Mucosal Immunity in HIV Controllers: The Right Place at the Right Time

doi:10.1097/COH.0b013e3283453e2b

Curr Opin HIV AIDS. Author manuscript; available in PMC 2011 December 22.

Published in final edited form as:

Curr Opin HIV AIDS. 2011 May; 6(3): 202–207.

doi: 10.1097/COH.0b013e3283453e2b

PMCID: PMC3245199

NIHMSID: NIHMS343319

Mucosal Immunity in HIV Controllers: The Right Place at the Right Time

Barbara L. Shacklett^1,²^* and April L. Ferre¹

¹Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616

²Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California at Davis, Davis, CA 95616

^* Corresponding Author: Barbara L. Shacklett, PhD, Associate Professor, Dept. of Medical Microbiology and Immunology, 3146 Tupper Hall, 1 Shields Ave., Davis, CA 95616 USA, Tel: (530) 752-6785, Fax: (530) 752-8692, Email: blshacklett/at/ucdavis.edu

The publisher's final edited version of this article is available at Curr Opin HIV AIDS

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Abstract

Purpose of review

The phenomenon of long-term non-progression in HIV infection has been recognized for some time, and the ability of rare individuals, designated “elite controllers”, to control HIV in the absence of therapy is the focus of numerous ongoing studies. This review focuses on studies of HIV-specific immune responses in mucosal tissues as a potential correlate of immune control, with an emphasis on recently published work.

Recent findings

Genetic studies have implicated a role for elements localized to the major histocompatibility complex (MHC) on chromosome 6 in the immune control of HIV infection. In parallel, functional studies have strongly implicated MHC class I-restricted, CD8+ T-cell responses as a major contributor to elite control. In addition, the localization of HIV-specific CD8+ and CD4+ T-cells with respect to the major sites of virus replication in the body may be critical in determining clinical outcome.

Summary

Recent findings suggest that MHC class I-restricted, CD8+ T-cells are a major component of immune control in “elite controllers”. In addition, the presence of these effector cells at or near critical viral reservoirs, such as mucosal tissues, may be critical in determining their effectiveness at limiting viral replication and dissemination.

Keywords: Mucosal immunity, Gut, GALT, CTL, T-cell

Introduction

Typical HIV disease progression is marked by a decline in CD4+ T-cells and the loss of control of viral replication. However, a small subset of infected individuals are able to establish durable control of viral replication (elite controllers), and/or maintain relatively normal CD4+ T-cell counts for periods of 10 or more years (long-term non-progressors [LTNP]) in the absence of antiretroviral therapy (ART) [1,2]. Elite controllers and LTNP represent <1% and 10–15% of the HIV infected population, respectively [1,2]. Despite effective control of plasma viremia, elite controllers show heightened levels of immune activation compared to healthy controls, exhibit an increased incidence of comorbid inflammatory diseases such as atherosclerosis, and in rare cases may progress to AIDS [3,4]. Thus, while most elite controllers remain relatively free of overt HIV disease, they are not completely free from the consequences of immune activation and inflammation.

Mucosal tissues of the reproductive and gastrointestinal tracts serve as the major portals of entry for HIV. Gut-associated lymphoid tissue (GALT) is the largest lymphoid organ in the body, comprised of immune inductive sites (Peyer’s patches and isolated lymphoid follicles) and effector sites in the lamina propria and epithelium (Figure 1). Because of its high density of CD4+ memory T-cells, most of which express HIV coreceptors CCR5 and CXCR4, the gut represents a major target for HIV infection. During the first weeks of infection, there is a rapid and profound loss of CD4+ T-cells from the intestinal lamina propria [5,6]. There is also considerable damage to epithelial integrity, resulting in “leaky gut” and translocation of bacterial products, such as lipopolysaccharide, into peripheral circulation [7,8]. Microbial translocation, leading to triggering of toll-like receptor signaling on cells of the immune system, has been implicated as a likely cause of the generalized activation that is a hallmark of chronic HIV infection [*9,**10]. Recent studies have highlighted the central role of the gastrointestinal mucosa as a reservoir for ongoing viral replication during chronic infection, the breakdown of gut epithelial barrier function and its relationship to immune activation, and finally, mucosal T-cell responses as a potential correlate of HIV control.

Figure 1

The Figure shows idealized drawings of rectal mucosa in uninfected individuals (left), HIV non-controllers (NC, center), and HIV controllers (C, right). Individual cell types are identified in the legend. For simplicity, innate effector cells such as (more ...)

Mucosal T-cell responses in HIV controllers: CD8+/CD4+ T-cell synergy

In both HIV-infected individuals and healthy controls, CD8+ T-cells from the gastrointestinal tract express low levels of perforin as compared to their counterparts in blood [11]. Nevertheless, HIV-specific CD8+ T-cells are abundant in rectal mucosa of chronically infected individuals [12,13]. Following in vitro stimulation, these cells express a broad range of cytokines/chemokines (IFNγ, IL-2, MIP1-β, and TNFα) and the degranulation marker CD107 [14,15]. A study of rectal HIV Gag-specific CD8+ T-cell responses in 15 HIV-positive individuals not on highly-active antiretroviral therapy (HAART), with a broad range of viral loads and CD4+ T-cell counts, revealed a positive correlation between total response magnitude (i.e., percent Gag-responsive CD8+ T-cells), polyfunctionality (i.e., production of 3 or more effector molecules, also referred to as response “quality”) and CD4+ T-cell count, as well as an inverse correlation between response magnitude and plasma viral load [15]. Thus, in this study, individuals with the highest blood CD4+ T-cell counts and lowest plasma viral loads had the strongest, most polyfunctional rectal CD8+ T-cell responses.

In a subsequent study, CD8+ T-cell responses from paired blood and rectal biopsy samples were obtained from 17 elite controllers (viral load [VL] <75 copies/mL), 11 viremic controllers (VL 75–2,000 copies/mL), 14 non-controllers (VL >10,000 copies/mL), and 10 HAART-treated subjects (VL <75 copies/mL) and assessed for their ability to degranulate and/or secrete multiple cytokines in response to HIV Gag stimulation [16]. There was considerable heterogeneity in all groups; however, mucosal CD8+ T-cell responses in controllers were significantly more robust and polyfunctional than in either non-controllers or HAART-suppressed individuals. Importantly, in this study there were no differences in the magnitude or quality of peripheral blood CD8+ T-cell responses between controllers and non-controllers. Additionally, controllers with “protective” class I HLA alleles (HLA-B13, B27, B57, B58, and B81) had significantly more polyfunctional mucosal Gag-specific CD8+ T-cells than controllers lacking these alleles, and showed a trend towards higher response magnitudes [16]. HIV controllers also had significant preservation of rectal CD4+ T-cells as compared to non-controllers. However, all HIV-positive groups had significantly lower rectal CD4+ T-cell percentages than seronegatives [16].

In a companion study, Ferre and colleagues evaluated Gag-specific CD4+ T-cell responses in rectal mucosa from the same patients [*17]. Controllers had significantly higher magnitude rectal CD4+ T-cell responses than patients on HAART, and the frequency of polyfunctional mucosal CD4+ T-cells was significantly greater in controllers than in either non-controllers or patients on HAART. Intriguingly, controllers with the strongest and most polyfunctional rectal CD4+ T-cell responses in this study possessed the HLA class II alleles HLA-DRB1*13 and/or HLA-DQB1*06 in addition to protective MHC class I alleles [*17]. Although this study was not statistically powered to distinguish the protective effects of MHC class I versus MHC class II alleles, an earlier report found an association between the HLA-DRB1*13/HLA-DQB1*06 haplotype, long-term nonprogression and strong p24-specific lymphoproliferative responses in the absence of any protective MHC class I alleles [18].

Taken together, these findings reveal that many HIV controllers, particularly those with “protective” HLA alleles, have strong, polyfunctional mucosal CD4+ and CD8+ T-cell responses that are not necessarily mirrored in blood. Additionally, both the magnitude and “quality” of mucosal CD4+ T-cell responses positively correlated with the strength of mucosal CD8+ T-cell responses. This suggests that mucosal CD4+ T-cell “help” supports the development and maintenance of robust CD8+ T-cell responses. Mucosal CD8+ T-cells, in turn, eradicate infected cells, thereby limiting de novo infection of CD4+ T-cells; accordingly, these two cell types likely act synergistically to limit virus production and preserve relatively high CD4+ T-cell frequencies in mucosal tissues of HIV controllers.

Gene expression analysis: distinct molecular signatures

Gene expression analyses of gastrointestinal tissue from controllers and non-controllers have also revealed molecular signatures of mucosal immunity that distinguish these two patient groups, while generally supporting an important role for mucosal cell-mediated immunity in HIV controllers [19,20]. Using microarray technology, Sankaran and colleagues studied gene expression profiles in blood and jejunal biopsies from four long-term nonprogressors, 15 ART-naïve HIV positive patients with VL >10,000 (i.e., non-controllers), and 8 seronegative controls [19]. Non-controllers showed increased expression of genes regulating immune activation, leukocyte trafficking, and inflammation as compared to patients characterized as long-term nonprogressors. As compared to healthy controls, both LTNP and non-controllers showed decreased expression of genes associated with nutrient absorption and lipid metabolism, suggesting significant effects of HIV infection on gastrointestinal function even in non-progressors.

In a more recent study, Loke and colleagues used a combination of flow cytometry assays and oligonucleotide expression arrays to compare gene expression in blood and rectosigmoid biopsies from 9 HIV controllers and 11 non-controllers [20]. Genes whose expression was strongly associated with controller status included those involved in T-cell immunity, MHC class I and II-related immunity, NK-cell responses, and cytokines/chemokines. Although mucosal HIV-specific immune responses were not measured, rectal CD4+ T-cells were tested for the ability to respond to polyclonal stimulation (PMA + Ionomycin) by producing cytokines such as IL-2, IFN-γ, TNF-α and IL-17. Notably, the ability of mucosal (but not blood) CD4+ T-cells to secrete multiple cytokines was strongly associated with high peripheral CD4+ T-cell count and controller status. There was a strong relationship between expression of markers of immune activation (e.g., CD38) in blood and rectal mucosa; the frequency of CD4+Foxp3+ putative Treg cells was also strongly associated with immune activation. These findings suggested that measurements of immune activation in blood are often reflective of those in mucosa, and might be used as surrogates to infer mucosal immune activation when gut biopsies are not available. The conclusions from this study also supported the hypothesis that mucosal CD4+ T-cell responses contribute significantly to immune control [20].

Targeting conserved, functionally constrained regions of Gag

In addition to the strength and “quality” of mucosal T-cell responses, the targeting of T-cell epitopes located in highly conserved regions of the viral proteome appears to be important for viral control. Extensive studies have characterized the immunodominant HIV epitopes restricted by HLA-B57 and HLA-B27 and recognized by CD8+ T-cells in blood. In the case of HLA-B27, a single immunodominant epitope in the capsid protein (p24), KK10, is typically recognized by cytotoxic T-cells (CTL) [21,22]. This epitope is located in a structurally constrained region involved in interactions between the viral capsid and the host protein cyclophilin A [21,22]. Viral escape from KK10-specific CTL frequently occurs late in infection and is associated with progression to AIDS. In the case of HLA-B57, four immunodominant epitopes are located within p24. One of these, TW10, is targeted by CTL early in infection and is also presented by HLA-B58, a close relative of B57. CTL escape mutations in TW10 occur rapidly and have a negative impact on viral fitness during the acute/early phase of infection; in addition, many escape variants also elicit strong CTL responses [**23–**27]. Thus, the combination of reduced viral fitness and strong CTL responses likely contributes to immune control.

Because the immunodominant HLA-B57 and B27-restricted epitopes were initially characterized using CTL from blood, it was important to determine whether these epitopes were also recognized by T-cells in mucosal tissues. Ferre and colleagues mapped CD8+ T-cell responses to HIV Gag, Env and Nef peptides in blood and rectal mucosa from 30 controllers and 14 non-controllers [*28]. Mucosal CD8+ T-cells from controllers more frequently targeted conserved regions in HIV Gag p24 and the zinc-finger domains of Gag p7, while those from non-controllers preferentially targeted Nef. Immunodominant CD8+ T-cell responses, including those directed towards KK10 and TW10, were shared between blood and rectal mucosa. Among controllers, mucosal CD8+ T-cell responses to HLA-B27 and -B57 restricted epitopes were consistently of greater magnitude than responses to other epitopes. Interestingly, mucosal CD4+ T-cells from controllers with HLA-DRB1*13 and/or HLA-DQB1*06 were also shown to target epitopes within p24 that overlap with immunodominant HLA-B27 and -B57 restricted epitopes [*17]. Thus, mucosal CD8+ and CD4+ T-cells from controllers preferentially target conserved, structurally constrained regions of the HIV Gag protein. The breadth of mucosal CD8+ T-cell responses (i.e., number of epitopes recognized) did not differ significantly between controllers and non-controllers. Thus, the total number of epitopes recognized may not be as critical as the targeting of specific conserved viral sequences, where escape mutations elicit a strong cost in viral fitness.

Mucosal tissues as a viral reservoir in HIV/SIV controllers

Although Elite Controllers are defined as having plasma viral loads below the limit of detection by standard assays, at least four studies have demonstrated that controllers harbor low levels of plasma viral RNA that may be detected using ultrasensitive methods [29–32]. Dinoso and colleagues measured viral RNA using an ultrasensitive RT-PCR based assay after concentrating virus from 7 mL of plasma by ultracentrifugation. They reported that 9 of 14 elite controllers had undetectable plasma viral loads using this method, as compared to 6 of 15 individuals on suppressive HAART [29]. Using a transcription-mediated amplification (TMA) assay with a 50% detection limit of 3.6 to 14 viral RNA copies/mL plasma, Hatano and colleagues found that 45 of 46 controllers harbored detectable HIV RNA [30]. Strikingly, 15 subjects had detectable HIV RNA at all time points tested, and most also had cell-associated HIV RNA and proviral DNA. Median plasma HIV RNA levels were higher in Elite Controllers than in a comparison group of HAART-suppressed patients, although this difference did not reach significance.

To date, no studies have systematically addressed levels of HIV RNA and DNA in mucosal tissues of HIV controllers using ultrasensitive methods. However, the robust HIV-specific T-cell responses detected in rectal mucosa of controllers suggest ongoing viral replication in these tissues, since such responses rapidly wane in patients on HAART [16,*17]. Several recent studies have quantified mucosal viral load in patients on HAART with well-suppressed viremia. A seminal study by Chun and colleagues revealed that HIV DNA persists in terminal ileum of patients on long-term successful HAART [33], despite plasma viral loads below 50 copies/ml. Furthermore, phylogenetic analysis of viral envelope (C2-V5) DNA sequences provided evidence for cross-infection of CD4+ T-cells from blood and gut, rather than strict anatomic compartmentalization. A subsequent study by Yukl and colleagues extended these findings to four tissue sites: duodenum, ileum, ascending colon, and rectum in 8 patients on ART with viral loads <40 copies/ml [34]. In this study, HIV DNA levels were significantly higher in ileum, colon and rectum than in PBMC, and median HIV RNA levels were highest in terminal ileum. Taken together, these studies demonstrate that the gastrointestinal mucosa remains an important reservoir for HIV DNA and RNA even in the absence of detectable plasma viremia. Studies of HIV controllers will likely reveal similar findings.

Among nonhuman primate models for AIDS, rhesus macaques of Chinese origin (ChRh) are relatively resistant to disease progression when infected with SIVmac; although the majority of infected macaques eventually develop simian AIDS, approximately 30% maintain low viral loads for at least 5–6 years [35–37]. Ling and colleagues have used this model to study mucosal CD4+ T-cell depletion and reconstitution in controllers, as well as viral replication and compartmentalization in the GI tract. In a recent study of nine ChRh inoculated with pathogenic SIVmac239, three animals spontaneously controlled viremia [36]. Like typical progressors, these SIV controllers experienced acute phase viremia and profound jejunal CD4+ T-cell depletion at two to four weeks post-infection. However, unlike progressors, controllers showed gradual restoration of intestinal CD4+/CCR5+ T-cells beginning at 2 months post-infection. In vivo depletion of CD8+ T-cells in two controllers led to transient viremia in both animals and the development of simian AIDS in one, implying a major role for CD8+ T-cells in controlling virus replication. Notably, the animal that developed AIDS failed to fully reconstitute intestinal CD8+ T-cells following antibody-mediated depletion.

In a follow-up study, Ling and colleagues used the ChRh model to quantify viral replication in both small and large intestine of SIV controllers [35]. Five of 7 controllers had fewer than 10 viral RNA copies/10⁶ PBMC. However, controllers consistently harbored cell-associated viral RNA in colonic mucosa (mean 767 vRNA copies/10⁶ cells) and associated mesenteric lymph nodes (mean 486 vRNA copies/10⁶ cells). These findings indicate that the gastrointestinal mucosa remains a major SIV reservoir even in controllers lacking detectable plasma viremia. In particular, colonic mucosa may be particularly susceptible to SIV/HIV infection due to the high frequency of target cells that are CD4+CCR5+ and have a “memory” phenotype [35].

Conclusions

A growing consensus from genomics and cellular immunology studies points to a major, although clearly not exclusive, role for cell-mediated immune responses in establishing and maintaining HIV controller status [38–42]. Furthermore, seminal studies of acute SIV infection point to the importance of in vivo effector-to-target ratio in determining the outcome of the “race between expansion of infection and the immune response generated to contain it” [43]. Recent studies have revealed that the gastrointestinal mucosa remains an important reservoir for viral replication even in individuals with viral load suppressed through HAART, and in SIV-infected macaques that control infection without therapy. Furthermore, the magnitude and quality of HIV-specific mucosal T-cell responses appear to correlate positively with controller status. Taken together, these findings support the view that T-cell responses occurring at the “right place and time”, i.e., in the gastrointestinal tract during chronic (and perhaps also acute) infection, may be a major component of HIV control.

Key Points

A growing consensus from genomics and cellular immunology studies points to a major role for cell-mediated immune responses in establishing and maintaining HIV controller status.
The gastrointestinal mucosa remains an important reservoir for viral replication even in individuals with viral load suppressed through HAART, and in SIV-infected macaques that control infection without therapy.
The magnitude and quality of HIV-specific mucosal T-cell responses appear to correlate positively with controller status.
T-cell responses occurring at the “right place and time”, i.e., in the gastrointestinal tract during chronic, and likely also acute infection, may be a major component of HIV control.

Acknowledgments

The authors thank the members of the Shacklett laboratory, as well as colleagues Steven G. Deeks, Peter W. Hunt, and Ruth M. Greenblatt, University of California, San Francisco, for thoughtful discussions. The authors’ research is supported by NIH/NIAID R01 AI057020 and NIH/NIAID P01 AI083050.

References and recommended reading

1. Deeks SG, Walker BD. Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy. Immunity. 2007;27:406–416. [PubMed]

2. Okulicz JF, Marconi VC, Landrum ML, et al. Clinical outcomes of elite controllers, viremic controllers, and long-term nonprogressors in the US Department of Defense HIV natural history study. J Infect Dis. 2009;200:1714–1723. [PubMed]

3. Hunt PW, Brenchley J, Sinclair E, et al. Relationship between T cell activation and CD4+ T cell count in HIV-seropositive individuals with undetectable plasma HIV RNA levels in the absence of therapy. J Infect Dis. 2008;197:126–133. [PMC free article] [PubMed]

4. Hsue PY, Hunt PW, Schnell A, et al. Role of viral replication, antiretroviral therapy, and immunodeficiency in HIV-associated atherosclerosis. AIDS. 2009;23:1059–1067. [PMC free article] [PubMed]

5. Brenchley JM, Price DA, Douek DC. HIV disease: fallout from a mucosal catastrophe? Nat Immunol. 2006;7:235–239. [PubMed]

6. Johnson RP, Kaur A. HIV: viral blitzkrieg. Nature. 2005;434:1080–1081. [PubMed]

7. Brenchley JM, Price DA, Schacker TW, et al. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med. 2006;12:1365–1371. [PubMed]

8. Nazli A, Chan O, Dobson-Belaire WN, et al. Exposure to HIV-1 directly impairs mucosal epithelial barrier integrity allowing microbial translocation. PLoS Pathog. 2010;6:e1000852. [PMC free article] [PubMed]

*9. Estes JD, Harris LD, Klatt NR, et al. Damaged intestinal epithelial integrity linked to microbial translocation in pathogenic simian immunodeficiency virus infections. PLoS Pathog. 2010;6 This study provided evidence for translocation of microbial products from the intestinal lumen into the lamina propria and beyond. The study contrasted SIV-infected rhesus macaques, which develop epithelial barrier destruction, immune activation, and progressive disease, with sooty mangabeys, which become chronically infected but develop neither gut ‘leakiness’ nor immune activation and remain disease-free. [PMC free article] [PubMed]

**10. Klatt NR, Harris LD, Vinton CL, et al. Compromised gastrointestinal integrity in pigtail macaques is associated with increased microbial translocation, immune activation, and IL-17 production in the absence of SIV infection. Mucosal Immunol. 2010;3:387–398. This study focused on the relationship between intestinal barrier compromise and immune activation in pigtail macaques, which rapidly progress to AIDS after SIV infection. Surprisingly, even before SIV infection, pigtail macaques have high levels of epithelial barrier damage and microbial translocation, suggesting that these features may predispose this species to develop progressive AIDS. [PMC free article] [PubMed]

11. Shacklett BL, Cox CA, Quigley MF, et al. Abundant expression of granzyme A, but not perforin, in granules of CD8+ T cells in GALT: implications for immune control of HIV-1 infection. J Immunol. 2004;173:641–648. [PubMed]

12. Shacklett BL, Cox CA, Sandberg JK, et al. Trafficking of HIV-1-specific CD8+ T-cells to gut-associated lymphoid tissue (GALT) during chronic infection. J Virol. 2003;77:5621–5631. [PMC free article] [PubMed]

13. Ibarrondo FJ, Anton PA, Fuerst M, et al. Parallel human immunodeficiency virus type 1-specific CD8+ T-lymphocyte responses in blood and mucosa during chronic infection. J Virol. 2005;79:4289–4297. [PMC free article] [PubMed]

14. Critchfield JW, Lemongello D, Walker DH, et al. Multifunctional HIVgag Specific CD8+ T-cell Responses in Rectal Mucosa and PBMC During Chronic HIV-1 Infection. J Virol. 2007;81:5460–5471. [PMC free article] [PubMed]

15. Critchfield JW, Young DH, Hayes TL, et al. Magnitude and complexity of rectal mucosa HIV-1-specific CD8+ T-cell responses during chronic infection reflect clinical status. PLoS ONE. 2008;3:e3577. [PMC free article] [PubMed]

16. Ferre AL, Hunt PW, Critchfield JW, et al. Mucosal immune responses to HIV-1 in elite controllers: a potential correlate of immune control. Blood. 2009;113:3978–3989. [PubMed]

*17. Ferre AL, Hunt PW, McConnell DH, et al. HIV controllers with HLA-DRB1*13 and HLA-DQB1*06 alleles have strong, polyfunctional mucosal CD4+ T-cell responses. J Virol. 2010;84:11020–11029. This study showed that controllers have abundant, polyfunctional HIV-specific CD4+ T-cells in rectal mucosa, and suggests that CD4+ and CD8+ T-cells act synergistically to control viral replication in mucosal tissues. [PMC free article] [PubMed]

18. Malhotra U, Holte S, Dutta S, et al. Role for HLA class II molecules in HIV-1 suppression and cellular immunity following antiretroviral treatment. J Clin Invest. 2001;107:505–517. [PMC free article] [PubMed]

19. Sankaran S, Guadalupe M, Reay E, et al. Gut mucosal T cell responses and gene expression correlate with protection against disease in long-term HIV-1-infected nonprogressors. Proc Natl Acad Sci U S A. 2005;102:9860–9865. [PubMed]

20. Loke P, Favre D, Hunt PW, et al. Correlating cellular and molecular signatures of mucosal immunity that distinguish HIV controllers from noncontrollers. Blood. 2010;115:e20–32. [PubMed]

21. Schneidewind A, Brockman MA, Sidney J, et al. Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. J Virol. 2008;82:5594–5605. [PMC free article] [PubMed]

22. Schneidewind A, Brockman MA, Yang R, et al. Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J Virol. 2007;81:12382–12393. [PMC free article] [PubMed]

*23. Brockman MA, Brumme ZL, Brumme CJ, et al. Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. J Virol. 2010;84:11937–11949. This study revealed that CTL responses restricted by protective MHC class I alleles select for escape mutations that contribute to decreased viral fitness during acute/early infection; however, compensatory mutations accumulate during chronic infection. These findings suggest that the effects of decreased viral fitness early in infection may have lasting benefits to the host. [PMC free article] [PubMed]

24. Brockman MA, Schneidewind A, Lahaie M, et al. Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A. J Virol. 2007;81:12608–12618. [PMC free article] [PubMed]

25. Miura T, Brockman MA, Brumme ZL, et al. HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. J Virol. 2009;83:140–149. [PMC free article] [PubMed]

26. Miura T, Brockman MA, Schneidewind A, et al. HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition. J Virol. 2009;83:2743–2755. [PMC free article] [PubMed]

*27. Miura T, Brumme ZL, Brockman MA, et al. Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J Virol. 2010;84:7581–7591. This paper examined viruses isolated during acute/early infection from individuals who subsequently became HIV controllers. Although several of these individuals did not have protective class I alleles, two harbored viruses with typical B57 signature mutations, suggesting they had acquired these viruses from B57+ donors. Drug resistance mutations that impair viral fitness were also found in early controllers. [PMC free article] [PubMed]

*28. Ferre AL, Lemongello D, Hunt PW, et al. Immunodominant HIV-specific CD8+ T-cell responses are common to blood and gastrointestinal mucosa, and Gag-specific responses dominate in rectal mucosa of HIV controllers. J Virol. 2010;84:10354–10365. In this study, CD8+ T-cell responses to Gag, Env and Nef were mapped in rectal mucosa and PBMC from controllers, non-controllers, and ART-treated subjects. Gag-specific responses, particularly directed towards p24 and p7, dominated in controllers, while responses in noncontrollers were more evenly distributed to Gag, Env and Nef. [PMC free article] [PubMed]

29. Dinoso JB, Kim SY, Siliciano RF, et al. A comparison of viral loads between HIV-1-infected elite suppressors and individuals who receive suppressive highly active antiretroviral therapy. Clin Infect Dis. 2008;47:102–104. [PMC free article] [PubMed]

30. Hatano H, Delwart EL, Norris PJ, et al. Evidence for persistent low-level viremia in individuals who control human immunodeficiency virus in the absence of antiretroviral therapy. J Virol. 2009;83:329–335. [PMC free article] [PubMed]

31. Migueles SA, Osborne CM, Royce C, et al. Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control. Immunity. 2008;29:1009–1021. [PMC free article] [PubMed]

32. Pereyra F, Palmer S, Miura T, et al. Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters. J Infect Dis. 2009;200:984–990. [PubMed]

33. Chun TW, Nickle DC, Justement JS, et al. Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J Infect Dis. 2008;197:714–720. [PubMed]

34. Yukl SA, Gianella S, Sinclair E, et al. Differences in HIV burden and immune activation within the gut of HIV-positive patients receiving suppressive antiretroviral therapy. J Infect Dis. 2010;202:1553–1561. [PMC free article] [PubMed]

35. Ling B, Mohan M, Lackner AA, et al. The large intestine as a major reservoir for simian immunodeficiency virus in macaques with long-term, nonprogressing infection. J Infect Dis. 2010;202:1846–1854. [PMC free article] [PubMed]

36. Ling B, Veazey RS, Hart M, et al. Early restoration of mucosal CD4 memory CCR5 T cells in the gut of SIV-infected rhesus predicts long term non-progression. AIDS. 2007;21:2377–2385. [PubMed]

37. Ling B, Veazey RS, Luckay A, et al. SIV(mac) pathogenesis in rhesus macaques of Chinese and Indian origin compared with primary HIV infections in humans. AIDS. 2002;16:1489–1496. [PubMed]

38. Goulder PJ, Watkins DI. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol. 2008;8:619–630. [PMC free article] [PubMed]

39. Thomas R, Apps R, Qi Y, et al. HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C. Nat Genet. 2009;41:1290–1294. [PMC free article] [PubMed]

40. Fellay J, Shianna KV, Ge D, et al. A whole-genome association study of major determinants for host control of HIV-1. Science. 2007;317:944–947. [PMC free article] [PubMed]

**41. Pereyra F, Jia X, McLaren PJ, et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010;330:1551–1557. This genome-wide analysis study identified >300 single-nucleotide polymorphisms within the MHC that were associated with HIV control. Specific amino acids in the HLA-B peptide binding groove explain many of these associations, and reveal the MHC class I-peptide interaction as critical to HIV control. [PMC free article] [PubMed]

42. Dalmasso C, Carpentier W, Meyer L, et al. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. PLoS One. 2008;3:e3907. [PMC free article] [PubMed]

43. Li Q, Skinner PJ, Ha SJ, et al. Visualizing antigen-specific and infected cells in situ predicts outcomes in early viral infection. Science. 2009;323:1726–1729. [PMC free article] [PubMed]