Despite antiretroviral therapy (ART), human immunodeficiency virus (HIV)-1 persists in a stable latent reservoir, primarily in resting memory CD4(+) T cells. This reservoir presents a major barrier to the cure of HIV-1 infection. To purge the reservoir, pharmacological reactivation of latent HIV-1 has been proposed and tested both in vitro and in vivo. A key remaining question is whether virus-specific immune mechanisms, including cytotoxic T lymphocytes (CTLs), can clear infected cells in ART-treated patients after latency is reversed. Here we show that there is a striking all or none pattern for CTL escape mutations in HIV-1 Gag epitopes. Unless ART is started early, the vast majority (>98%) of latent viruses carry CTL escape mutations that render infected cells insensitive to CTLs directed at common epitopes. To solve this problem, we identified CTLs that could recognize epitopes from latent HIV-1 that were unmutated in every chronically infected patient tested. Upon stimulation, these CTLs eliminated target cells infected with autologous virus derived from the latent reservoir, both in vitro and in patient-derived humanized mice. The predominance of CTL-resistant viruses in the latent reservoir poses a major challenge to viral eradication. Our results demonstrate that chronically infected patients retain a broad-spectrum viral-specific CTL response and that appropriate boosting of this response may be required for the elimination of the latent reservoir.

/pdf/broad-ctl-response-is-required-to-clear-latent-hiv-1-due-to-2egoyve5e4.pdf

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations

The new field of viral dynamics, based on within-host modeling of viral infections, began with models of human immunodeficiency virus (HIV), but now includes many viral infections. Here we review developments in HIV modeling, emphasizing quantitative findings about HIV biology uncovered by studying acute infection, the response to drug therapy and the rate of generation of HIV variants that escape immune responses. We show how modeling has revealed many dynamical features of HIV infection and how it may provide insight into the ultimate cure for this infection.

/pdf/modeling-the-within-host-dynamics-of-hiv-infection-27aeiewyk4.pdf

Modeling the within-host dynamics of HIV infection

Magnitude and Kinetics of CD8+ T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point

During early human immunodeficiency virus (HIV) infection multiple CD8+ T cell responses are elicited almost simultaneously. These responses exert strong selective pressures on different parts of HIV’s genome, and select for mutations that escape recognition and are thus beneficial to the virus. Some studies reveal that the later these escape mutations emerge, the more slowly they go to fixation. This pattern of escape rate decrease(ERD) can arise by distinct mechanisms. In particular, in large populations with high beneficial mutation rates interference among different escape strains –an effect that can emerge in evolution with asexual reproduction and results in delayed fixation times of beneficial mutations compared to sexual reproduction– could significantly impact the escape rates of mutations. In this paper, we investigated how interference between these concurrent escape mutations affects their escape rates in systems with multiple epitopes, and whether it could be a source of the ERD pattern. To address these issues, we developed a multilocus Wright-Fisher model of HIV dynamics with selection, mutation and recombination, serving as a null-model for interference. We also derived an interference-free null model assuming initial neutral evolution before immune response elicitation. We found that interference between several equally selectively advantageous mutations can generate the observed ERD pattern. We also found that the number of loci, as well as recombination rates substantially affect ERD. These effects can be explained by the underexponential decline of escape rates over time. Lastly, we found that the observed ERD pattern in HIV infected individuals is consistent with both independent, interference-free mutations as well as interference effects. Our results confirm that interference effects should be considered when analyzing HIV escape mutations. The challenge in estimating escape rates and mutation-associated selective coefficients posed by interference effects cannot simply be overcome by improved sampling frequencies or sizes. This problem is a consequence of the fundamental shortcomings of current estimation techniques under interference regimes. Hence, accounting for the stochastic nature of competition between mutations demands novel estimation methodologies based on the analysis of HIV strains, rather than mutation frequencies.

/pdf/investigating-the-consequences-of-interference-between-1swgjk0dfb.pdf

Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection.

BACKGROUND A central challenge to emerging efforts to cure HIV infection is the persistence of quiescent but replication-competent proviral genomes in resting CD4 + T lymphocytes and, to an unknown extent, in other cell populations. Targeted approaches are sought to reverse latency, induce viral antigen expression within formerly latently infected cells, and use immune clearance mechanisms to eradicate persistent infection. Small-molecule HIV latency-reversing agents (LRAs) capable of modulating pathways that control HIV-1 latency are the first tools to be studied in this effort. However, despite the successful reversal of latency, the only clinical interventions to date producing a significant decrease in the viral reservoir involved bone marrow transplantation. Moreover, whether the HIV-1 RNA expression induced by LRAs leads to durable viral protein presentation on the surface of infected cells sufficient to allow immune mediated clearance is unknown. Because multiple mechanisms are involved in maintaining the transcriptional silence of HIV-1, a combination of LRAs may be necessary to effectively perturb persistent HIV-1 infection. Defining the cells that harbor persistent HIV-1 is technically challenging, burdening the development of antilatency therapy. Last, immune interventions designed to clear persistently infected cells have yet to be combined with LRAs in a successful, coordinated therapeutic strategy. ADVANCES Histone deacetylase (HDAC) inhibitors have been the most widely investigated LRAs, inducing cell-associated HIV-1 RNA in four clinical studies. The complex nature of the mechanisms that restrict HIV-1 expression of the population of latent integrated proviruses suggests the hypothesis that combinations of agents could more effectively disrupt latency. Numerous in vitro studies support this hypothesis, but thus far, only one animal model study used several LRAs; although results appeared promising, the effect of this combination was not directly assessed. A study of latently infected cells obtained from HIV-1 + donors on antiretroviral therapy revealed that instantaneous reversal of latency across all cells harboring integrated proviruses may be challenging and suggests that effective LRA strategies will likely need to be delivered serially over time. This study also illustrates the limitations of assessing the persistence of latent infection via HIV-1 RNA expression because a majority of such RNA transcripts are defective and therefore irrelevant. New approaches,such as novel techniques that can quantitate the frequency of rare cells in a large population that are capable of expressing viral antigen, may surmount this challenge. Other recent efforts have examined the obstacles to clearance of persistent, latent infection. For example, the latent reservoir harbors viral mutant subspecies that have previously escaped the extant antiviral immune response. Tissue sanctuaries that may be poorly accessed by the cytotoxic T lymphocyte (CTL) response have been described, as has the potential for some LRAs to interfere with CTL activity. Whether the extent of antigen presentation induced by the current generation of LRAs is sufficient to allow targeting and clearance of infected cells remains unknown. OUTLOOK Although the challenges of latent HIV-1 infection are daunting, the stability of the latent pool over years of antiviral therapy gives hope that an effective perturbation of the homeostasis that maintains the latent pool may allow substantial depletion, and eventually eradication, of persistent infection. The steady advances in animal models of HIV-1 latency, tools for the assessment of persistent infection, LRAs to disrupt latency, and emerging immunotherapeutics to clear persistently infected cells suggest that the first effective combination studies may be close at hand. Such studies will likely represent progress toward the goal of HIV-1 cure while also revealing new challenges to be overcome.

/pdf/latency-reversal-and-viral-clearance-to-cure-hiv-1-2u3s1y8u7d.pdf

Latency reversal and viral clearance to cure HIV-1

HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell–mediated in vivo control of HIV-1. Primary HIV-1–specific T cell responses were fully mapped in 17 individuals, and the time to virus escape, which ranged from days to years, was measured for each epitope. While higher magnitude of an individual T cell response was associated with more rapid escape, the most significant T cell measure was its relative immunodominance measured in acute infection. This identified subject-level or “vertical” immunodominance as the primary determinant of in vivo CD8+ T cell pressure in HIV-1 infection. Conversely, escape was slowed significantly by lower population variability, or entropy, of the epitope targeted. Immunodominance and epitope entropy combined to explain half of all the variability in time to escape. These data explain how CD8+ T cells can exert significant and sustained HIV-1 pressure even when escape is very slow and that within an individual, the impacts of other T cell factors on HIV-1 escape should be considered in the context of immunodominance.

/pdf/vertical-t-cell-immunodominance-and-epitope-entropy-4yz9nzwpnr.pdf

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape

HIV infection is characterized by a gradual deterioration of immune function, mainly in the CD4 compartment. To better understand the dynamics of HIV-specific T cells, we analyzed the kinetics and polyfunctional profiles of Gag-specific CD4 + and CD8 + T cell responses in 12 subtype C-infected individuals with different disease-progression profiles, ranging from acute to chronic HIV infection. The frequencies of Gag-responsive CD4 + and CD8 + T cells showed distinct temporal kinetics. The peak frequency of Gag-responsive IFN-γ + CD4 + T cells was observed at a median of 28 d (interquartile range: 21–81 d) post-Fiebig I/II staging, whereas Gag-specific IFN-γ + CD8 + T cell responses peaked at a median of 253 d (interquartile range: 136–401 d) and showed a significant biphasic expansion. The proportion of TNF-α–expressing cells within the IFN-γ + CD4 + T cell population increased ( p = 0.001) over time, whereas TNF-α–expressing cells within IFN-γ + CD8 + T cells declined ( p = 0.005). Both Gag-responsive CD4 + and CD8 + T cells showed decreased Ki67 expression within the first 120 d post-Fiebig I/II staging. Prior to the disappearance of Gag-responsive Ki67 + CD4 + T cells, these cells positively correlated ( p = 0.00038) with viremia, indicating that early Gag-responsive CD4 events are shaped by viral burden. No such associations were observed in the Gag-specific CD8 + T cell compartment. Overall, these observations indicated that circulating Gag-responsive CD4 + and CD8 + T cell frequencies and functions are not synchronous, and properties change rapidly at different tempos during early HIV infection.

/pdf/distinct-kinetics-of-gag-specific-cd4-and-cd8-t-cell-4ux5y8vqeo.pdf

Victoria E. Whale

Papers

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape

Distinct Kinetics of Gag-Specific CD4+ and CD8+ T Cell Responses during Acute HIV-1 Infection