Modeling HIV persistence, the latent reservoir, and viral blips

Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection

HIV type 1 (HIV-1) persists within resting CD4(+) T cells despite antiretroviral therapy (ART). To better understand the kinetics by which resting cell infection (RCI) is established, we developed a mathematical model that accurately predicts (r = 0.65, P = 2.5 × 10(-4)) the initial frequency of RCI measured about 1 year postinfection, based on the time of ART initiation and the dynamic changes in viremia and CD4(+) T cells. In the largest cohort of patients treated during acute seronegative HIV infection (AHI) in whom RCI has been stringently quantified, we found that early ART reduced the generation of latently infected cells. Although RCI declined after the first year of ART in most acutely infected patients, there was a striking absence of decline when initial RCI frequency was less than 0.5 per million. Notably, low-level viremia was observed more frequently as RCI increased. Together these observations suggest that (i) the degree of RCI is directly related to the availability of CD4(+) T cells susceptible to HIV, whether viremia is controlled by the immune response and/or ART; and (ii) that two pools of infected resting CD4(+) T cells exist, namely, less stable cells, observable in patients in whom viremia is not well controlled in early infection, and extremely stable cells that are established despite early ART. These findings reinforce and extend the concept that new approaches will be needed to eradicate HIV infection, and, in particular, highlight the need to target the extremely small but universal, long-lived latent reservoir.

Epigenetic regulation of HIV-1 transcription

After entry into the target cell and reverse transcription, HIV-1 genes are integrated into the host genome. It is now well established that the viral promoter activity is directly governed by its chromatin environment. Nuc-1, a nucleosome located immediately downstream of the HIV-1 transcriptional initiation site directly impedes long-terminal repeat (LTR) activity. Epigenetic modifications and disruption of Nuc-1 are a prerequisite to the activation of LTR-driven transcription and viral expression. The compaction of chromatin and its permissiveness for transcription are directly dependent on the post-translational modifications of histones such as acetylation, methylation, phosphorylation and ubiquitination. Understanding the molecular mechanisms underlying HIV-1 transcriptional silencing and activation is thus a major challenge in the fight against AIDS and will certainly lead to new therapeutic tools.

PREDICTING THE PROBABILITY OF PERSISTENCE OF HIV INFECTION WITH THE STANDARD MODEL

It is not well understood why the transmission of HIV may have a small probability of occurrence despite frequent high risk exposures or ongoing contact between members of a discordant couple. We explore the possible contributions made by distributions of system parameters beginning with the standard three-component differential equation model for the growth of a HIV virion population in an infected host in the absence of drug therapy. The overall dynamical behavior of the model is determined by the set of values of six parameters, some of which describe host immune system properties and others which describe virus properties. There may be one or two critical points whose natures play a key role in determining the outcome of infection and in particular whether the HIV population will persist or become extinct. There are two cases which may arise. In the first case, there is only one critical point P1at biological values and this is an asymptotically stable node. The system ends up with zero virions and so the host becomes HIV-free. In the second case, there are two critical points P1and P2at biological values. Here P1is an unstable saddle point and P2is an asymptotically stable spiral point with a non-zero virion level. In this case the HIV population persists unless parameters change. We let the parameter values take random values from distributions based on empirical data, but suitably truncated, and determine the probabilities of occurrence of the various combinations of critical points. From these simulations the probability that an HIV infection will persist, across a population, is estimated. It is found that with conservatively estimated distributions of parameters, within the framework of the standard 3-component model, the chances that a within-host HIV population will become extinct is between 0.6% and 6.9%. With less conservative parameter estimates, the probability is estimated to be as high as 24%. The many complicating factors related to the transmission and possible spontaneous elimination of the virus and the need for experimental data to clarify whether transient infections may occur are discussed. More realistic yet complicated higher dimensional models are likely to yield smaller probabilities of extinction.

Quantitative analysis of viral persistence and transient viral load rebound from HIV clinical data

Highly active antiretroviral therapy (HAART) suppresses HIV RNA viral load below the limit of detection for many patients. However, clinical data demonstrates that the HIV virus is not eradicated by HAART, even in patients who have had no detectable virus for 7 years [1]. One possible reason is that a stable resting latent reservoir with a long half-life exists in resting memory CD4(+)T cells [2]. In this paper, we propose a mathematical model with a constant contribution of a stable latent reservoir and identified this constant by using one patient's data from AutoVac HAART interruption study [3]. Many patients also have transient rebounds of plasma viral RNA (viral blips) under otherwise successful control of the virus by HAART. Activation of latently infected cells can explain these transient rebounds of viral load. Little quantitative analysis about the activation of reservoir has been done based on any clinical experiment data. Here, we model the activation dynamics of the reservoir by a time-independent activation rate and estimate this rate by using the clinical data from the AutoVac HAART interruption study [3].

A model of HIV-1 infection with two time delays: mathematical analysis and comparison with patient data

Mathematical models have made considerable contributions to our understanding of HIV dynamics. Introducing time delays to HIV models usually brings challenges to both mathematical analysis of the models and comparison of model predictions with patient data. In this paper, we incorporate two delays, one the time needed for infected cells to produce virions after viral entry and the other the time needed for the adaptive immune response to emerge to control viral replication, into an HIV-1 model. We begin model analysis with proving the positivity and boundedness of the solutions, local stability of the infection-free and infected steady states, and uniform persistence of the system. By developing a few Lyapunov functionals, we obtain conditions ensuring global stability of the steady states. We also fit the model including two delays to viral load data from 10 patients during primary HIV-1 infection and estimate parameter values. Although the delay model provides better fits to patient data (achieving a smaller error between data and modeling prediction) than the one without delays, we could not determine which one is better from the statistical standpoint. This highlights the need of more data sets for model verification and selection when we incorporate time delays into mathematical models to study virus dynamics.

Maximum likelihood estimation of long-term HIV dynamic models and antiviral response

HIV dynamics studies, based on differential equations, have significantly improved the knowledge on HIV infection. While first studies used simplified short-term dynamic models, recent works considered more complex long-term models combined with a global analysis of whole patient data based on nonlinear mixed models, increasing the accuracy of the HIV dynamic analysis. However statistical issues remain, given the complexity of the problem. We proposed to use the SAEM (stochastic approximation expectation-maximization) algorithm, a powerful maximum likelihood estimation algorithm, to analyze simultaneously the HIV viral load decrease and the CD4 increase in patients using a long-term HIV dynamic system. We applied the proposed methodology to the prospective COPHAR2-ANRS 111 trial. Very satisfactory results were obtained with a model with latent CD4 cells defined with five differential equations. One parameter was fixed, the 10 remaining parameters (eight with between-patient variability) of this model were well estimated. We showed that the efficacy of nelfinavir was reduced compared to indinavir and lopinavir.

Profaning the ultimate sanctuary: HIV latency in hematopoietic stem cells

The early establishment of a reservoir of latently infected T cells is a sobering obstacle to HIV eradication, in spite of the efficacy of current antiretroviral therapies. That latent proviruses might also hide in multipotent hematopoietic stem cells suggests an even more formidable challenge and potentially has therapeutic implications.

Joint effects of mitosis and intracellular delay on viral dynamics: two-parameter bifurcation analysis

To understand joint effects of logistic growth in target cells and intracellular delay on viral dynamics in vivo, we carry out two-parameter bifurcation analysis of an in-host model that describes infections of many viruses including HIV-I, HBV and HTLV-I. The bifurcation parameters are the mitosis rate r of the target cells and an intracellular delay τ in the incidence of viral infection. We describe the stability region of the chronic-infection equilibrium E* in the two-dimensional (r, τ) parameter space, as well as the global Hopf bifurcation curves as each of τ and r varies. Our analysis shows that, while both τ and r can destabilize E* and cause Hopf bifurcations, they do behave differently. The intracellular delay τ can cause Hopf bifurcations only when r is positive and sufficiently large, while r can cause Hopf bifurcations even when τ = 0. Intracellular delay τ can cause stability switches in E* while r does not.

Role of β-catenin/TCF-4 signaling in HIV replication and pathogenesis: insights to informing novel anti-HIV molecular therapeutics

A greater understanding of the interaction between HIV and host signaling pathways that restrict virus production may lead to new methods to purge virus from latent reservoirs and enhance survival/function of cells targeted by HIV. This review highlights the role of the Wnt/β-catenin pathway as a host factor that represses HIV replication in multiple targets, especially those relevant to HIV in the central nervous system.

A stochastic model of latently infected cell reactivation and viral blip generation in treated HIV patients

Motivated by viral persistence in HIV+ patients on long-term anti-retroviral treatment (ART), we present a stochastic model of HIV viral dynamics in the blood stream. We consider the hypothesis that the residual viremia in patients on ART can be explained principally by the activation of cells latently infected by HIV before the initiation of ART and that viral blips (clinically-observed short periods of detectable viral load) represent large deviations from the mean. We model the system as a continuous-time, multi-type branching process. Deriving equations for the probability generating function we use a novel numerical approach to extract the probability distributions for latent reservoir sizes and viral loads. We find that latent reservoir extinction-time distributions underscore the importance of considering reservoir dynamics beyond simply the half-life. We calculate blip amplitudes and frequencies by computing complete viral load probability distributions, and study the duration of viral blips via direct numerical simulation. We find that our model qualitatively reproduces short small-amplitude blips detected in clinical studies of treated HIV infection. Stochastic models of this type provide insight into treatment-outcome variability that cannot be found from deterministic models.

A mathematical model of HIV dynamics in the presence of a rescuing virus with replication deficiency

Recently, an enzyme (Cre recombinase) has been developed by directed evolution that successfully removes the HIV genome from the nuclear DNA of infected cells. To explore this idea further, we hypothesized that a replication deficient virus (called "police virus"), added externally, can deliver such a recombinase which excises the integrated HIV DNA from the genome of infected cells. Such a "police virus" could attack and remove the integrated provirus which is not possible using contemporary strategies. The hypothesis was tested by developing a mathematical model that describes the dynamics of virus-host cell interaction and the consequences of introducing the "police virus". The simulations show that such a therapeutic vector may eradicate all HIV viruses from the system in the long term. All components of the HIV infection (free virus, latently, and actively infected cells) can be cleared and the system ends up only with susceptible CD4+ cells. The proposed model may provide new insights in the dynamical behavior and future alternative treatments of HIV.

The large intestine as a major reservoir for simian immunodeficiency virus in macaques with long-term, nonprogressing infection

Although patients with human immunodeficiency virus type 1 infection who are receiving antiretroviral therapy and those with long-term, nonprogressive infection (LTNPs) usually have undetectable viremia, virus persists in tissue reservoirs throughout infection. However, the distribution and magnitude of viral persistence and replication in tissues has not been adequately examined. Here, we used the simian immunodeficiency virus (SIV) macaque model to quantify and compare viral RNA and DNA in the small (jejunum) and large (colon) intestine of LTNPs. In LTNPs with chronic infection, the colon had consistently higher viral levels than did the jejunum. The colon also had higher percentages of viral target cells (memory CD4(+) CCR5(+) T cells) and proliferating memory CD4(+) T cells than did the jejunum, whereas markers of cell activation were comparable in both compartments. These data indicate that the large intestine is a major viral reservoir in LTNPs, which may be the result of persistent, latently infected cells and higher turnover of naive and central memory CD4(+) T cells in this major immunologic compartment.

Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles

Gene therapy is an emerging alternative to conventional anti-HIV-1 drugs, and can potentially control the virus while alleviating major limitations of current approaches. Yet, HIV-1's ability to rapidly acquire mutations and escape therapy presents a critical challenge to any novel treatment paradigm. Viral escape is thus a key consideration in the design of any gene-based technique. We develop a computational model of HIV's evolutionary dynamics in vivo in the presence of a genetic therapy to explore the impact of therapy parameters and strategies on the development of resistance. Our model is generic and captures the properties of a broad class of gene-based agents that inhibit early stages of the viral life cycle. We highlight the differences in viral resistance dynamics between gene and standard antiretroviral therapies, and identify key factors that impact long-term viral suppression. In particular, we underscore the importance of mutationally-induced viral fitness losses in cells that are not genetically modified, as these can severely constrain the replication of resistant virus. We also propose and investigate a novel treatment strategy that leverages upon gene therapy's unique capacity to deliver different genes to distinct cell populations, and we find that such a strategy can dramatically improve efficacy when used judiciously within a certain parametric regime. Finally, we revisit a previously-suggested idea of improving clinical outcomes by boosting the proliferation of the genetically-modified cells, but we find that such an approach has mixed effects on resistance dynamics. Our results provide insights into the short- and long-term effects of gene therapy and the role of its key properties in the evolution of resistance, which can serve as guidelines for the choice and optimization of effective therapeutic agents.

A primary obstacle to the success of any anti-HIV treatment is HIV's ability to rapidly resist it by generating new viral strains whose vulnerability to the treatment is reduced. Gene therapies represent a novel class of treatments for HIV infection that may supplement or replace present therapies, as they alleviate some of their major shortcomings. The design of gene therapeutic agents that effectively reduce viral resistance can be aided by a quantitative elucidation of the processes by which resistance is acquired following therapy initiation. We developed a computational model that describes a patient's response to therapy and used it to quantify the influence of therapy parameters and strategies on the development of viral resistance. We find that gene therapy induces different clinical conditions and a much slower viral response than present therapies. These dictate different design principles such as a greater significance to the virus' competence in the absence of therapy. We also show that one can effectively delay emergence of resistance by delivering distinct therapeutic genes into separate cell populations. Our results highlight the differences between traditional and gene therapies and provide a basic understanding of how key controllable parameters and strategies affect resistance development.

HIV persistence and the prospect of long-term drug-free remissions for HIV-infected individuals

HIV infection can persist in spite of efficacious antiretroviral therapies. Although incomplete inhibition of viral replication may contribute to this phenomenon, this is largely due to the early establishment of a stable reservoir of latently infected cells. Thus, life-long antiviral therapy may be needed to control HIV. Such therapy is prone to drug resistance and cumulative side effects and is an unbearable financial burden for regions of the world hit hardest by the epidemic. This review discusses our current understanding of HIV persistence and the limitations of potential approaches to eradicate the virus and accordingly pleads for a joint multidisciplinary effort toward two highly related goals: the development of an HIV prophylactic vaccine and the achievement of long-term drug-free remissions in HIV-infected individuals.

Drug-class specific impact of antivirals on the reproductive capacity of HIV

Predictive markers linking drug efficacy to clinical outcome are a key component in the drug discovery and development process. In HIV infection, two different measures, viral load decay and phenotypic assays, are used to assess drug efficacy in vivo and in vitro. For the newly introduced class of integrase inhibitors, a huge discrepancy between these two measures of efficacy was observed. Hence, a thorough understanding of the relation between these two measures of drug efficacy is imperative for guiding future drug discovery and development activities in HIV. In this article, we developed a novel viral dynamics model, which allows for a mechanistic integration of the mode of action of all approved drugs and drugs in late clinical trials. Subsequently, we established a link between in vivo and in vitro measures of drug efficacy, and extract important determinants of drug efficacy in vivo. The analysis is based on a new quantity-the reproductive capacity-that represents in mathematical terms the in vivo analog of the read-out of a phenotypic assay. Our results suggest a drug-class specific impact of antivirals on the total amount of viral replication. Moreover, we showed that the (drug-)target half life, dominated by immune-system related clearance processes, is a key characteristic that affects both the emergence of resistance as well as the in vitro-in vivo correlation of efficacy measures in HIV treatment. We found that protease- and maturation inhibitors, due to their target half-life, decrease the total amount of viral replication and the emergence of resistance most efficiently.

Intracellular transactivation of HIV can account for the decelerating decay of virus load during drug therapy

Linking the intracellular transactivation circuit of HIV into a virus dynamics model can account for activation of infected cells and reversion into latency.

We hypothesize that the activation of latently infected cells is governed by the basal transcription rate of the integrated provirus rather than through extracellular stimuli.

This systems approach to modelling virus dynamics offers a promising framework to infer the extracellular dynamics of cell populations from their intracellular reaction networks.

The viral reservoir of latently infected cells is considered to be one of the major barriers for eradicating the virus from patients infected with HIV. During prolonged antiretroviral therapy, it has been shown that the pool of latently infected cells decays very slowly and at a decreasing rate. The underlying mechanisms causing this decelerating decay are still unclear (Lassen et al, 2004a, 2004b; Han et al, 2007). A recent study has shown that HIV can exhibit a switch-like behavior where infected cells can either be activated or become resting in a latent state (Weinberger et al, 2005). To investigate the effect of this switch-like behavior on the viral infection dynamics, we devise a new model that links the intracellular transactivation of the virus with the extracellular virus dynamics (Box 1). The model can explain the typical decelerating decay of HIV that is observed during antiretroviral therapy. We find that the activation of latently infected cells is governed by the basal transcription rate of the inserted provirus. Therefore, our analysis suggests that increasing the basal transcription rate of the HIV provirus could serve as a new therapeutic intervention for eradicating the pool of latently infected cells. In addition, our systems approach to modeling virus dynamics offers a promising framework for inferring the extracellular dynamics of cell populations from their intracellular reaction networks.

Basic virus dynamics models have been essential in understanding quantitative issues of HIV replication. However, several parts of the viral life cycle remain elusive. One of the most critical steps is the start of viral transcription, which is governed by the regulatory protein trans-activator of transcription (Tat) that induces a positive feedback loop. It has been shown that this feedback loop can alternate between two states leading to a transient activation of viral transcription. Using Monte Carlo simulations, we integrate the transactivation circuit into a new virus dynamics model having an age-dependent transactivation rate and reversion into latency. The cycling of infected cells between an activated and latent state results in the typical decelerating decay of virus load following therapy. Further, we hypothesize that the activation of latently infected cells is governed by the basal transcription rate of the integrated provirus rather than the intra- or extracellular environment. Finally, our systems approach to modeling virus dynamics offers a promising framework to infer the extracellular dynamics of cell populations from their intracellular reaction networks.

Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy

BACKGROUND

Several diseases, many of which nowadays pandemic, consist of multifactorial pathologies. Paradigmatic examples come from the immune response to pathogens, in which cases the effects of different infections combine together, yielding complex mutual feedback, often a positive one that boosts infection progression in a scenario that can easily become lethal. HIV is one such infection, which weakens the immune system favouring the insurgence of opportunistic infections, amongst which Tuberculosis (TB). The treatment with antiretroviral therapies has shown effective in reducing mortality. An in-depth understanding of complex systems, like the one consisting of HIV, TB and related therapies, is an open great challenge, on the boundaries of bioinformatics, computational and systems biology.

RESULTS

We present a simplified formalisation of the highly dynamic system consisting of HIV, TB and related therapies, at the cellular level. The progression of the disease (AIDS) depends hence on interactions between viruses, cells, chemokines, the high mutation rate of viruses, the immune response of individuals and the interaction between drugs and infection dynamics. We first discuss a deterministic model of dual infection (HIV and TB) which is able to capture the long-term dynamics of CD4 T cells, viruses and Tumour Necrosis Factor (TNF). We contrast this model with a stochastic approach which captures intrinsic fluctuations of the biological processes. Furthermore, we also integrate automated reasoning techniques, i.e. probabilistic model checking, in our formal analysis. Beyond numerical simulations, model checking allows general properties (effectiveness of anti-HIV therapies) to be verified against the models by means of an automated procedure. Our work stresses the growing importance and flexibility of model checking techniques in bioinformatics. In this paper we i) describe HIV as a complex case of infectious diseases; ii) provide a number of different formal descriptions that suitably account for aspects of interests; iii) suggest that the integration of different models together with automated reasoning techniques can improve the understanding of infections and therapies through formal analysis methodologies.

CONCLUSION

We argue that the described methodology suitably supports the study of viral infections in a formal, automated and expressive manner. We envisage a long-term contribution of this kind of approaches to clinical Bioinformatics and Translational Medicine.

Theoretical aspects of immunity

The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the dynamics of the immune system. We describe how the immune system recognizes antigens by searching the large space of receptor molecules. We consider in some detail the theories that quantify the immune response to influenza and dengue fever. We review theoretical descriptions of the complementary evolution of pathogens that occurs in response to immune system pressure. Methods including bioinformatics, molecular simulation, random energy models, and quantum field theory contribute to a theoretical understanding of aspects of immunity.

Viral sanctuaries during highly active antiretroviral therapy in a nonhuman primate model for AIDS

Highly active antiretroviral therapy (HAART) enables long-term suppression of plasma HIV-1 loads in infected persons, but low-level virus persists and rebounds following cessation of therapy. During HAART, this virus resides in latently infected cells, such as resting CD4(+) T cells, and in other cell types that may support residual virus replication. Therapeutic eradication will require elimination of virus from all reservoirs. We report here a comprehensive analysis of these reservoirs in fluids, cells, and tissues in a rhesus macaque model that mimics HAART in HIV-infected humans. This nonhuman primate model uses RT-SHIV, a chimera of simian immunodeficiency virus containing the HIV-1 reverse transcriptase (RT). Methods were developed for extraction, preamplification, and real-time PCR analyses of viral DNA (vDNA) and viral RNA (vRNA) in tissues from RT-SHIV-infected macaques. These methods were used to identify viral reservoirs in RT-SHIV-infected macaques treated with a potent HAART regimen consisting of efavirenz, emtricitabine, and tenofovir. Plasma virus loads at necropsy ranged from 11 to 28 copies of vRNA per ml. Viral RNA and DNA were detected during HAART, in tissues from numerous anatomical locations. Additional analysis provided evidence for full-length viral RNA in tissues of animals with virus suppressed by HAART. The highest levels of vDNA and vRNA in HAART-treated macaques were in lymphoid tissues, particularly the spleen, lymph nodes, and gastrointestinal tract tissues. This study is the first comprehensive analysis of the tissue and organ distribution of a primate AIDS virus during HAART. These data demonstrate widespread persistence of residual virus in tissues during HAART.

Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy

Although potent combination therapy is usually able to suppress plasma viral loads in HIV-1 patients to below the detection limit of conventional clinical assays, a low level of viremia frequently can be detected in plasma by more sensitive assays. Additionally, many patients experience transient episodes of viremia above the detection limit, termed viral blips, even after being on highly suppressive therapy for many years. An obstacle to viral eradication is the persistence of a latent reservoir for HIV-1 in resting memory CD4(+) T cells. The mechanisms underlying low viral load persistence, slow decay of the latent reservoir, and intermittent viral blips are not fully characterized. The quantitative contributions of residual viral replication to viral and the latent reservoir persistence remain unclear. In this paper, we probe these issues by developing a mathematical model that considers latently infected cell activation in response to stochastic antigenic stimulation. We demonstrate that programmed expansion and contraction of latently infected cells upon immune activation can generate both low-level persistent viremia and intermittent viral blips. Also, a small fraction of activated T cells revert to latency, providing a potential to replenish the latent reservoir. By this means, occasional activation of latently infected cells can explain the variable decay characteristics of the latent reservoir observed in different clinical studies. Finally, we propose a phenomenological model that includes a logistic term representing homeostatic proliferation of latently infected cells. The model is simple but can robustly generate the multiphasic viral decline seen after initiation of therapy, as well as low-level persistent viremia and intermittent HIV-1 blips. Using these models, we provide a quantitative and integrated prospective into the long-term dynamics of HIV-1 and the latent reservoir in the setting of potent antiretroviral therapy.

HIV reservoirs, latency, and reactivation: prospects for eradication

Current antiretroviral therapy effectively suppresses but does not eradicate HIV-1 infection. During therapy patients maintain a persistent low-level viremia requiring lifelong adherence to antiretroviral therapies. This viremia may arise from latently infected reservoirs such as resting memory CD4+ T-cells or sanctuary sites where drug penetration is suboptimal. Understanding the mechanisms of HIV latency will help efforts to eradicate the infection. This review examines the dynamics of persistent viremia, viral reservoirs, the mechanisms behind viral latency, and methods to purge the viral reservoirs. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, vol. 85, issue 1, 2010.