Antiretroviral therapy suppresses HIV-1 replication but cannot eradicate a latent reservoir of long-lived infected cells, and the reservoir is not eliminated by the infected person's own CD8+ cytotoxic T lymphocytes even though most reactive epitopes in replication-competent reservoir virus carry no escape mutations. The problem is to determine, mechanistically, why the replication-competent reservoir survives T-cell immune surveillance during therapy - candidate mechanisms being transcriptional latency limiting antigen presentation, viral interference with antigen display, such as removal of MHC class I molecules from the cell surface by the viral Nef protein, cell-intrinsic resistance of reservoir-harboring cells to CTL killing, archived CTL escape variation, clonal and homeostatic proliferation of infected cells, and anatomical sanctuary sites such as B-cell follicles - and to establish the epitope breadth and tissue trafficking a T-cell response would need in order to prevent immune escape and control viral rebound after treatment interruption. The primary sources report the reservoir as largely sensitive (at the epitope-sequence level) and as inherently resistant (at the whole-cell killing level); the 2023-2026 literature, including two 2026 studies reaching opposing conclusions on intrinsic CTL resistance, leaves both parts of the problem open.

Background

Antiretroviral therapy (ART) suppresses HIV-1 replication to undetectable levels but cannot cure infection, because a latent reservoir persists: a small population of long-lived cells, mostly resting memory CD4+ T cells, harboring chromosomally integrated HIV-1 proviral DNA that is transcriptionally silent. Only a minority of proviruses are genetically intact and replication-competent (on the order of one replication-competent provirus per million resting CD4+ T cells in most treated people), but this pool suffices to reignite systemic infection within weeks of stopping ART. Cure research therefore asks whether the reservoir can be eliminated by the immune system's main antiviral effector T cell, the CD8+ cytotoxic T lymphocyte (CTL), which kills cells that display viral peptides on MHC class I molecules at the cell surface.

CTLs exert strong selection pressure on HIV-1 during untreated infection, driving the emergence of CTL escape mutations - amino-acid substitutions in viral epitopes that reduce or abolish T-cell recognition - and such variants can be archived in the reservoir when infected cells become latent. The dominant cure paradigm, shock and kill, proposes to reverse latency pharmacologically so that reservoir cells express viral antigens and are eliminated by CTLs. Early support came from Shan et al. (Immunity 2012): in an in vitro latency model, patient-derived CTLs that were pre-stimulated eliminated reactivated reservoir cells. Two subsequent human studies, using different readouts, pulled the field in opposite directions. Huang et al. (J Clin Invest 2018) found that potent latency-reversing agents plus autologous CD8+ T cells (the participants' own T cells) reduced total HIV DNA ex vivo yet failed to deplete replication-competent virus, even though the same CD8+ T cells efficiently killed newly infected cells - ruling out viral escape and CD8 dysfunction as explanations in that assay and implying inherent resistance of the cells that harbor replication-competent virus. Warren et al. (eLife 2020), sequencing outgrowth viruses from 25 people on long-term ART and functionally testing every reactive epitope, found that 68% of T-cell epitopes in the replication-competent reservoir carry no detectable escape mutation, concluding that the reservoir is largely sensitive, in epitope sequence, to the circulating T cells of the same person. These two results probe different levels - epitope sequence versus whole-cell killing - so they are complementary rather than strictly contradictory; what remains unresolved is why both hold at once, mechanistically, in vivo.

Several non-exclusive candidate explanations have since been established as individually real. Transcriptional latency itself limits antigen presentation in most intact-provirus cells. Nef, an HIV-1 accessory protein, removes MHC class I from the surface of productively infected cells, so even antigen-expressing reservoir cells may be poorly visible to CTLs. Cells harboring genome-intact proviruses are enriched for surface-marker combinations conferring resistance to CTL and natural-killer-cell killing and for immune-checkpoint markers (inhibitory surface receptors that restrain cellular activation) that limit proviral transcription, with compartmentalized signatures in blood versus lymph nodes (Sun et al., Nature 2023), consistent with ongoing immune selection. Clonal expansion of infected cells - driven by antigen recognition or by homeostatic proliferation, the normal self-renewal of memory T cells - maintains large infected clones independently of immune evasion. Anatomical sanctuary sites add a further layer: in lymphoid tissue, productive infection concentrates in B-cell follicles (the germinal-center regions where infected follicular helper CD4+ T cells reside and from which most CTLs are excluded, because follicle entry requires the chemokine receptor CXCR5), and compartments such as the central nervous system are poorly accessible to blood-borne effectors (Fukazawa et al., Nat Med 2015; Leong et al., Nat Immunol 2016; Petrovas et al., Sci Transl Med 2017). Integration site also matters: proviruses integrated in certain zinc-finger genes (genes encoding zinc-finger DNA-binding transcription factors) show low inducibility and can evade CD8+ T cells despite antigen exposure (Dragoni et al., J Clin Invest 2023). What no study has done is determine, in in-vivo-relevant terms, which of these mechanisms, individually or in combination, allow the reservoir to persist under CD8 surveillance on ART, and establish the T-cell breadth (epitope coverage, including of archived escape variants) and tissue trafficking that would prevent escape upon viral rebound. Reviews in 2023-2025 frame exactly this as the open question - HIV persistence: silence or resistance (Pasternak and Berkhout 2023); immune targeting of reservoir cells (Armani-Tourret et al. 2024); immune-mediated strategies to the reservoir problem (Kulpa et al. 2025); and the passenger hypothesis, in which most reservoir dynamics reflect normal CD4+ T-cell population biology rather than immune evasion (Schiffer et al. 2025).

Problem Statement

The problem has two linked parts and must be answered without reducing it to a single cell type, tissue, model system, or intervention.

Part 1 - Mechanistic decomposition of reservoir persistence under CD8+ T-cell surveillance. Determine, mechanistically and with in-vivo-relevant evidence, which of the candidate mechanisms (individually or in combination) allow the replication-competent HIV-1 latent reservoir to persist during suppressive antiretroviral therapy despite CTL pressure: (a) transcriptional latency limiting antigen expression and MHC class I presentation; (b) viral interference with antigen presentation in expressing cells, for example Nef-mediated MHC class I downregulation; (c) cell-intrinsic resistance of reservoir-harboring cells to CTL-mediated killing, for example pro-survival programs or low-oxidative-stress metabolic states; (d) archived CTL escape variation and its effect on recognition; (e) antigen-driven and homeostatic clonal proliferation of infected cells; and (f) anatomical sanctuary sites, for example B-cell follicles and the central nervous system, that limit effector access or function. The answer must explain how the reservoir can be largely unmutated at reactive T-cell epitopes (the viral peptides recognized by that person's T cells) - sequence-level sensitivity to the same person's autologous circulating T cells (Warren et al. 2020) - while replication-competent reservoir cells resist elimination by those same CD8+ T cells ex vivo (Huang et al. 2018).

Part 2 - Effector requirement for rebound control. Establish what breadth of T-cell specificity (epitope coverage across the reservoir, including archived escape variants) and what tissue trafficking and local effector function (for example follicle entry, tissue residency) a T-cell response would require in order to prevent immune escape and control viral rebound upon analytical interruption of ART (a closely monitored, temporary halt of therapy, also called an analytical treatment interruption).

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