greater number of viral peptides will be recognized if the infected individual is heterozygous for HLA antigens.

More importantly, there are qualitative differences in the ability of individual class I molecules to recognize and present viral peptides from highly conserved regions of the virus. These differences are observed in the spectrum of rapid, intermediate, and slow progressors in the HIV-infected human population (Table 2). Independent cohort studies have demonstrated the effects of specific HLA class I alleles on the rate of progression to AIDS with acceleration conferred by a subset of HLA-B*35 (HLA-B*3502, HLA-B*3503, and HLA-B*3504) specificities (33, 34). Most notably, HLA-B*27 and HLA-B*57 have been associated with long-term survival. Both of these class I molecules restrict CTL responses to HIV by presenting peptides selected from highly conserved regions of Gag. Mutations that allow escape from these CTL-specific responses arise only at great cost to viral fitness, reflected in lower viral loads (13) and survival benefit.

Evidence is emerging that HIV-1 is continuing to adapt under pressure from HLA-restricted immune responses in the human population. In a study that examined the relationship between HIV reverse transcriptase sequence polymorphisms and HLA genotypes, virus load was found to be predicted by the degree of HLA-associated selection of viral reverse transcriptase sequence (35). In a broader context, these results indicate that HLA alleles in the host population play an important role in shaping patterns of adaptation of viral sequences both within the host and at large.

Recent data have also started to suggest a potential influence that the HIV-1 epidemic may have on descendants of the HIV-infected population. In examining the relative contributions of HLA-A, HLA-B, and HLA-C alleles on restricting effective antiviral CTL, Kiepiela et al. (36) observed that HLA-B but not HLA-A allele expression influenced the rate of disease progression in that cohort. Thus, certain HLA-B alleles that favor long-term survival with HIV infection, in the absence of treatment, will be positively selected and will continue to evolve more rapidly over time. This coevolution of virus and host would be predicted to continue over generations until a relative equilibrium is reached between host resistance genes and virus infection. This would perhaps be similar to the asymptomatic lentivirus infections currently observed in naturally infected African nonhuman primates.

Disease Resistance in African Nonhuman Primates

Studies of SIVs in their natural hosts have been difficult and limited because of ethical issues and the endangered status of some species. For the most part, SIV natural history studies have been restricted to chimpanzees, sooty mangabeys, and African green monkeys. The chimpanzee is the closest living relative of humans, and two of its subspecies—P. t. schweinfurthii in East Africa and P. t. troglodytes in Western Central Africa—have certain wild communities with infected individuals (1). Although we should be cautious with generalizations, differences in transmission patterns may exist between the naturally infected monkey and ape populations (5). The prevalence of naturally occurring SIVsm in sooty mangabeys and SIVagm in African green monkeys appears to be relatively high, between 30 and 60%, increasing with age. However, SIVcpz infection across remaining free-ranging chimpanzee populations appears to be relatively low and regionally focal, restricted to certain troupes or communities in which it may reach levels greater than 20% (1, 37, 38).

Few naturally infected chimpanzees have been available for study (1), and much of the knowledge of the immune responses to lentivirus in this species has come from animals infected with HIV-1 strains in the late 1980s and 1990s (39). In contrast to pathogenic HIV-1 infection of humans or SIVmac infection of rhesus macaques, the hallmarks of lentivirus infection in chimpanzees include the absence of overt CD4 T cell loss, a lack of generalized immune activation, and the preservation of secondary lymphoid structure, specifically with respect to MHC class II antigen presenting cells (APCs) in infected lymph nodes (39, 40). In addition, there is little increase in apoptosis or anergy and no marked loss of interleukin (IL)-2–producing CD4+ T cells after infection (Table 1) (41, 42). These findings further underscore the importance of maintaining intact dendritic cell function and CD4 T cell interaction, which are symptoms of early immune dysfunction in infected AIDS-susceptible species (40).

Notably, CD8+ CTLs in chimpanzees recognize highly conserved HIV-1 Gag epitopes, which correspond to almost identical epitopes presented by HLA-B*57 and HLA-B*27 alleles of humans with nonprogression or slow progression to AIDS (43). A phylogenetic analysis of MHC class I alleles in chimpanzees as compared with humans reveals an overall reduction of HLA-A, HLA-B, and HLA-C lineages in chimpanzees. Furthermore, comparative analysis of intron 2 sequences strongly supports marked reduction in the MHC class I repertoire, especially in the HLA-B locus (44). These data imply that chimpanzees may have experienced a selective sweep, possibly caused by a viral epidemic in the distant past. We could envision such a selective sweep of the modern day human population in the HIV-1 pandemic (in the absence of antiretroviral therapy), with a strong positive selection for HLA-B alleles beneficial for long-term survival (36).

It is becoming clearer that infected chimpanzees are relatively resistant to developing AIDS, not because they control virus load better than humans (45), but because they avoid the immunopathological events that affect the function of lymphoid tissue in humans and macaques that progress to AIDS. Thus, certain African nonhuman primates, such as chimpanzees, serve as natural lentivirus reservoirs and sustain lentivirus infection without the immunopathology (40, 42) (Table 1). Mature CD4 T cells of chimpanzees are susceptible to SIVcpz or HIV-1 infection and cytopathology, but unlike macaques and humans, chimpanzees retain the renewal capacity to replace and sustain sufficient numbers of immunologically competent CD4 T cells to maintain immunological integrity (39).

How Will Humans Evolve in the Era of Medical Intervention?

New generations of more effective antiviral drug combinations are being developed, as are strategies to reduce virus load and facilitate restoration of CD4+ T cell numbers. The opportunity to convert an HIV-1 viremic patient into an aviremic individual by antiviral chemotherapy is an achievable clinical aim (46). Concern remains over the resident proviral population in long-lived lymphocytes and in APCs. Under antiretroviral treatment, aviremic CD4+ T cell tropic primate lentiviruses may also share features with the true “slow” replicating lentiviruses of ruminants. The prototypic lentiviruses of sheep and goats infect and persist in APCs such as dendritic and monotype/macrophage lineages without overt plasma viremia (47). Disease development is asymptomatic until late stages and is extremely protracted. Even in the absence of viremia and CD4 T cell loss, symptoms associated with chronic inflammation develop insidiously in diverse tissues resulting in a range of clinical conditions including encephalitis, pneumonia, and arthritis. It is important to consider that after solving the side effects of antiviral therapies such as lipodystrophy, HIV-infected aviremic humans might develop such classical lentivirus symptoms over a longer period of time.

Clearly, prophylactic strategies such as vaccines to prevent infection are the ultimate public health goals. Failing this, there is abundant evidence of previous retroviral epidemics embedded within the human genome. These suggest that there are further undisclosed antiretroviral defenses, which have coevolved and will continue to coevolve in human populations in response to retroviral insurgents.

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