Dissociation of HIV-1 from follicular dendritic cells during HAART: mathematical analysis

Acute hepatitis B virus infection in humanized chimeric mice has multiphasic viral kinetics

Chimeric urokinase type plasminogen activator (uPA)/severely severe combined immunodeficiency (SCID) mice reconstituted with humanized livers are useful for studying hepatitis B virus (HBV) infection in the absence of an adaptive immune response. However, the detailed characterization of HBV infection kinetics necessary to enable in-depth mechanistic studies in this in vivo HBV infection model is lacking. To characterize HBV kinetics post-inoculation (p.i.) to steady state, 42 mice were inoculated with HBV. Serum HBV DNA was frequently measured from 1 minute to 63 days p.i. Total intrahepatic HBV DNA, HBV covalently closed circular DNA (cccDNA), and HBV RNA was measured in a subset of mice at 2, 4, 6, 10, and 13 weeks p.i. HBV half-life (t_1/2 ) was estimated using a linear mixed-effects model. During the first 6 hours p.i., serum HBV declined in repopulated uPA/SCID mice with a t_1/2 = 62 minutes (95% confidence interval [CI] = 59-67). Thereafter, viral decline slowed followed by a 2-day lower plateau. Subsequent viral amplification was multiphasic with an initial mean doubling time of t₂ = 8 ± 3 hours followed by an interim plateau before prolonged amplification (t₂ = 2 ± 0.5 days) to a final HBV steady state of 9.3 ± 0.3 log copies (cps)/mL. Serum HBV and intrahepatic HBV DNA were positively correlated (R² = 0.98).

CONCLUSION

HBV infection in uPA/SCID chimeric mice is highly dynamic despite the absence of an adaptive immune response. Serum HBV t_1/2 in humanized uPA/SCID mice was estimated to be ∼1 hour regardless of inoculum size. The HBV acute infection kinetics presented here is an important step in characterizing this experimental model system so that it can be effectively used to elucidate the dynamics of the HBV life cycle and thus possibly reveal effective antiviral drug targets. (Hepatology 2018).

How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response

Many HIV-1-infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest-affinity receptors tend to acquire the most antigen from the follicular dendritic cell (FDC) network and present the highest density of cognate peptides to follicular helper T (Tfh) cells, which provide survival signals to the B cell. bnAbs are therefore expected to evolve only when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than other lineages of more specific B cells. Here we develop mathematical models of Tfh cells in germinal centers to explicitly define the mechanisms of selection in this complex evolutionary process. Our results suggest that broadly reactive B cells presenting a high density of peptides bound to major histocompatibility complex class II molecules (pMHC) are readily outcompeted by B cells responding to lineages of HIV-1 that transiently dominate the within host viral population. Conversely, if broadly reactive B cells acquire a large variety of several HIV-1 proteins from the FDC network and present a high diversity of several pMHC, they can be rescued by a large fraction of the Tfh cell repertoire in the germinal center. Under such circumstances the evolution of bnAbs is much more consistent. Increasing either the magnitude of the Tfh cell response or the breadth of the Tfh cell repertoire markedly facilitates the evolution of bnAbs. Because both the magnitude and breadth can be increased by vaccination with several HIV-1 proteins, this calls for experimental testing.IMPORTANCE Many HIV-infected patients slowly evolve antibodies that can neutralize a large variety of viruses. Such broadly neutralizing antibodies (bnAbs) could in the future become therapeutic agents. bnAbs appear very late, and patients are typically not protected by them. At the moment, we fail to understand why this takes so long and how the immune system selects for broadly neutralizing capacity. Typically, antibodies are selected based on affinity and not on breadth. We developed mathematical models to study two different mechanisms by which the immune system can select for broadly neutralizing capacity. One of these is based upon the repertoire of different follicular helper T (Tfh) cells in germinal centers. We suggest that broadly reactive B cells may interact with a larger fraction of this repertoire and demonstrate that this would select for bnAbs. Intriguingly, this suggests that broadening the Tfh cell repertoire by vaccination may speed up the evolution of bnAbs.

The comparisons of hepatitis C virus RNA level between intraoperative blood salvage (cell saver) and systemic hepatitis C virus RNA kinetics during liver transplantation

BACKGROUND

Cell Saver (CS; Haemonemic Corp, Braintree, Mass, United States) is frequently used to decrease transfusion requirements of homologous blood during liver transplantation (OLT). However, the use of CS in hepatitis C virus (HCV)-infected recipients is still debated owing to the potential elevation of HCV RNA level. In this study, we compared HCV RNA levels of CS blood with a series of blood samples obtained from HCV-infected OLT recipients.

METHODS

Twelve HCV-infected patients with >50,000 copies/mL of HCV RNA were enrolled. HCV RNA was measured immediately after induction (I), at the end of anhepatic period (II), at the end of operation (III), and from the first returned blood in CS (CSb). HCV RNA level at each time period was compared.

RESULTS

HCV RNA levels ranged from 77,931 to 9,072,000 copies/mL at I. When compared to I, HCV RNA levels were reduced to 11.1% ± 13.0% and 0.7% ± 1.0% at II and III, respectively. Also, the RNA level reduced to 3.0% ± 2.0% of I after CS processing. The HCV RNA level at I was significantly higher than the levels at II, III, and CSb (P = .012, each), and the level at II was significantly higher than the level at III (P = .012). The HCV RNA level at CSb showed no statistical difference with the levels at II, but it was significantly higher than the level at III (P = .042).

CONCLUSIONS

The use of CS in HCV-infected OLT recipients seems to carry no additional risk with respect to intraoperative HCV RNA kinetics.

Receptor concentration and diffusivity control multivalent binding of Sv40 to membrane bilayers

Incoming Simian Virus 40 particles bind to their cellular receptor, the glycolipid GM1, in the plasma membrane and thereby induce membrane deformation beneath the virion leading to endocytosis and infection. Efficient membrane deformation depends on receptor lipid structure and the organization of binding sites on the internalizing particle. To determine the role of receptor diffusion, concentration and the number of receptors required for stable binding in this interaction, we analyze the binding of SV40 to GM1 in supported membrane bilayers by computational modeling based on experimental data. We measure the diffusion rates of SV40 virions in solution by fluorescence correlation spectroscopy and of the receptor in bilayers by single molecule tracking. Quartz-crystal microbalance with dissipation (QCM-D) is used to measure binding of SV40 virus-like particles to bilayers containing the viral receptor GM1. We develop a phenomenological stochastic dynamics model calibrated against this data, and use it to investigate the early events of virus attachment to lipid membranes. Our results indicate that SV40 requires at least 4 attached receptors to achieve stable binding. We moreover find that receptor diffusion is essential for the establishment of stable binding over the physiological range of receptor concentrations and that receptor concentration controls the mode of viral motion on the target membrane. Our results provide quantitative insight into the initial events of virus-host interaction at the nanoscopic level.

Modeling the within-host dynamics of HIV infection

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.

Contribution of follicular dendritic cells to persistent HIV viremia

HIV-1 infections cannot be completely eradicated by drug therapy, as the virus persists in reservoirs. Low-level plasma viremia has been detected in patients treated for over 7 years, but the cellular compartments that support this low-level viremia have not been identified. The decay of HIV-1 during treatment appears to occur in four phases, with the 3rd and 4th phases occurring when the virus is below the limit of detection of conventional assays. Here, we focus on the 3rd phase of decay, which has been estimated to have a half-life of 39 months. We show that follicular dendritic cells (FDC), which have been identified as an HIV reservoir, can be the main source of the low-level viremia detected during the 3rd phase of decay and contribute to viremia at even longer times. Our calculations show that the kinetics of leakage of virus from FDC is consistent with three types of available clinical data.

GLOBAL DYNAMICS OF AN IN-HOST HIV-1 INFECTION MODEL WITH THE LONG-LIVED INFECTED CELLS AND FOUR INTRACELLULAR DELAYS

In this paper, we investigate global dynamics for an in-host HIV-1 infection model with the long-lived infected cells and four intracellular delays. Our model admits two possible equilibria, an uninfected equilibrium and infected equilibrium depending on the basic reproduction number. We derive that the global dynamics are completely determined by the values of the basic reproduction number: if the basic reproduction number is less than one, the uninfected equilibrium is globally asymptotically stable, and the virus is cleared; if the basic reproduction number is larger than one, then the infection persists, and the infected equilibrium is globally asymptotically stable.

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.

A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells

The term serial engagement was introduced to describe the ability of a single peptide, bound to a MHC molecule, to sequentially interact with TCRs within the contact region between a T cell and an APC. In addition to ligands on surfaces, soluble multivalent ligands can serially engage cell surface receptors with sites on the ligand, binding and dissociating from receptors many times before all ligand sites become free and the ligand leaves the surface. To evaluate the role of serial engagement in Syk activation, we use a detailed mathematical model of the initial signaling cascade that is triggered when FcepsilonRI is aggregated on mast cells by multivalent Ags. Although serial engagement is not required for mast cell signaling, it can influence the recruitment of Syk to the receptor and subsequent Syk phosphorylation. Simulating the response of mast cells to ligands that serially engage receptors at different rates shows that increasing the rate of serial engagement by increasing the rate of dissociation of the ligand-receptor bond decreases Syk phosphorylation. Increasing serial engagement by increasing the rate at which receptors are cross-linked (for example by increasing the forward rate constant for cross-linking or increasing the valence of the ligand) increases Syk phosphorylation. When serial engagement enhances Syk phosphorylation, it does so by partially reversing the effects of kinetic proofreading. Serial engagement rapidly returns receptors that have dissociated from aggregates to new aggregates before the receptors have fully returned to their basal state.

Current estimates for HIV-1 production imply rapid viral clearance in lymphoid tissues

It has recently been estimated that a single HIV-1 infected cell produces between and more than viral particles over its life span. Since body-wide estimates of the ratio of free virus to productively infected cells are smaller than and much smaller than , individual virions must be cleared rapidly. This seems difficult to reconcile with the fact that most of the total body virus is trapped on follicular dendritic cells where it can survive for many months. It has also been difficult to reconcile the vast difference in the rates at which the virus is cleared from the blood in rhesus macaques and in chronically infected patients. Here we attempt to reconcile these seemingly contradictory observations by considering the virion clearance rate in various organs and the virion exchange rates between them. The main results are that the per capita clearance rate of free virus in lymphoid tissue should be fast, the virion exchange rate between lymphoid tissue and the blood should be slow, and the comparatively slow previous estimates for the virion clearance rate from the blood correspond to the rate of virion efflux from the blood to other organs where the virus is ultimately cleared.

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.

Back-burning to cure HIV: temporary depletion of all CD4+ cells and elimination of the extracellular reservoir with HIV immunotoxin therapy

Temporary elimination of all host cells for the human immunodeficiency virus (HIV) combined with dislodging HIV from its extracellular reservoir could cure acquired immunodeficiency syndrome (AIDS). This combination would be effective because the virus is dependent on host cell integration or on the membrane protection of B cells or of follicular dendritic cells (FDCs) for its survival and because the CD4(+) host cells are leukocytes that are naturally renewable through hematopoiesis. By treating HIV patients with a combination of humanized antibodies it should be possible to achieve both goals. To deplete HIV host cells, a humanized antibody against CD4 should be fused to an apoptosis-inducing toxin; and to void the extracellular reservoir, a fragment of a humanized antibody against CD21 should be used. Because only CD4(+) cells would be destroyed, hematopoietic stem cells would be spared, and would spontaneously replace the depleted cells. We call this hypothetical new HIV treatment "HIV Immunotoxin Therapy (HIT)". Once the HIV viral load reaches zero, the HIT would be withdrawn and IL-2 or luteinizing hormone releasing hormone analogues (LHRH-A) might be administered to accelerate the natural replacement of the CD4(+) T(H) cells and macrophages. Killing all HIV host cells may seem counterintuitive at first, because it requires the purposeful destruction of the very cells that we ultimately hope to preserve for AIDS patients, but just as controlled back-burning purposefully creates a trap to stop a wildfire from burning out of control, this method could provide a mechanism to extinguish HIV.

A simple macroscopic model for the diffusion and adsorption kinetics of r-adenovirus

The diffusion of viruses toward cells is a limiting step of the infection process. To be modeled correctly, this step must be evaluated in combination with the adsorption of the virus to the cell surface, which is a rapid but reversible step. In this paper, the recombinant adenovirus (rAd) diffusion and its adsorption to 293S cells in suspension were both measured and modeled. First, equilibrium experiments permitted to determine the number of receptors on the surface of 293S (R(T) = 3,500 cell(-1)) and the association constant (K(A) = 1.9 x 10(11) M(-1)) for rAd on these cells based on a simple monovalent adsorption model. Non-specific binding of the virus to the cell surface was not found to be significant. Second, total virus particle degradation rates between 5.2 x 10(-3) and 4.0 x 10(-2) min(-1) were measured at 37 degrees C in culture medium, but no significant virus degradation was observed at 4 degrees C. Third, free viral particle disappearance rates from a mixed suspension of virus and cells were measured at different virus concentrations. Experimental data were compared to a phenomenological dynamic model comprising both the diffusion and the adsorption steps. The diffusion to adsorption ratio, a fitted parameter, confirmed that the contact process of a virus with a cell is indeed diffusion controlled. However, the characteristic diffusion time constants obtained, based on a reversible adsorption model, were eightfolds smaller than those reported in the literature, based on diffusion models that assume irreversible adsorption.

Emergence of HIV-1 Drug Resistance During Antiretroviral Treatment

Treating HIV-infected patients with a combination of several antiretroviral drugs usually contributes to a substantial decline in viral load and an increase in CD4(+) T cells. However, continuing viral replication in the presence of drug therapy can lead to the emergence of drug-resistant virus variants, which subsequently results in incomplete viral suppression and a greater risk of disease progression. In this paper, we use a simple mathematical model to study the mechanism of the emergence of drug resistance during therapy. The model includes two viral strains: wild-type and drug-resistant. The wild-type strain can mutate and become drug-resistant during the process of reverse transcription. The reproductive ratio [Symbol: see text](0) for each strain is obtained and stability results of the steady states are given. We show that drug-resistant virus is more likely to arise when, in the presence of antiretroviral treatment, the reproductive ratios of both strains are close. The wild-type virus can be suppressed even when the reproductive ratio of this strain is greater than 1. A pharmacokinetic model including blood and cell compartments is employed to estimate the drug efficacies of both the wild-type and the drug-resistant strains. We investigate how time-varying drug efficacy (due to the drug dosing schedule and suboptimal adherence) affects the antiviral response, particularly the emergence of drug resistance. Simulation results suggest that perfect adherence to regimen protocol will well suppress the viral load of the wild-type strain while drug-resistant variants develop slowly. However, intermediate levels of adherence may result in the dominance of the drug-resistant virus several months after the initiation of therapy. When more doses of drugs are missed, the failure of suppression of the wild-type virus will be observed, accompanied by a relatively slow increase in the drug-resistant viral load.

Viral and latent reservoir persistence in HIV-1-infected patients on therapy

Despite many years of potent antiretroviral therapy, latently infected cells and low levels of plasma virus have been found to persist in HIV-infected patients. The factors influencing this persistence and their relative contributions have not been fully elucidated and remain controversial. Here, we address these issues by developing and employing a simple, but mechanistic viral dynamics model. The model has two novel features. First, it assumes that latently infected T cells can undergo bystander proliferation without transitioning into active viral production. Second, it assumes that the rate of latent cell activation decreases with time on antiretroviral therapy due to the activation and subsequent loss of latently infected cells specific for common antigens, leaving behind cells that are successively less frequently activated. Using the model, we examined the quantitative contributions of T cell bystander proliferation, latent cell activation, and ongoing viral replication to the stability of the latent reservoir and persisting low-level viremia. Not surprisingly, proliferation of latently infected cells helped maintain the latent reservoir in spite of loss of latent infected cells through activation and death, and affected viral dynamics to an extent that depended on the magnitude of latent cell activation. In the limit of zero latent cell activation, the latent cell pool and viral load became uncoupled. However, as the activation rate increased, the plasma viral load could be maintained without depleting the latent reservoir, even in the absence of viral replication. The influence of ongoing viral replication on the latent reservoir remained insignificant for drug efficacies above the "critical efficacy" irrespective of the activation rate. However, for lower drug efficacies viral replication enabled the stable maintenance of both the latent reservoir and the virus. Our model and analysis methods provide a quantitative and qualitative framework for probing how different viral and host factors contribute to the dynamics of the latent reservoir and the virus, offering new insights into the principal determinants of their persistence.

Ecological and evolutionary principles in immunology

Experimental immunology has given rise to detailed insights into how immune cells react to infectious agents and fight pathogens. At the same time, however, the interplay between infectious agents and immune responses can be viewed as an ecological system in vivo. This is characterized by complex interactions between species of immune cells and populations of pathogens. This review discusses how an understanding of the immune system can be aided by the application of ecological and evolutionary principles: competition, predation, and the evolution of viruses in vivo. These concepts can shed light onto important immunological concepts such as the correlates of efficient virus control, immunodominance, the relationship between viral evolution and the development of pathology, as well as the ability of the immune system to control immunosuppressive infections.

Kinetics of hepatitis C virus reinfection after liver transplantation

Improved understanding of hepatitis C virus (HCV) dynamics during and after liver transplantation can be useful in optimizing antiviral therapy in transplant recipients. We analyzed serum HCV ribonucleic acid (RNA) levels during and after cadaveric liver transplantation in 6 HCV patients. After removal of the liver and before the new liver started producing virions, HCV RNA levels dropped with an average half-life (t(1/2)) of 0.8 hours. Viral loads then continued to drop up to 23 hours postimplantation (t(1/2) = 3.4 hours), and began to rise (doubling-time = 2.0 days) as soon as 15 hours after the anhepatic phase. In 3 patients the viral load reached a plateau before rising, suggesting that a nonhepatic source supplied virions and balanced their intrinsic clearance. However, from the decline in viral load over the first 24 hours of the postanhepatic phase, we estimate that nonhepatic sources can at most correspond to 4% of total viral production, 96% of which occurs in the liver, even after we corrected for fluid exchanges during surgery. As the new liver was reinfected, production increased and viral load rose to a new steady state. Using nonlinear regression, we were able to fit the patients' HCV RNA data to a viral dynamic model and estimate the de novo infection rate (mean 1.5 x 10(-6) mL/virion/day), as well as the average percentage of hepatocytes infected at the posttransplantation steady state (19%). In conclusion, we have quantified liver reinfection dynamics in the absence of posttransplantation antiviral therapy. Our findings support the notion that early antiviral therapy may delay or prevent reinfection.

The majority of human immunodeficiency virus type 1 particles present within splenic germinal centres are produced locally

In most stages of human immunodeficiency virus (HIV) infection, cell-free viral particles can be detected in germinal centres (GCs) that are principally retained, in the form of immune complexes, on the surface of follicular dendritic cells (FDCs). The source of this virus remains unknown, although it is agreed that the FDCs themselves are not infected productively. By sequencing HIV viral DNA, genomic RNA and spliced mRNA isolated from individual splenic white pulps, it was shown here that the majority of HIV-1 viral particles are produced locally within the supporting lymphoid structure and do not result from trapping of circulating viruses or immune complexes. These findings underline the exquisite spatial organization of HIV-1 replication in vivo, suggesting a local origin for viruses trapped in splenic GCs.

HIV-1 dynamics at different time scales under antiretroviral therapy

We exploit a model that considers three compartments: blood plasma (BP), lymphoid tissue-interstitial spaces (LT-IS), and follicular dendritic cells (FDC), for the HIV-1 dynamics under the application of highly active antiretroviral therapy (HAART) which allowed us to unravel distinct viral dynamics occurring in short- (2 days), middle- (21 days), and long-term (183 days) time scales. The different time scales are determined by the viral clearance rate, the ratio of productively infected CD4(+) T cells to chronically infected cells, and the dissociation rate of HIV-1 complexes from FDC. This generates a scenario in which, after an initial transient stage, the viral BP dynamics decouples and becomes governed by the lymphoid tissue (LT) dynamics; in a later stage, a new decoupling occurs in which the LT-IS dynamics is slaved to that of the FDC dynamics. We observed an initial increase in the viremia after HAART in a patient who did not receive protease inhibitors (PI). By means of the above-mentioned model we were able to highlight the relevant parameters which need to be estimated at three different time scales after HAART.

Folate targeting of drug carriers: A mathematical model

The binding of folate-targeted drug carriers to a receptor-bearing cell surface is modeled using a deterministic approach. The model accounts for the presence of multiple folate ligands on the carrier surface, the anchoring and presentation of the ligands on flexible polymeric tethers, and the combination of both clustered and homogeneous spatial distributions of receptors on the cell surface. The model was validated against an experimental system where folate-bearing liposomes were used as delivery vehicles to deliver drug to tumor cells in vitro. Unknown parameters of the model were then estimated by a least-squares fit to the experimental data. A parametric study systematically varying the estimated parameters around the best-fit values indicated that the model was sensitive to these parameters, lending credence to their estimated values. This study indicates that drug uptake is dependent on several factors including the ligand number, the exposure time, and carrier concentration. For the specific case of folate targeting, the cumulative uptake of folate ligands is important, causing a decrease in the carrier uptake rate once a threshold cumulative uptake is crossed.

Brownian adhesive dynamics (BRAD) for simulating the receptor-mediated binding of viruses

Current viral docking models have relied upon the assumption that bond formation and breakage are independent of viral and docking surface geometry, as well as the forces exerted on the bonds. This assumption, known as the equivalent site hypothesis (ESH), is examined in detail using a newly developed simulation technique-Brownian adhesive dynamics (BRAD). The simulation couples the thermal motion of viral particles with adhesive dynamics models to characterize the effect of bonding on viral motion. We use the binding of HIV-like particles to CD4 expressing cells as a model system to illustrate the utility of BRAD. Comparison of the transition rates between bound states predicted by ESH and the rates resulting from BRAD simulations show dramatic differences; at values of the equilibrium crosslinking constant, K(x)R(T), where ESH suggests all virus adhesion proteins will be bound (K(x)R(T) = 10(6)), BRAD predicts not all virus adhesion proteins will be bound. At values of the equilibrium crosslinking constant used in typical ESH calculations of virus docking (K(x)R(T) = 1) we find BRAD simulations predict no binding. The mean bond density from BRAD models is often much lower than that predicted by ESH for equivalent parameter values. BRAD suggests that the viruses are much less well bound than ESH predicts. The differences suggest that binding models for viruses need to be reexamined closely. BRAD is a simulation technique that will be useful for quantifying the receptor-mediated binding of a wide variety of viruses to cells.

The effect of cellular receptor diffusion on receptor-mediated viral binding using Brownian adhesive dynamics (BRAD) simulations

Brownian adhesive dynamics (BRAD) is a new method for simulating the attachment of viruses to cell surfaces. In BRAD, the motion of the virus is subject to stochastic bond formation and breakage, and thermal motion owing to collisions from the solvent. In the model, the virus is approximated as a rigid sphere and the cell surface is approximated as a rigid plane coated with receptors. In this article, we extend BRAD to allow for the mobility of receptors in the plane of the membrane, both before and after they are ligated by viral attachment proteins. Allowing the proteins to move within the membrane produced several differences in behavior from when the receptors are immobilized. First, the mean steady-state bond number is unaffected by changes in cellular receptor density because proteins are now free to diffuse into the contact area, and the extent of binding is dictated by the availability of viral attachment proteins. Second, the time required to reach steady-state binding increases as both the cellular receptor number decreases and the receptor mobility decreases. This is because receptor diffusion is a slower process than the binding kinetics of the proteins. Decreasing the rate of protein binding was found to decrease the fraction of viruses bound to steady state, but not the extent of binding for those viruses that were bound. Increasing the binding rate increased the fraction of viruses bound, until no further viruses could bind. Alterations in receptor binding kinetics had no discernable effect on the mean steady-state bond number between virus and cell, because interactions were of sufficiently high affinity that all available receptor-viral attachment proteins were destined to bind at steady state.

Peripheral blood Dendritic cells are not a major reservoir for HIV type 1 in infected individuals on virally suppressive HAART

Dendritic cells (DCs) are potent antigen-presenting cells, and their physiological localization in tissues that interact with the external environment is important as a first barrier against pathogens such as human immunodeficiency virus type I (HIV-1). Several models have been proposed to explain the possible role of DCs as a reservoir for HIV-1 in patients on virally suppressive highly active antiretroviral therapy (HAART). However, the low yield of cell isolates has made this evaluation a difficult task. The present study analyzes whether peripheral blood DCs from HIV-1-infected individuals on virally suppressive HAART, with plasma HIV-1 RNA levels of less than 50 copies/ml, carry either HIV-1 provirus and/or HIV-1 virions. Peripheral blood DCs were isolated from a cohort of 10 HIV-1-seropositive men taking suppressive HAART. In five patients, plasmacytoid and myeloid dendritic cells were isolated to attempt to identify their respective roles in HIV-1 residual disease. Viral out-growth assays were performed in vitro, as well as gag and R/U5 polymerase chain reaction (PCR) amplification of viral RNA and DNA, respectively, from DC and peripheral blood mononuclear cell (PBMC) extracts. Fluorescence activated cell-sorting (FACS) data revealed cellular yields from 85.90 to 95.18%, of relatively pure DCs isolated from patients' PBMCs. Although HIV-1 RNA gag and DNA RU/5 were detected in all PBMC samples isolated from the patients, proviral DNA and viral RNA forms were not detected in any of the DC isolates. In addition, no replication-competent virus was demonstrated in DC coculture assays, while virus was isolated from each patients' CD8+ T-lymphocyte-depleted PBMC cocultures. Furthermore, HIV-1 gag proviral DNA was not detected in either plasmacytoid or myeloid DC subfractions. The current study suggests that in HIV-1-infected individuals treated with suppressive HAART, peripheral blood DCs do not carry HIV-1 proviral DNA or viral particles attached to their surface. These populations of peripheral blood DCs are likely not a major HIV-1 reservoir in patients on HAART with clinically undetectable plasma viral RNA.

Detection of peripheral HIV-1-specific memory B cells in patients untreated or receiving highly active antiretroviral therapy

OBJECTIVES

To examine whether polyclonal activation of circulating B cells, in a process that involves CD40-CD40 ligand and cytokine interactions, could induced HIV-1-specific memory B cells to synthesize HIV-1-specific antibodies.

METHODS

B cells from 26 HIV-1-infected patients were cultured with a CD40L-transfected cell line plus interleukins 2 and 10 and tested for their secretion of HIV-1- and Toxoplasma gondii-specific antibodies.

RESULTS

In vitro activated B lymphocytes from HIV-1-infected patients secreted anti-HIV-1-specific antibodies. B cells from HIV-1-infected patients as well as those from controls chronically infected by T. gondii synthesized T. gondii-specific antibodies. HIV-1-specific IgG-, IgA- or IgM-secreting B cells represented approximately 1 x 10(-4) to 1 x 10(-5) of total circulating B cells and 1 x 10(-2) to 1 x 10(-3) of immunoglobulin-secreting cells. HIV-1-specific memory B cells were found in 9/9 untreated patients and in 8/17 patients receiving highly active antiretroviral therapy (HAART). The other nine patients showed a normal CD40-CD40L B cell response and six of them produced T. gondii-specific antibody B cells. The follow-up of seven patients indicated that HIV-1-specific memory B cells became undetectable after 8 to 46 months of HAART, whereas T. gondii-specific memory B cells persisted in parasite coinfected patients.

CONCLUSIONS

Circulating memory HIV-1-specific B cells were detected in untreated patients and in about half of the patients taking HAART, suggesting that persistent low-level ongoing viral replication is not sufficient to maintain HIV-1-specific memory B cells.

The contribution of monocyte infection and trafficking to viral persistence, and maintenance of the viral reservoir in HIV infection

Cellular viral reservoirs and anatomic sanctuary sites allow continuing HIV-1 replication in patients with suppressed plasma viremia who are receiving highly active antiretroviral therapy and prevent eradication of HIV-1 by these regimens. Cells of macrophage lineage, including monocytes subsets within the blood, play a role in HIV-1 persistence. Evidence of sequence evolution in blood monocytes, in comparison to resting CD4+ T cells, demonstrates their distinct contribution to plasma viremia. There is evidence to suggest that a specific monocyte subset, of CD14loCD16hi phenotype, is more susceptible to HIV-1 infection than the majority of blood monocytes. Trafficking of monocytes through various tissues following their emigration from the bloodstream allows these cells to differentiate into tissue macrophages, or potentially to egress from the tissues as migratory dendritic cells. This review provides an evaluation of the contribution of monocytes to HIV-1 persistence and the HIV-1 reservoir, essential for the effective design of therapeutic eradication strategies.

Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: intrinsic stability predicts lifelong persistence

Viral replication and latently infected cellular reservoirs persist in HIV-infected patients achieving undetectable plasma virus levels with potent antiretroviral therapy. We exploited a predictable drug resistance mutation in the HIV reverse transcriptase to label and track cells infected during defined intervals of treatment and to identify cells replenished by ongoing replication. Decay rates of subsets of latently HIV-infected cells paradoxically decreased with time since establishment, reflecting heterogeneous lymphocyte activation and clearance. Residual low-level replication can replenish cellular reservoirs; however, it does not account for prolonged clearance rates in patients without detectable viremia. In patients receiving potent antiretroviral therapy, the latent pool has a heterogeneous and dynamic composition that comprises a progressively increasing proportion of stable lymphocytes. Eradication will not be achieved with complete inhibition of viral replication alone.

In a subset of subjects on highly active antiretroviral therapy, human immunodeficiency virus type 1 RNA in plasma decays from 50 to <5 copies per milliliter, with a half-life of 6 months

Three of five virally suppressed human immunodeficiency virus type I (HIV-1)-infected patients treated with highly active antiretroviral therapy and followed intensively with a supersensitive reverse transcriptase PCR assay with a lower limit of quantitation of 5 copies/ml showed statistically significant viral load decays below 50 copies/ml, with half-lives of 5 to 8 months and a mean of 6 months. This range of half-lives is consistent with the estimated half-life of the latent HIV-1 reservoir in the peripheral blood. Those patients without decay of viral load in plasma may have significant cryptic HIV-1 residual replication.

Development of a pharmacodynamic model for HIV treatment with nucleoside reverse transcriptase and protease inhibitors

There is a need for models useful for predicting the efficacy of agents developed for treating human immunodeficiency virus (HIV) based on information obtained during the drug development process. A pharmacodynamic model that superimposes the pharmacokinetics of anti-HIV nucleoside reverse transcription (RT) and protease inhibitors over a previously published predator-prey model of HIV and CD4 dynamics was developed to address this need. This model was applied to in vitro measurements and patient-derived pharmacokinetics of the unbound antiviral drugs to simulate HIV-1 and CD4 counts versus time and dose. The primary mechanism for nucleoside RT inhibitors was assumed to be competitive inhibition of HIV-1-RT by the active nucleoside triphosphates (NTP). Cellular accumulation and breakdown rates of the NTP were estimated from previous in vivo pharmacokinetic studies. Median inhibition concentrations for the HIV-1 RT enzyme were estimated from previously published cell-free binding studies. The concentration of active protease inhibitor available for binding with HIV-1 protease was assumed equal to the unbound fraction in the plasma. The resulting simulations for mono- and dual nucleoside therapy with zidovudine and lamivudine single dose regimen with the protease inhibitor indinavir, produced similar HIV and CD4 response profiles to those reported in large Phase II and III clinical trials. Based on these findings this pharmacodynamic model can be applied to predict starting doses for a new agent based on simulated biological responses as a function of time for dosage regimens comprising one or two agents. However, the model overestimated the efficacy of highly effective drug combinations where all three agents are combined as in highly active anti-retroviral therapy.

Dynamics of spontaneous HIV-1 specific and non-specific B-cell responses in patients receiving antiretroviral therapy

OBJECTIVES

As spontaneous anti-HIV-1 antibody and IgG secretion by peripheral blood mononuclear cells (PBMC) reflect immune system activation by HIV-1 antigens, we evaluated the impact of antiretroviral therapies on HIV-1 specific and non-specific B cell responses.

METHODS

Anti-HIV-1 antibody and non-specific IgG were measured by ELISA in supernatants of PBMC cultured during 7 day from 30 patients initiating an antiretroviral therapy at baseline, 8, 16, 24, 36 and 48 weeks.

RESULTS

An early and sustained fall in plasma viral load to below the detection limit (20 copies/ml) was observed in 17 sustained responder patients (SR), whereas HIV-1 RNA remained detectable in 13 others incomplete responders. In both groups, HIV-1 specific antibody secretion decreased significantly in parallel with plasma viral load and polyclonal immunoglobulin production became similar to that of PBMC controls. However, HIV-1 specific antibody production became negative in only six SR, exhibiting a greater increase of CD4 T-cell counts and higher levels of the spontaneous HIV-1 specific IgA secretion at baseline than the other SR.

CONCLUSIONS

Antiretroviral therapy induced a rapid and dramatic decrease of spontaneous HIV-1 specific and non-specific B cell responses. These results pointed out that HIV-1 specific antibody secretion persisted in 11 out of 17 SR patients, suggesting persistent immune system activation by residual HIV-1 antigens.

HIV-1 reservoirs

In most infected individuals, HIV-1 replicates high levels throughout the duration of infection, including the clinically quiescent phase of disease. The level of this active viral replication correlates directly with disease progression and survival. The advent of combination therapeutics for HIV-1 (i.e., highly active antiretroviral therapy [HAART]) has led to dramatic reductions in viral replication in vivo and morbidity and mortality, at least in the developed world.

Human immunodeficiency virus type 1 bound to B cells: relationship to virus replicating in CD4+ T cells and circulating in plasma

Human immunodeficiency virus type 1 (HIV-1) virions bind to B cells in the peripheral blood and lymph nodes through interactions between CD21 on B cells and complement-complexed virions. B-cell-bound virions have been shown to be highly infectious, suggesting a unique mode of HIV-1 dissemination by B cells circulating between peripheral blood and lymphoid tissues. In order to investigate the relationship between B-cell-bound HIV-1 and viruses found in CD4+ T cells and in plasma, we examined the genetic relationships of HIV-1 found in the blood and lymph nodes of chronically infected patients with heteroduplex mobility and tracking assays and DNA sequence analysis. In samples from 13 of 15 patients examined, HIV-1 variants in peripheral blood-derived B cells were closely related to virus in CD4+ T cells and more divergent from virus in plasma. In samples from five chronically viremic patients for whom analyses were extended to include lymph node-derived HIV-1 isolates, B-cell-associated HIV-1 and CD4+-T-cell-associated HIV-1 in the lymph nodes were equivalent in their divergence from virus in peripheral blood-derived B cells and generally more distantly related to virus in peripheral blood-derived CD4+ T cells. These results indicates virologic cross talk between B cells and CD4+ T cells within the microenvironment of lymphoid tissues and, to a lesser extent, between cells in lymph nodes and the peripheral blood. These findings also indicate that most of the virus in plasma originates from cells other than CD4(+) T cells in the peripheral blood and lymph nodes.

The challenge of viral reservoirs in HIV-1 infection

A viral reservoir is a cell type or anatomical site in association with which a replication-competent form of the virus accumulates and persists with more stable kinetic properties than the main pool of actively replicating virus. This article reviews several cell types and anatomical sites proposed as potential reservoirs for HIV-1. It is now clear that HIV-1 persists in a small reservoir of latently infected resting memory CD4(+) T cells, which shows minimal decay even in patients on highly active antiretroviral therapy (HAART). The persistence of virus in this reservoir is consistent with the biology of these cells and the long-term persistence of immunologic memory. The viral replication that continues in patients on suppressive HAART may also contribute to the stability of this reservoir. There may be other reservoirs, but the latent reservoir in resting CD4(+) T cells appears to be sufficient to guarantee lifetime persistence of HIV-1 in the majority of patients on current HAART regimens, and unless new approaches are developed, eradication will not be possible. The clinical implications of this and other HIV-1 reservoirs are discussed.

Retention of antigen on follicular dendritic cells and B lymphocytes through complement-mediated multivalent ligand-receptor interactions: theory and application to HIV treatment

In HIV-infected patients, large quantities of HIV are associated with follicular dendritic cells (FDCs) in lymphoid tissue. During antiretroviral therapy, most of this virus disappears after six months of treatment, suggesting that FDC-associated virus has little influence on the eventual outcome of long-term therapy. However, a recent theoretical study using a stochastic model for the interaction of HIV with FDCs indicated that some virus may be retained on FDCs for years, where it can potentially reignite infection if treatment is interrupted. In that study, an approximate expression was used to estimate the time an individual virion remains on FDCs during therapy. Here, we determine the conditions under which this approximation is valid, and we develop expressions for the time a virion spends in any bound state and for the effect of rebinding on retention. We find that rebinding, which is influenced by diffusion, may play a major role in retention of HIV on FDCs. We also consider the possibility that HIV is retained on B cells during therapy, which like FDCs also interact with HIV. We find that virus associated with B cells is unlikely to persist during therapy.

Modelling viral and immune system dynamics

During the past 6 years, there have been substantial advances in our understanding of human immunodeficiency virus 1 and other viruses, such as hepatitis B virus and hepatitis C virus, that cause chronic infection. The use of mathematical modelling to interpret experimental results has made a significant contribution to this field. Mathematical modelling is also improving our understanding of T-cell dynamics and the quantitative events that underlie the immune response to pathogens.

Reservoirs of human immunodeficiency virus type 1: the main obstacles to viral eradication

Highly active antiretroviral therapy (HAART) has led to profound decreases in morbidity and mortality rates in human immunodeficiency virus type 1 (HIV-1)-infected persons, at least in the developed world. Many infected persons have plasma levels of HIV-1 RNA that are less than the limits of detection of most clinical assays as a result of combination antiretroviral therapy. Nonetheless, HIV-1 has not been eradicated by HAART. This has been shown to be because of latent HIV-1 replication-competent provirus in resting CD4+ T lymphocytes, cryptic viral replication below the limits of detection of most clinical assays, and, possibly, the presence of viral sanctuary sites. An understanding of these reservoirs for HIV-1 in the setting of virally suppressive HAART will be critical for the development of new approaches to induce HIV-1 remissions and for the exploration of the possibility of viral eradication in the future.

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.

Release of virus from lymphoid tissue affects human immunodeficiency virus type 1 and hepatitis C virus kinetics in the blood

Kinetic parameters of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infections have been estimated from plasma virus levels following perturbation of the chronically infected (quasi-) steady state. We extend previous models by also considering the large pool of virus localized in the lymphoid tissue (LT) compartment. The results indicate that the fastest time scale of HIV-1 plasma load decay during therapy probably reflects the clearance rate of LT virus and not, as previously supposed, the clearance rate of virus in plasma. This resolves the discrepancy between the clearance rate estimates during therapy and those based on plasma apheresis experiments. In the extended models plasma apheresis measurements are indeed expected to reflect the plasma decay rate. We can reconcile all current HIV-1 estimates with this model when, on average, the clearance rate of virus in plasma is approximately 20 day(-1), that of LT virus is approximately 3 day(-1), and the death rate of virus-producing cells is approximately 0.5 day(-1). The fast clearance in the LT compartment increases current estimates for total daily virus production. Because HCV is produced in the liver, we let virus be produced into the blood compartment of our model. The results suggest that extending current HCV models with an LT compartment is not likely to affect current estimates for kinetic parameters and virus production. Estimates for treatment efficacy might be affected, however.

Persistence of infectious HIV on follicular dendritic cells

Follicular dendritic cells (FDCs) trap Ags and retain them in their native state for many months. Shortly after infection, HIV particles are trapped on FDCs and can be observed until the follicular network is destroyed. We sought to determine whether FDCs could maintain trapped virus in an infectious state for long periods of time. Because virus replication would replenish the HIV reservoir and thus falsely prolong recovery of infectious virus, we used a nonpermissive murine model to examine maintenance of HIV infectivity in vivo. We also examined human FDCs in vitro to determine whether they could maintain HIV infectivity. FDC-trapped virus remained infectious in vivo at all time points examined over a 9-mo period. Remarkably, as few as 100 FDCs were sufficient to transmit infection throughout the 9-mo period. Human FDCs maintained HIV infectivity for at least 25 days in vitro, whereas virus without FDCs lost infectivity after only a few days. These data indicate that HIV retained on FDCs can be long lived even in the absence of viral replication and suggest that FDCs stabilize and protect HIV, thus providing a long-term reservoir of infectious virus. These trapped stores of HIV may be replenished with replicating virus that persists even under highly active antiretroviral therapy and would likely be capable of causing infection on cessation of drug therapy.

Influence of follicular dendritic cells on decay of HIV during antiretroviral therapy

Drug treatment of HIV type 1 (HIV-1) infection leads to a rapid initial decay of plasma virus followed by a slower second phase of decay. To investigate the role of HIV-1 retained on follicular dendritic cells (FDCs) in this process, we have developed and analyzed a mathematical model for HIV-1 dynamics in lymphoid tissue (LT) that includes FDCs. Analysis of clinical data using this model indicates that decay of HIV-1 during therapy may be influenced by release of FDC-associated virus. The biphasic character of viral decay can be explained by reversible multivalent binding of HIV-1 to receptors on FDCs, indicating that the second phase of decay is not necessarily caused by long-lived or latently infected cells. Furthermore, viral clearance and death of short-lived productively infected cells may be faster than previously estimated. The model, with reasonable parameter values, is consistent with kinetic measurements of viral RNA in plasma, viral RNA on FDCs, productively infected cells in LT, and CD4(+) T cells in LT during therapy.

Detachment of human immunodeficiency virus type 1 from germinal centers by blocking complement receptor type 2

After the transition from the acute to the chronic phase of human immunodeficiency virus (HIV) infection, complement mediates long-term storage of virions in germinal centers (GC) of lymphoid tissue. The contribution of particular complement receptors (CRs) to virus trapping in GC was studied on tonsillar specimens from HIV-infected individuals. CR2 (CD21) was identified as the main binding site for HIV in GC. Monoclonal antibodies (MAb) blocking the CR2-C3d interaction were shown to detach 62 to 77% of HIV type 1 from tonsillar cells of an individual in the presymptomatic stage. Although they did so at a lower efficiency, these antibodies were able to remove HIV from tonsillar cells of patients under highly active antiretroviral therapy, suggesting that the C3d-CR2 interaction remains a primary entrapment mechanism in treated patients as well. In contrast, removal of HIV was not observed with MAb blocking CR1 or CR3. Thus, targeting CR2 may facilitate new approaches toward a reduction of residual virus in GC.