HIV infection: how effective is drug combination treatment?

Rationale, current state and opportunities in combining biologic disease modifying antirheumatic drugs in rheumatoid and psoriatic arthritis

The advent of biologic disease modifying antirheumatic drugs (bDMARDs) has considerably improved patient outcomes in inflammatory arthritis. However, not all patients reach the state of remission, as disease can be resistant even to single cytokine inhibition by bDMARDs. Simultaneous or sequential inhibition of multiple cytokines may be considered in situations where disease control is not adequate under singular inhibition of cytokines. Although there have been some disappointing experiences in the past with combination of bDMARDs, the ongoing improvement of our understanding about inflammatory pathways and the overall better safety understanding of bDMARDs seem to make new biologic treatment combinations possible. This review covers the rationale and current evidence for bDMARDs combination in inflammatory arthritis.

Pharmacometrics: The Already-Present Future of Precision Pharmacology

The use of mathematical modeling to represent, analyze, make predictions or providing information on data obtained in drug research and development has made pharmacometrics an area of great prominence and importance. The main purpose of pharmacometrics is to provide information relevant to the search for efficacy and safety improvements in pharmacotherapy. Regulatory agencies have adopted pharmacometrics analysis to justify their regulatory decisions, making those decisions more efficient. Demand for specialists trained in the field is therefore growing. In this review, we describe the meaning, history, and development of pharmacometrics, analyzing the challenges faced in the training of professionals. Examples of applications in current use, perspectives for the future, and the importance of pharmacometrics for the development and growth of precision pharmacology are also presented.

Kinetics of Asian and African Zika virus lineages over single-cycle and multi-cycle growth in culture: Gene expression, cell killing, virus production, and mathematical modeling

Since 2014, an Asian lineage of Zika virus has caused outbreaks, and it has been associated with neurological disorders in adults and congenital defects in newborns. The resulting threat of the Zika virus to human health has prompted the development of new vaccines, which have yet to be approved for human use. Vaccines based on the attenuated or chemically inactivated virus will require large-scale production of the intact virus to meet potential global demands. Intact viruses are produced by infecting cultures of susceptible cells, a dynamic process that spans from hours to days and has yet to be optimized. Here, we infected Vero cells adhesively cultured in well-plates with two Zika virus strains: a recently isolated strain from the Asian lineage, and a cell-culture-adapted strain from the African lineage. At different time points post-infection, virus particles in the supernatant were quantified; further, microscopy images were used to quantify cell density and the proportion of cells expressing viral protein. These measurements were performed across multiple replicate samples of one-step infections every four hours over 60 h and for multi-step infections every four to 24 h over 144 h, generating a rich data set. For each set of data, mathematical models were developed to estimate parameters associated with cell infection and virus production. The African-lineage strain was found to produce a 14-fold higher yield than the Asian-lineage strain in one-step growth and a sevenfold higher titer in multi-step growth, suggesting a benefit of cell-culture adaptation for developing a vaccine strain. We found that image-based measurements were critical for discriminating among different models, and different parameters for the two strains could account for the experimentally observed differences. An exponential-distributed delay model performed best in accounting for multi-step infection of the Asian strain, and it highlighted the significant sensitivity of virus titer to the rate of viral degradation, with implications for optimization of vaccine production. More broadly, this study highlights how image-based measurements can contribute to the discrimination of virus-culture models for the optimal production of inactivated and attenuated whole-virus vaccines.

On the extinction probability in models of within-host infection: the role of latency and immunity

Not every exposure to virus establishes infection in the host; instead, the small amount of initial virus could become extinct due to stochastic events. Different diseases and routes of transmission have a different average number of exposures required to establish an infection. Furthermore, the host immune response and antiviral treatment affect not only the time course of the viral load provided infection occurs, but can prevent infection altogether by increasing the extinction probability. We show that the extinction probability when there is a time-dependent immune response depends on the chosen form of the model-specifically, on the presence or absence of a delay between infection of a cell and production of virus, and the distribution of latent and infectious periods of an infected cell. We hypothesise that experimentally measuring the extinction probability when the virus is introduced at different stages of the immune response, alongside the viral load which is usually measured, will improve parameter estimates and determine the most suitable mathematical form of the model.

Notwithstanding Circumstantial Alibis, Cytotoxic T Cells Can Be Major Killers of HIV-1-Infected Cells

Several experiments suggest that in the chronic phase of human immunodeficiency virus type 1 (HIV-1) infection, CD8⁺ cytotoxic T lymphocytes (CTL) contribute very little to the death of productively infected cells. First, the expected life span of productively infected cells is fairly long, i.e., about 1 day. Second, this life span is hardly affected by the depletion of CD8⁺ T cells. Third, the rate at which mutants escaping a CTL response take over the viral population tends to be slow. Our main result is that all these observations are perfectly compatible with killing rates that are much faster than one per day once we invoke the fact that infected cells proceed through an eclipse phase of about 1 day before they start producing virus. Assuming that the major protective effect of CTL is cytolytic, we demonstrate that mathematical models with an eclipse phase account for the data when the killing is fast and when it varies over the life cycle of infected cells. Considering the steady state corresponding to the chronic phase of the infection, we find that the rate of immune escape and the rate at which the viral load increases following CD8⁺ T cell depletion should reflect the viral replication rate, ρ. A meta-analysis of previous data shows that viral replication rates during chronic infection vary between 0.5 ≤ ρ ≤ 1 day⁻¹. Balancing such fast viral replication requires killing rates that are several times larger than ρ, implying that most productively infected cells would die by cytolytic effects.

IMPORTANCE Most current data suggest that cytotoxic T cells (CTL) mediate their control of human immunodeficiency virus type 1 (HIV-1) infection by nonlytic mechanisms; i.e., the data suggest that CTL hardly kill. This interpretation of these data has been based upon the general mathematical model for HIV infection. Because this model ignores the eclipse phase between the infection of a target cell and the start of viral production by that cell, we reanalyze the same data sets with novel models that do account for the eclipse phase. We find that the data are perfectly consistent with lytic control by CTL and predict that most productively infected cells are killed by CTL. Because the killing rate should balance the viral replication rate, we estimate both parameters from a large set of published experiments in which CD8⁺ T cells were depleted in simian immunodeficiency virus (SIV)-infected monkeys. This confirms that the killing rate can be much faster than is currently appreciated.

What do mathematical models tell us about killing rates during HIV-1 infection?

Over the past few decades the extent to which cytotoxic T lymphocytes (CTLs) control human immunodeficiency virus (HIV) replication has been studied extensively, yet their role and mode of action remain controversial. In some studies, CTLs were found to kill a large fraction of the productively infected cells relative to the viral cytopathicity, whereas in others CTLs were suggested to kill only a small fraction of infected cells. In this review, we compile published estimates of CTL-mediated death rates, and examine whether these studies permit determining the rate at which CTLs kill HIV-1 infected cells. We highlight potential misinterpretations of the CTL-killing rates from the escape rates of mutants, and from perturbations of the steady state viral load during chronic infection. Our major conclusion is that CTL-mediated killing rates remain unknown. But contrary to current consensus, we argue that killing rates higher than one per day are perfectly consistent with the experimental data, which would imply that the majority of the productively infected cells could still die from CTL-mediated killing rather than from viral cytopathicity.

Global dynamics of a delayed within-host viral infection model with both virus-to-cell and cell-to-cell transmissions

A within-host viral infection model with both virus-to-cell and cell-to-cell transmissions and three distributed delays is investigated, in which the first distributed delay describes the intracellular latency for the virus-to-cell infection, the second delay represents the intracellular latency for the cell-to-cell infection, and the third delay describes the time period that viruses penetrated into cells and infected cells release new virions. The global stability analysis of the model is carried out in terms of the basic reproduction number R0. If R0≤1, the infection-free (semi-trivial) equilibrium is the unique equilibrium and is globally stable; if R0>1, the chronic infection (positive) equilibrium exists and is globally stable under certain assumptions. Examples and numerical simulations for several special cases are presented, including various within-host dynamics models with discrete or distributed delays that have been well-studied in the literature. It is found that the global stability of the chronic infection equilibrium might change in some special cases when the assumptions do not hold. The results show that the model can be applied to describe the within-host dynamics of HBV, HIV, or HTLV-1 infection.

Exploring the effect of biological delays in kinetic models of influenza within a host or cell culture

BACKGROUND

For a typical influenza infection in vivo, viral titers over time are characterized by 1-2 days of exponential growth followed by an exponential decay. This simple dynamic can be reproduced by a broad range of mathematical models which makes model selection and the extraction of biologically-relevant infection parameters from experimental data difficult.

RESULTS

We analyze in vitro experimental data from the literature, specifically that of single-cycle viral yield experiments, to narrow the range of realistic models of infection. In particular, we demonstrate the viability of using a normal or lognormal distribution for the time a cell spends in a given infection state (e.g., the time spent by a newly infected cell in the latent state before it begins to produce virus), while exposing the shortcomings of ordinary differential equation models which implicitly utilize exponential distributions and delay-differential equation models with fixed-length delays.

CONCLUSIONS

By fitting published viral titer data from challenge experiments in human volunteers, we show that alternative models can lead to different estimates of the key infection parameters.

Biomarkers of HIV replication

PURPOSE OF REVIEW

Viremia provides a biomarker for HIV-1 replication in various tissues. The purpose of this review is to discuss the relationship between viremia and viral replication at a theoretical level and to review recent advances in understanding this relationship, particularly in the context of highly active antiretroviral therapy (HAART).

RECENT FINDINGS

Recent studies have focused on understanding the extremely low level of residual viremia that can be detected in patients on HAART. The two major explanations for this residual viremia are that it represents ongoing cycles of replication that continue despite HAART or that it represents release of virus from stable reservoirs. The recent finding that intensification of HAART does not further reduce residual viremia supports that latter hypothesis. Direct sequence analysis of the residual viremia has provided new insights into the complex relationship between residual viremia and viral reservoirs.

SUMMARY

In patients with untreated HIV-1 infection, the level of viremia is a direct indication of the level of viral replication and a predictor of the rate of CD4 depletion. However, when viral replication is suppressed by HAART, the level of residual viremia is to a large extent an indication of virus release from stable viral reservoirs.

Design considerations in building in silico equivalents of common experimental influenza virus assays

Experimentation in vitro is a vital part of the process by which the clinical and epidemiological characteristics of a particular influenza virus strain are determined. We detail the considerations which must be made in designing appropriate theoretical/mathematical models of these experiments and show how modeling can increase the information output of such experiments. Starting from a traditional system of ordinary differential equations, common to infectious disease modeling, we broaden the approach by using an agent-based model, applicable to more general experimental geometries and assumptions about the biological properties of viruses, cell and their interaction. Within this framework, we explore the limits of the assumptions made by more traditional models and the conditions under which these assumptions begin to break down, requiring the use of more sophisticated models. We apply the agent-based model to experimental plaque growth of two influenza strains, one resistant to the antiviral oseltamivir, and extract the values of key infection parameters specific to each strain.

Effect of raltegravir-containing intensification on HIV burden and T-cell activation in multiple gut sites of HIV-positive adults on suppressive antiretroviral therapy

OBJECTIVE

To determine whether raltegravir-containing antiretroviral therapy (ART) intensification reduces HIV levels in the gut.

DESIGN

Open-label study in HIV-positive adults on ART with plasma HIV RNA below 40 copies/ml.

METHODS

Seven HIV-positive adults received 12 weeks of ART intensification with raltegravir alone or in combination with efavirenz or darunavir. Gut cells were obtained by upper and lower endoscopy with biopsies from duodenum, ileum, colon, and rectum at baseline and 12 weeks. Study outcomes included plasma HIV RNA, HIV DNA and RNA from peripheral blood mononuclear cells (PBMC) and four gut sites, T-cell subsets, and activation markers.

RESULTS

Intensification produced no consistent decrease in HIV RNA in the plasma, PBMC, duodenum, colon, or rectum. However, five of seven participants had a decrease in unspliced HIV RNA per 10 CD4(+) T cells in the ileum. There was a trend towards decreased T-cell activation in all sites, which was greatest for CD8(+) T cells in the ileum and PBMC, and a trend towards increased CD4(+) T cells in the ileum.

CONCLUSION

Most HIV RNA and DNA in the blood and gut is not the result of ongoing replication that can be impacted by short-term intensification with raltegravir. However, the ileum may support ongoing productive infection in some patients on ART, even if the contribution to plasma RNA is not discernible.

Modeling HIV persistence, the latent reservoir, and viral blips

HIV-1 eradication from infected individuals has not been achieved with the prolonged use of highly active antiretroviral therapy (HAART). The cellular reservoir for HIV-1 in resting memory CD4(+) T cells remains a major obstacle to viral elimination. The reservoir does not decay significantly over long periods of time but is able to release replication-competent HIV-1 upon cell activation. Residual ongoing viral replication may likely occur in many patients because low levels of virus can be detected in plasma by sensitive assays and transient episodes of viremia, or HIV-1 blips, are often observed in patients even with successful viral suppression for many years. Here we review our current knowledge of the factors contributing to viral persistence, the latent reservoir, and blips, and mathematical models developed to explore them and their relationships. We show how mathematical modeling has helped improve our understanding of HIV-1 dynamics in patients on HAART and of the quantitative events underlying HIV-1 latency, reservoir stability, low-level viremic persistence, and emergence of intermittent viral blips. We also discuss treatment implications related to these studies.

Implications of decoupling the intracellular and extracellular levels in multi-level models of virus growth

Virus infections are characterized by two distinct levels of detail: the intracellular level describing how viruses hijack the host machinery to replicate, and the extracellular level describing how populations of virus and host cells interact. Deterministic, population balance models for viral infections permit incorporation of both the intracellular and extracellular levels of information. In this work, we identify assumptions that lead to exact, selective decoupling of the interaction between the intracellular and extracellular levels, effectively permitting solution of first the intracellular level, and subsequently the extracellular level. This decoupling leads to (1) intracellular and extracellular models of viral infections that have been previously reported and (2) a significant reduction in the computational expense required to solve the model. However, the decoupling restricts the behaviors that can be modeled. Simulation of a previously reported multi-level model demonstrates this decomposition when the intracellular level of description consists of numerous reaction events. Additionally, examples demonstrate that viruses can persist even when the intracellular level of description cannot sustain a steady-state production of virus (i.e., has only a trivial equilibrium). We expect the combination of this modeling framework with experimental data to result in a quantitative, systems-level understanding of viral infections and cellular antiviral strategies that will facilitate controlling both these infections and antiviral strategies.

Stability analysis of within-host parasite models with delays

We provide a global analysis of systems of within-host parasitic infections. The systems studied have parallel classes of different length of latently infected target cells. These systems can also be thought as systems arising from within-host parasitic systems with distributed continuous delays. We compute the basic reproduction ratio R0 for the systems under consideration. If R0< or =1 the parasite is cleared, if R0>1 and if a sufficient condition is satisfied we conclude to the global asymptotic stability (GAS) of the endemic equilibrium. For some generic class of models this condition reduces to R0>1. These results make possible to revisit some parasitic models including intracellular delays and to study their global stability.

Appropriate models for the management of infectious diseases

BACKGROUND

Mathematical models have become invaluable management tools for epidemiologists, both shedding light on the mechanisms underlying observed dynamics as well as making quantitative predictions on the effectiveness of different control measures. Here, we explain how substantial biases are introduced by two important, yet largely ignored, assumptions at the core of the vast majority of such models.

METHODS AND FINDINGS

First, we use analytical methods to show that (i) ignoring the latent period or (ii) making the common assumption of exponentially distributed latent and infectious periods (when including the latent period) always results in underestimating the basic reproductive ratio of an infection from outbreak data. We then proceed to illustrate these points by fitting epidemic models to data from an influenza outbreak. Finally, we document how such unrealistic a priori assumptions concerning model structure give rise to systematically overoptimistic predictions on the outcome of potential management options.

CONCLUSION

This work aims to highlight that, when developing models for public health use, we need to pay careful attention to the intrinsic assumptions embedded within classical frameworks.

A parameter sensitivity methodology in the context of HIV delay equation models

A sensitivity methodology for nonlinear delay systems arising in one class of cellular HIV infection models is presented. Theoretical foundations for a typical sensitivity investigation and illustrative computations are given.

Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads

Highly active antiretroviral therapy (HAART) can suppress plasma human immunodeficiency virus type 1 (HIV-1) levels to below the detection limit of ultrasensitive clinical assays. However, HIV-1 persists in cellular reservoirs, and in adults, persistent low-level viremia is detected with more sensitive assays. The nature of this viremia is poorly understood, and it is unclear whether viremia persists in children on HAART, particularly those who start therapy shortly after birth. We therefore developed a reverse transcriptase PCR (RT-PCR) assay that allows genotyping of HIV-1 protease even when viremia is present at levels as low as 5 copies of HIV-1 RNA/ml. We demonstrated that viremia persists in children with plasma virus levels below the limit of detection of clinical assays. Viremia was detected even in children who began HAART in early infancy and maintained such strong suppression of viremia that HIV-1-specific antibody responses were absent or minimal. The low-level plasma virus lacked protease inhibitor resistance mutations despite the frequent use of nelfinavir, which has a low mutational barrier to resistance. Protease sequences resembled those of viruses in the latent reservoir in resting CD4(+) T cells. Thus, in most children on HAART with clinically undetectable viremia, there is continued virus production without evolution of resistance in the protease gene.

Simulating the effect of vaccine-induced immune responses on HIV infection

The need for anti-HIV-1 vaccines is universally recognized. Although several potential vaccine formulations are being tested in clinical trials, the complexity of the viral system and the length of the experimentation required and its costs makes the goal of obtaining such a vaccine still elusive. We have built a mathematical model for the simulation of HIV-1 infection spreading into the body, which allows us study in silico the effect of hypothetical anti-HIV-1 vaccines having different properties. In particular, vaccines eliciting a cytolytic T-cell response, a humoral response, or both can be simulated. The vaccines considered can be envisaged either as preventive or therapeutic and can have different strength. The kinetic parameters used for solving the model are those of HIV-1 infection obtained from experimental and clinical observations. The vaccines are instead characterized by parameters that can be varied in order to mimic different behaviors: the rate of killing of the single effector cell and the rate of neutralization of the single antibody molecule; and the level of the immune response raised. The model allows us to predict which characteristics of immunogenicity a preventive or therapeutic vaccine should possess to be efficacious, and which are the key factors that most likely will affect its ability to control the spread of the infection. We discuss here the conclusions that can be drawn from a such a model and some of its limitations.

Incorporation of variability into the modeling of viral delays in HIV infection dynamics

We consider classes of functional differential equation models which arise in attempts to describe temporal delays in HIV pathogenesis. In particular, we develop methods for incorporating arbitrary variability (i.e., general probability distributions) for these delays into systems that cannot readily be reduced to a finite number of coupled ordinary differential equations (as is done in the method of stages). We discuss modeling from first principles, introduce several classes of non-linear models (including discrete and distributed delays) and present a discussion of theoretical and computational approaches. We then use the resulting methodology to carry out simulations and perform parameter estimation calculations, fitting the models to a set of experimental data. Results obtained confirm the statistical significance of the presence of delays and the importance of including delays in validating mathematical models with experimental data. We also show that the models are quite sensitive to the mean of the distribution which describes the delay in viral production, whereas the variance of this distribution has relatively little impact.

Mathematical analysis of delay differential equation models of HIV-1 infection

Models of HIV-1 infection that include intracellular delays are more accurate representations of the biology and change the estimated values of kinetic parameters when compared to models without delays. We develop and analyze a set of models that include intracellular delays, combination antiretroviral therapy, and the dynamics of both infected and uninfected T cells. We show that when the drug efficacy is less than perfect the estimated value of the loss rate of productively infected T cells, delta, is increased when data is fit with delay models compared to the values estimated with a non-delay model. We provide a mathematical justification for this increased value of delta. We also provide some general results on the stability of non-linear delay differential equation infection models.

Selection of a T-Cell Line Resistant to Stavudine and Zidovudine by Prolonged Treatment with Stavudine

It has been demonstrated that prolonged treatment with nucleoside analogues, such as 3′-azido-3′-deoxythymi-dine (zidovudine), 2’,3′-dideoxycytidine (zalcitabine) and 9-(2-phosphonylmethoxyethyl) adenine (PMEA), may cause selection of cells that are resistant to their anti-HIV activity. A human T-lymphoblastoid cell line that is resistant to the antiviral and cytotoxic activity of 2’,3′-didehydro-3′-deoxythymidine (stavudine) has developed as a result of prolonged treatment. These cells, called CEMstavudine, are also less sensitive to zidovudine. The cellular/pharmacological resistance acquired by the CEMstavudine cells is relatively low and appears to correlate with a reduction in thymidine kinase (TK) activity, rather than with a decreased expression of TK mRNA.

Correlation between reduction in plasma HIV-1 RNA concentration 1 week after start of antiretroviral treatment and longer-term efficacy

BACKGROUND

Early assessment of antiretroviral drug efficacy is important for prevention of the emergence of drug-resistant virus and unnecessary exposure to ineffective drug regimens. Current US guidelines for changing therapy are based on measurements of plasma HIV-1 RNA concentrations 4 or 8 weeks after the start of treatment with cut-off points of 0.75 or 1.00 log, respectively. We investigated the possibility of assessing drug efficacy from measurements of plasma HIV-1 concentrations made during the first week on therapy.

METHODS

The kinetics of virus decay in plasma during the first 12 weeks of treatment was analysed for 124 HIV-1-infected patients being treated for the first time with a protease inhibitor. Patients with a continuous decline of HIV-1 concentrations and in whom HIV-1 was either undetectable or declined by more than 1.5 log at 12 weeks were defined as good responders; the rest were poor responders.

FINDINGS

The individual virus decay rate constants (k) at day 6 correlated significantly (r>0.66, p<0.0001) with changes in HIV-1 concentrations at 4, 8, and 12 weeks, and correctly predicted 84% of the responses with a cut-off value of k=0.21 per day (in log scale). Reduction in plasma HIV-1 of less than 0.72 log by day 6 after initiation of therapy predicted poor long-term responses in more than 99% of patients.

INTERPRETATION

These results suggest that changes in HIV-1 concentration at day 6 after treatment initiation are major correlates of longer-term virological responses. They offer a very early measure of individual long-term responses, suggesting that treatment could be optimised after only a few days of therapy.

Short-term measures of relative efficacy predict longer-term reductions in human immunodeficiency virus type 1 RNA levels following nelfinavir monotherapy

We calculated the relative efficacy of treatment, defined as the rate of decline of virus levels in plasma during treatment relative to the rate of decline during highly potent combination therapy, in human immunodeficiency virus type 1 (HIV-1) patients treated for 56 days with different doses of the protease inhibitor nelfinavir. Relative efficacies based on the rate of decline of HIV-1 RNA levels in plasma over the first 14 to 21 days correlated with drug dose and viral load reduction by day 56. Calculation of relative treatment efficacies over the first 2 to 3 weeks of treatment can allow rapid assessment of new antiretroviral agents and dosing regimens, reducing the need to keep subjects in clinical trials on monotherapy for prolonged periods of time. Relative efficacy may also serve as a measure of treatment efficacy in patients in initiating established therapies.

The dependence of viral parameter estimates on the assumed viral life cycle: limitations of studies of viral load data

Estimation of viral parameters, such as the basic reproductive number (R0) and infected cell life span, is central to the quantitative study of the within-host dynamics of viral diseases such as human immunodeficiency virus, hepatitis B or hepatitis C. As these parameters can rarely be determined directly, they are usually estimated indirectly by fitting mathematical models to viral load data. This paper investigates how parameter estimates obtained by such procedures depend on the assumptions made concerning the viral life cycle. It finds that estimates of the basic reproductive number obtained using viral load data collected during the initial stages of infection can depend quite sensitively on these assumptions. The use of models which neglect the intracellular delay before virion production can lead to severe underestimates of R0 and, hence, to overly optimistic predictions of how efficacious treatment must be in order to prevent or eradicate the disease. These results are also of importance for attempts at estimating R0 from similar epidemiological data as there is a correspondence between within-host and between-host models. Estimates of the life span of infected cells obtained from viral load data collected during drug treatment studies also depend on the assumptions made in modelling the virus life cycle. The use of more realistic descriptions of the life cycle is seen to increase estimates of infected cell life span, in addition to providing a new explanation for the shoulder phase seen during drug treatment. This study highlights the limitations of what can be learnt by fitting mathematical models to infectious disease data without detailed independent knowledge of the life cycle of the infectious agent.

Effect of drug efficacy and the eclipse phase of the viral life cycle on estimates of HIV viral dynamic parameters

Fits of mathematic models to the decline in HIV-1 RNA after antiretroviral therapies have yielded estimates for the life span of productively infected cells of 1 to 2 days. In a previous report, we described the mathematic properties of an extended model that accounts for imperfect viral suppression and the eclipse phase of the viral life cycle (the intracellular delay between initial infection and release of progeny virions). In this article, we fit this extended model to detailed data on the decline of plasma HIV-1 RNA after treatment with the protease inhibitor ritonavir. Because the therapy in this study was most likely not completely suppressive, we allowed the drug efficacy parameter to vary from 70% to 100%. Estimates for the clearance rate of free virus, c, increased with the addition of the intracellular delay (as reported previously) but were not appreciably affected by changes in the drug efficacy parameter. By contrast, the estimated death rate of virus-producing cells, delta, increased from an average of 0.49 day-1 to 0.90 day-1 (an increase of 84%) because the drug efficacy parameter was reduced from 100% to 70%. Neglecting the intracellular delay, the comparable increase in delta was only about 55%. The inferred increases in delta doubled when the model was extended to account for possible increases in target cell densities after treatment initiation. This work suggests that estimates for delta may be greater than previously reported and that the half-life of a cell in vivo that is producing virus, on average, may be 1 day.

Immune-Based Therapies for the Management of HIV Infection: Highly Active Antiretroviral Therapy and Beyond

The widespread use of highly active antiretroviral therapy (HAART) has had a significant impact on reducing the incidence of opportunistic infections in patients with the Acquired Immunodeficiency Syndrome (AIDS) and reducing the overall morbidity and mortality associated with this disease. However, the use of HAART is often associated with adverse effects, significant drug interactions, high cost and the emergence of viral resistance in a significant percentage of treatment recipients. In addition, the clinical efficacy of HAART in terms of viral eradication appears to be limited due to the presence of reservoirs of latent virus within HAART-experienced patients. Because of these and other limitations associated with antiretroviral therapies, new therapeutic strategies are being developed to restore the normal function of the immune system and improve patient outcomes. The purpose of this article is to review some of the more promising investigational immune-based therapies and their potential role in the management of Human Immunodeficiency Virus infection.

An in vitro rapid-turnover assay for human immunodeficiency virus type 1 replication selects for cell-to-cell spread of virus

We have developed a rapid-turnover culture system where the life span of a human immunodeficiency virus type 1-infected cell is controlled by periodic addition of a cytotoxic agent, mitomycin C. These mitomycin C-exposed cells are cocultured with a constant number of uninfected cells as new targets for the virus. Passage of the virus-infected cells under these conditions led to the emergence of a viral variant that was able to replicate efficiently in this culture system. After biologic and molecular cloning, we were able to identify a single frameshift mutation in the vpu open reading frame that was sufficient for growth of the mutant virus in the rapid-turnover assay. This virus variant spread more efficiently by cell-to-cell transfer than the parental virus did. Electron micrographs of cells infected with the delta vpu virus revealed a large number of mature viral capsids attached to the plasma membrane. The presence of these mature virus particles on the cell surface led to enhanced fusion and formation of giant syncytia with uninfected cells. Enhanced cell-to-cell transfer of the delta vpu virus provides an explanation for the survival of this mutant virus in the rapid-turnover culture system. The in vitro rapid-turnover culture system is a good representation of the in vivo turnover kinetics of infected cells and their continual replacement by host lymphopoietic mechanisms.

Immunological benefits of antiretroviral therapy in very early stages of asymptomatic chronic HIV-1 infection

OBJECTIVES

To assess whether an almost complete restoration of immune system can be achieved when antiretroviral therapy is initiated at very early stages of asymptomatic chronic HIV-1 infection.

DESIGN

T cell subsets and cell-mediated responses were analysed at baseline and after 12 months of either a double or a triple antiretroviral therapy in 26 asymptomatic HIV-1-infected patients with CD4 T cell counts > 500 x 10(6) cells/l and a baseline plasma viral load > 10000 copies/ml.

RESULTS

Triple therapy was significantly more effective in reducing plasma HIV RNA to undetectable levels, in returning CD4:CD8 ratio to nearly normal levels, in reducing activated cells (CD38) and in increasing naive (CD45RA+CD45RO-) and memory (CD45RA-CD45RO+) CD4 cells. Both double and triple therapies caused a clear decrease in memory (CD45RA-CD45RO+) CD8 cells as well as a significant increase in the CD28 subset of CD8 cells. At baseline, there was an important increase in cells producing interferon-gamma (IFNgamma) with no significant abnormalities in T lymphocytes producing interleukin 2 (IL-2), tumour necrosis factor alpha and interleukin 4. Both types of therapy reduced IFNgamma- and IL2-producing CD4 T lymphocytes while IFNgamma-producing CD8 cells remained increased. Even before therapy, these HIV-1-positive patients lacked significant abnormalities in the T cell responsiveness to polyclonal stimuli as well as in the secretion of CCR5 chemokines by peripheral blood mononuclear cells.

CONCLUSIONS

Initiating highly active antiretroviral therapy at very early stages of chronic HIV-1 infection allows rapid and almost complete normalization of T cell subsets and preservation of T cell functions. These early-treated patients could be excellent candidates for receiving additional HIV-specific immune-based therapies, which might be essential for the control of HIV infection.

Liquid chromatographic determination of FP-21399 in plasma of patients with HIV infection

A high-performance liquid chromatographic (HPLC) analysis method for the novel anti-HIV drug FP-21399 in human plasma was developed. The method employed the combination of organic solvent extraction and solid phase extraction. Analysis of FP 21399 and two major metabolites was achieved within 18 min using a reverse phase Puresil Cl 8 analytical column (4.6 x 150 mm, 5 microm, Waters) with a mobile phase of water-acetonitrile containing 20 mM triethylamine acetate (apparent pH 7.0). Linear gradient of mobile phase was applied as water-acetonitrile from 78:22 (v/v) to 55:45 over 8 min, and held at this ratio for the next 4 min. An ultraviolet-visible detector was operated at 265 mn from 0 to 8 min and at 600 mn from 8 min and after. The retention time of FP-21399 was 8.8 min and a linear response was observed over the concentration range 0.01 100 microg ml(-1) (r = 0.994). Lower limit of quantitation was found to be 0.01 microg ml(-1). Intra- and inter-assay precision varied in the range of 0.2 to 8% and 1-12%, respectively. The bias ranged from -17-3% for all analyses. A series of clinical plasma specimens were successfully analyzed using this method. The strategies for the method optimization on HIPLC separation and extraction procedure are discussed as well.

Reservoirs for HIV-1: mechanisms for viral persistence in the presence of antiviral immune responses and antiretroviral therapy

The success of combination antiretroviral therapy for HIV-1 infection has generated interest in mechanisms by which the virus can persist in the body despite the presence of drugs that effectively inhibit key steps in the virus life cycle. It is becoming clear that viral reservoirs established early in the infection not only prevent sterilizing immunity but also represent a major obstacle to curing the infection with the potent antiretroviral drugs currently in use. Mechanisms of viral persistence are best considered in the context of the dynamics of viral replication in vivo. Virus production in infected individuals is largely the result of a dynamic process involving continuous rounds of de novo infection of and replication in activated CD4(+) T cells with rapid turnover of both free virus and virus-producing cells. This process is largely, but not completely, interrupted by effective antiretroviral therapy. After a few months of therapy, plasma virus levels become undetectable in many patients. Analysis of viral decay rates initially suggested that eradication of the infection might be possible. However, there are several potential cellular and anatomical reservoirs for HIV-1 that may contribute to long-term persistence of HIV-1. These include infected cell in the central nervous system and the male urogenital tract. However, the most worrisome reservoir consists of latently infected resting memory CD4(+) T cells carrying integrated HIV-1 DNA. Definitive demonstration of the presence of this form of latency required development of methods for isolating extremely pure populations of resting CD4(+) T cells and for demonstrating that a small fraction of these cells contain integrated HIV-1 DNA that is competent for replication if the cells undergo antigen-driven activation. Most of the latent virus in resting CD4(+) T cells is found in cells of the memory phenotype. The half-life of this latent reservoir is extremely long (44 months). At this rate, eradication of this reservoir would require over 60 years of treatment. Thus, latently infected resting CD4(+) T cells provide a mechanism for life-long persistence of replication-competent forms of HIV-1, rendering unrealistic hopes of virus eradication with current antiretroviral regimens. The extraordinary stability of the reservoir may reflect gradual reseeding by a very low level of ongoing viral replication and/or mechanisms that contribute to the intrinsic stability of the memory T cell compartment. Given the substantial long-term toxicities of current combination therapy regimens, novel approaches to eradicating this latent reservoir are urgently needed.

The role of telomerase expression and telomere length maintenance in human and mouse

The molecular regulation of telomere length has been well elucidated by a series of elegant studies over the past decade. More recently, experimental evidence has accrued that addresses the challenging question of if and how telomere length regulation may contribute to normal human aging or to human disease. Recent studies in mice have provided a mammalian precedent indicating that telomerase deficiency can lead to in vivo dysfunction, most probably as a consequence of progressive telomere shortening. In humans, the evidence that telomere shortening might lead to in vivo dysfunction is far less direct, although the recent description of telomerase deficiency and telomere shortening associated with the DKC syndrome is suggestive of such a link. Methodologies exist and continue to be developed that are increasingly capable of manipulating telomerase activity and telomere length in human cells. It remains to be determined whether scientifically rigorous and (equally important) medically ethical approaches will emerge to directly assess the ability of telomere length modulation to correct functional disorders of human cellular function ex vivo or more challenging still, in vivo.

Early HIV infection in vivo: branching-process model for studying timing of immune responses and drug therapy

We propose a stochastic, branching-process model of early events in vivo in human or simian immunodeficiency virus (HIV or SIV) infection and study the influence that the time of appearance of virus-specific antibodies or cytotoxic cells, or of administration of antiretroviral drugs, has on the probability of progression to a chronic infection. In some biological scenarios, our model predicts that a few days' delay in response or intervention would make little difference, while in others it would be highly deleterious. We show that prophylactic efficacy does not require perfect efficiency at neutralizing infectious virus. Data from a trial of PMPA, a potent antiretroviral drug, as post-exposure therapy for SIV infection in macaques, reported by C.-C. Tsai, P. Emau, K.E. Follis, T.W. Beck, R. E. Beneveniste, N. Bischofberger, J.D. Lifson, W.R. Morton (J. Virol. 72 (1998) 4265), provides a test of the model. We show that their observations are consistent with a branching-process without invoking supplementary viral- or host-variability. Finally, most animal trials of antiviral drugs or vaccines use very high viral inoculums; our model demonstrates that in such experiments we risk greatly underestimating the efficacy of these agents.

Glycyrrhizin improves the resistance of MAIDS mice to opportunistic infection of Candida albicans through the modulation of MAIDS-associated type 2 T cell responses

Compared with normal mice, MAIDS mice (mice infected with LP-BM5 murine leukemia virus) exhibited an increase up to 100 times greater in susceptibility to infection with Candida albicans. The impaired resistance of MAIDS mice to the infection was recovered to levels observed in normal mice by the administration of glycyrrhizin (GR), an active component of licorice roots. MAIDS mice inoculated with CD4(+) T cells from GR-treated mice were also resistant to C. albicans infection. Normal mice inoculated with CD4(+) T helper type 2 cells (Th2 cells) from MAIDS mice were susceptible to C. albicans infection at the same levels shown in MAIDS mice. The susceptibility of normal mice inoculated with type 2 T cells was reversible by (i) administration of GR and (ii) inoculation of CD4(+) T cells from GR-treated mice and injection of a mixture of mAbs targeted against type 2 cytokines (IL-4 and IL-10). Type 2 cytokines were not detected in sera of MAIDS mice inoculated with CD4(+) T cells from GR-treated mice, while they were present in sera of MAIDS mice treated with saline. These results suggest that, by inducing CD4(+) T cells which suppress type 2 cytokine production by MAIDS-associated Th2 cells, GR improves the resistance of MAIDS mice to C. albicans infection.

Cellular Factors for Resistance against Antiretroviral Agents

Substantial advancements have been made in our understanding of the complex replication cycle of, and immunopathology associated with HIV infection as well as the drugs used to treat the disease. The nucleoside reverse transcriptase inhibitors remain the cornerstones of current antiviral treatment modalities. Unfortunately, their long-term use often leads to adverse reactions and the emergence of virus mutants with decreased susceptibility to therapeutic agents. In addition to viral resistance, prolonged antiviral treatment may affect metabolic changes in the host cells that can diminish the efficacy of the treatment. Thus, both viral and cellular resistance mechanisms must be considered in the context of failing antiviral chemotherapy. This review article concerns the intracellular pharmacology of antiviral nucleoside analogues in human lymphoid cells and the possible impact of a newly identified nucleotide transporter on drug resistance.

A model of HIV-1 pathogenesis that includes an intracellular delay

Mathematical modeling combined with experimental measurements have yielded important insights into HIV-1 pathogenesis. For example, data from experiments in which HIV-infected patients are given potent antiretroviral drugs that perturb the infection process have been used to estimate kinetic parameters underlying HIV infection. Many of the models used to analyze data have assumed drug treatments to be completely efficacious and that upon infection a cell instantly begins producing virus. We consider a model that allows for less then perfect drug effects and which includes a delay in the initiation of virus production. We present detailed analysis of this delay differential equation model and compare the results to a model without delay. Our analysis shows that when drug efficacy is less than 100%, as may be the case in vivo, the predicted rate of decline in plasma virus concentration depends on three factors: the death rate of virus producing cells, the efficacy of therapy, and the length of the delay. Thus, previous estimates of infected cell loss rates can be improved upon by considering more realistic models of viral infection.

Therapeutic vaccines in HIV.1 infection

In this review we address questions which must be considered if better attempts are to be made to treat all persons presently infected with human immunodeficiency virus (HIV). There are thirty million people in the world presently living with HIV, only 10% of whom are likely to be able to access currently available drug therapy. Even when available, such therapy causes considerable inconvenience and undesirable clinical side effects, and fails to eradicate virus from a small reservoir of latently infected cells. Thus, we must ask what forms of alternative therapy might be used. One strategy that may be considered is to reduce virus levels as low as possible using highly active antiretroviral therapy (HAART), followed by modulation of host immunity with immunotherapy in order to effect an appropriate and efficient response mimicking that found in long-term asymptomatic patients, with the aim of indefinitely maintaining the asymptomatic period following discontinuation of chemotherapy, or even of eradicating the virus from the latent reservoirs. In 1987, long before the advent of highly active antiretroviral therapy, J. Salk proposed the use of a 'suitable potent non-infectious (HIV) immunogen' to delay or prevent the development of AIDS in infected individuals (1). The objective of administering such an agent was to 'enhance and prolong the presence of (immunologically) protective factors'. The stated aim at that time was 'to destroy virus and viral antigen producing cells by the induction of the immune system's cytotoxic mechanisms known to rid the host of virus and virus producing cells'. Twelve years later, and after a quarter of a century living with HIV, and with the advent of HAART, is it time to use our knowledge of the host's own immune system to fight this seemingly intractable invader?