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Biomedical subjects

Alan S Perelson

Publications and source records attributed to Alan S Perelson.

At least 37 records · Page 2Linked to original sources
PubMed2005

Duration of an intermittent episode of viremia.

HIV-1 infected patients after being treated with potent combinations of antiretroviral drugs for 2-6 months typically reach a state in which virus can no longer be detected within their blood. These patients with undetectable virus occasionally have viral load measurements that are above the limit of detection of current assays. Such measurements are called blips. Here we examine the possibility that such blips represent infrequent measurements taken during a period of time in which there is a transient elevation of virus in the patient's blood, i.e., a so-called transient episode of viremia. By analyzing time series of blips from a large number of patients, we conclude that transient episodes of viremia exist and that on average they extend for a period of about 3 weeks.

Anti-HIV Agents↗
PubMed2005

Opportunistic infection as a cause of transient viremia in chronically infected HIV patients under treatment with HAART.

When highly active antiretroviral therapy is administered for long periods of time to HIV-1 infected patients, most patients achieve viral loads that are "undetectable" by standard assay (i.e., HIV -1 RNA<50 copies/ml). Yet despite exhibiting sustained viral loads below the level of detection, a number of these patients experience unexplained episodes of transient viremia or viral "blips". We propose here that transient activation of the immune system by opportunistic infection may explain these episodes of viremia. Indeed, immune activation by opportunistic infection may spur HIV replication, replenish viral reservoirs and contribute to accelerated disease progression. In order to investigate the effects of intercurrent infection on chronically infected HIV patients under treatment with highly active antiretroviral therapy (HAART), we extend a simple dynamic model of the effects of vaccination on HIV infection [Jones, L.E., Perelson, A.S., 2002. Modeling the effects of vaccination on chronically infected HIV-positive patients. JAIDS 31, 369-377] to include growing pathogens. We then propose a more realistic model for immune cell expansion in the presence of pathogen, and include this in a set of competing models that allow low baseline viral loads in the presence of drug treatment. Programmed expansion of immune cells upon exposure to antigen is a feature not previously included in HIV models, and one that is especially important to consider when simulating an immune response to opportunistic infection. Using these models we show that viral blips with realistic duration and amplitude can be generated by intercurrent infections in HAART treated patients.

AIDS-Related Opportunistic Infections↗
PubMed2005

Mathematical modeling of primary hepatitis C infection: noncytolytic clearance and early blockage of virion production.

BACKGROUND & AIMS: Although hepatitis C virus kinetics and immune determinants during primary infection have been described, the virus-host interplay is not fully understood. We used mathematical modeling to elucidate and quantify virus-host dynamics. METHODS: Ten chimpanzees were infected intrahepatically with H77-RNA (n = 3) or intravenously with infected serum. Blood samples were taken 1-3 times per week for 6 months. A new model was fitted to the observed HCV RNA and alanine aminotransferase (ALT) kinetics. RESULTS: After infection, viral levels increased in a biphasic manner with a transient decline in between. This can be explained by a partial block (mean, 91%) of virion production, possibly due to an endogenous type I interferon response. After reaching maximum levels, a long viral plateau (mean, 6.1 log cp/mL) can be explained by blind homeostasis and lack of susceptible cells. Modest elevations in ALT levels (21-93 IU/L) were concurrently observed, indicating a shorter half-life of infected versus noninfected hepatocytes (mean ratio, 2.6). Following the ALT flare, viral titers rapidly declined to a lower (mean, 4.5 log cp/mL; n = 6) or undetectable level (n = 4). This decline is compatible with increased cell death (mean minimal estimate half-life, 28.7 days) and noncytolytic clearance (mean maximal estimate half-life, 24.1 days) of infected cells. CONCLUSIONS: Our results quantify virus-host dynamics during primary HCV infection and suggest that endogenous type I interferon slows virus production in the early acute phase. Partial or effective virus control correlates with the half-life of infected cells regulated by both cytolytic and noncytolytic mechanisms.

Alanine Transaminase↗
PubMed2005

High-potency human immunodeficiency virus vaccination leads to delayed and reduced CD8+ T-cell expansion but improved virus control.

CD8(+) T lymphocytes are thought to play an important role in the control of acute and chronic human immunodeficiency virus infections. However, there is a significant delay between infection and the first observed increase in virus-specific CD8(+) T-cell numbers. Prior to this time, viral kinetics are not significantly different between controls and vaccinees. Surprisingly, higher initial virus-specific CD8(+) T-cell numbers lead to a longer delay prior to initial CD8(+) T-cell expansion, and slower CD8(+) T-cell increases. Nevertheless, higher initial CD8(+) T-cell numbers were associated with reduced peak and chronic viral loads and reduced CD4(+) T-cell depletion.

AIDS Vaccines↗
PubMed2005

Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture.

Human immunodeficiency virus (HIV) causes complex metabolic changes in infected CD4(+) T cells that lead to cell cycle arrest and cell death by necrosis. To study the viral functions responsible for deleterious effects on the host cell, we quantitated the course of HIV type 1 infection in tissue cultures by using flow cytometry for a virally encoded marker protein, heat-stable antigen (HSA). We found that HSA appeared on the surface of the target cells in two phases: passive acquisition due to association and fusion of virions with target cells, followed by active protein expression from transcription of the integrated provirus. The latter event was necessary for decreased target cell viability. We developed a general mathematical model of viral dynamics in vitro in terms of three effective time-dependent rates: those of cell proliferation, infection, and death. Using this model we show that the predominant contribution to the depletion of viable target cells results from direct cell death rather than cell cycle blockade. This allows us to derive accurate bounds on the time-dependent death rates of infected cells. We infer that the death rate of HIV-infected cells is 80 times greater than that of uninfected cells and that the elimination of the vpr protein reduces the death rate by half. Our approach provides a general method for estimating time-dependent death rates that can be applied to study the dynamics of other viruses.

Antigens, CD↗
PubMed2004

Modelling how ribavirin improves interferon response rates in hepatitis C virus infection.

Nearly 200 million individuals worldwide are currently infected with hepatitis C virus (HCV). Combination therapy with pegylated interferon and ribavirin, the latest treatment for HCV infection, elicits long-term responses in only about 50% of patients treated. No effective alternative treatments exist for non-responders. Consequently, significant efforts are continuing to maximize response to combination therapy. However, rational therapy optimization is precluded by the poor understanding of the mechanism(s) of ribavirin action against HCV. Ribavirin alone induces either a transient early decline or no decrease in HCV viral load, but in combination with interferon it significantly improves long-term response rates. Here we present a model of HCV dynamics in which, on the basis of growing evidence, we assume that ribavirin decreases HCV infectivity in an infected individual in a dose-dependent manner. The model quantitatively predicts long-term response rates to interferon monotherapy and combination therapy, fits observed patterns of HCV RNA decline in patients undergoing therapy, reconciles conflicting observations of the influence of ribavirin on HCV RNA decline, provides key insights into the mechanism of ribavirin action against HCV, and establishes a framework for rational therapy optimization.

Dose-Response Relationship, Drug↗
PubMed2004

A stochastic model of cytotoxic T cell responses.

We have constructed a stochastic stage-structured model of the cytotoxic T lymphocyte (CTL) response to antigen and the maintenance of immunological memory. The model follows the dynamics of a viral infection and the stimulation, proliferation, and differentiation of naïve CD8(+) T cells into effector CTL, which can eliminate virally infected cells. The model is capable of following the dynamics of multiple T cell clones, each with a T cell receptor represented by a digit string. MHC-viral peptide complexes are also represented by strings and a string match rule is used to compute the affinity of a T cell receptor for a viral epitope. The avidities of interactions are also computed by taking into consideration the density of MHC-viral peptides on the surface of an infected cell. Lastly, the model allows the probability of T cell stimulation to depend on avidity but also incorporates the notion of an antigen-independent programmed proliferative response. We compare the model to experimental data on the cytotoxic T cell response to lymphocytic choriomeningitis virus infections.

Antigens, Viral↗
PubMed2004

Virus dynamics and immune responses during treatment in patients coinfected with hepatitis C and HIV.

Mathematical modeling of the biological effect of interferon on virus decay permits the quantification of the efficacy (epsilon) of blocking virion production in different patient populations. The viral dynamic and immunologic responses of hepatitis C virus (HCV) infection to daily interferon therapy were characterized in twelve patients co-infected with human immunodeficiency virus (HIV). Three out of the twelve patients (25%) achieved an early viral response, a two-log reduction in HCV RNA by week 12. The mean epsilon of IFN-alpha in blocking HCV and HIV production were 72% and 74%, respectively. For HCV epsilon was highest (97%) in the one patient who had a sustained viral response, while it was reduced in the other two patients (68% and 77%). Baseline HCV RNA and the number of CD3+CD56+16+ cells were inversely related (r = -0.89, p = 0.03), and baseline HCV-specific immune responses were significantly higher in the three patients with 2-log viral load reductions. These data suggest that: 1) interferon efficacy at blocking virion production is correlated with treatment outcome in HIV/HCV co-infected patients, 2) that immunodeficient patients can respond to standard IFN-alpha, 3) that both innate and adaptive immune responses may be important determinants of HCV RNA decline in response to interferon.

Adult↗
PubMed2004

Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay.

We present a model of HIV dynamics under antiretroviral therapy that combines drug pharmacokinetics and intracellular delay. A two compartment pharmacokinetic model is employed to determine the time evolution of the intracellular concentrations of the active forms of drugs, and thereby drug efficacy. The viral replication period is divided into pre- and post-drug action parts, allowing for the introduction of an intracellular delay in drug action. The standard model of viral dynamics is modified to account for the drug dependence of intracellular delay and continuously varying drug efficacy. Model calculations reveal that viral load decay in HIV infected patients under monotherapy can exhibit remarkably complex patterns depending on the relative magnitudes of the pharmacokinetic, intracellular, and intrinsic viral dynamic time-scales. The commonly assumed exponential decay is only a special case. However, uncertainties in measurement and the low sampling frequencies employed in present clinical studies preclude the identification of these patterns from existing clinical viral load data.

Adenine↗
PubMed2004

Intensification of antiretroviral therapy accelerates the decay of the HIV-1 latent reservoir and decreases, but does not eliminate, ongoing virus replication.

This study evaluated whether intensification of standard antiretroviral therapy with abacavir, with or without efavirenz, leads to better viral suppression and acceleration of the rate of HIV-1 decay. Ten HIV-1-infected individuals were enrolled in a prospective, open-label study and received standard, combination antiretroviral therapy with either 3 or 4 agents. The rate of decay of the HIV-1 latent reservoir and the frequency of intermittent viremia were compared between 5 patients who underwent treatment intensification and 5 control subjects with comparable baseline characteristics. When compared with control patients, the median half-life (t1/2) of the latent reservoir decreased from 31 to 10 months (P = 0.016) in subjects who had treatment intensification. The frequency of intermittent viremia/year also decreased in 4 of 5 individuals following intensification (2.4/y vs. 0.8/y). These data suggest that ongoing virus replication during standard antiretroviral therapy is due, in part, to the inadequate antiviral potency of current regimens. Despite better viral suppression, treatment intensification did not completely block viral replication, as evidenced by continuing intermittent viremia in some individuals. Additional studies are needed to understand the host- and pathogen-related determinants of incomplete pharmacologic control of HIV-1 replication.

Adult↗
PubMed2004

The life span of ganglionic glia in murine sensory ganglia estimated by uptake of bromodeoxyuridine.

Studies of ganglionic glia turnover in the sensory nervous system have implications for understanding nervous system maintenance and repair. These glial cells of the sensory ganglia in the peripheral nervous system (PNS) comprise satellite cells (SCs) and, to a lesser extent, Schwann cells. SCs proliferate in response to trauma such as axotomy; however, the half-life of these glial cells under normal circumstances has not been estimated. To estimate the half-life of sensory ganglionic glial cells, we employed the DNA precursor analog 5-bromo-2'-deoxyuridine (BrdU) to measure the rate of turnover of these cells. BrdU was administered to inbred C57BL6 and outbred Swiss white mice via their drinking water. BrdU incorporation into ganglionic glia in the PNS was estimated by immunofluorescent staining of nervous tissue sections, and the fraction of ganglionic glial cells that acquired BrdU label was measured as a function of time. Mathematical modeling of the rate of uptake of BrdU into murine ganglionic glia enables calculation of the half-life of these cells. The kinetics of BrdU uptake is linear, consistent with ganglionic glia being a homogenous population. The value of the proliferation rate (p) plus death rate (d) derived from the slope of BrdU uptake as a function of time is approximately 2.4 x 10(-3) cells per day. Assuming that p = d (because ganglionic glial numbers are in equilibrium and they are assumed to neither emigrate from, or immigrate into, sensory ganglia), then the daily death rate is d = 1.2 x 10(-3) cells/day, which implies a half-life for ganglionic glia of about 600 days. Thus murine ganglionic glia in the untraumatized state appear to behave as a homogenous, slowly replicating population.

Animals↗
PubMed2004

Some scaling principles for the immune system.

Using recent progress in biological scaling, we explore the way in which the immune system of an animal scales with its mass (M). It is shown that the number of cells in a single clone of B cells should scale as M and that the B-cell repertoire scales as ln (cM), where c is a constant. The time that a B cell needs to circulate once through the organism is shown to scale as M(1/4)ln (cM). It is suggested that the scaling of other cell populations in the immune system could be derived from these scaling relations for B cells.

Animals↗
PubMed2004

Hepatitis B virus kinetics and mathematical modeling.

In this article, we review modeling and interpretation of kinetics data obtained from patients with chronic hepatitis B virus infection that has been treated with lamivudine, adefovir dipivoxil, and lamivudine plus famciclovir combination therapy.

Adenine↗
PubMed2004

Modelling the impact of antigen kinetics on T-cell activation and response.

Cytotoxic T lymphocyte (CTL) responses are thought to be important for the control of many viral and other infections. Qualitative aspects of the CTL response, including the epitope specificity, affinity, and clonal composition, may affect the ability of T cells to mediate infection control. Although it is clear that the mode of introduction and the dose of antigen can affect these qualitative aspects of the response, little is understood of the mechanisms. We have developed an in silico model of the CTL response, which we use to study the impact of antigen dose, antigen kinetics and repeated antigen delivery on the response. The results suggest that recent observations on differences in response to killed antigen can be explained simply by differences in timing of T-cell activation. These findings may provide insight into how different vaccination strategies can quantitatively and qualitatively affect the outcome of the immune response.

Antigens, Viral↗
PubMed2004

Effects of antibody on viral kinetics in simian/human immunodeficiency virus infection: implications for vaccination.

Passive antibody treatment of macaques prior to simian/human immunodeficiency virus infection produces "sterilizing immunity" in some animals and long-term reductions in viral loads in others. Analysis of viral kinetics suggests that antibody mediates sterilizing immunity by its effects on the initial viral inoculum. By contrast, reduction in peak viral load later in infection prevents CD4 depletion and contributes to long-term viral control.

Animals↗
PubMed2004

Multiplicity of human immunodeficiency virus infections in lymphoid tissue.

Human immunodeficiency virus type 1 (HIV-1)-infected splenocytes in humans were recently shown to harbor three to four proviruses per cell on average (A. Jung et al., Nature 418:144, 2002). However, the mechanisms that lead to such extensive multiple infections are not understood. Here, we find by using mathematical analysis that two mechanisms quantitatively capture the distribution of proviral genomes in HIV-1-infected splenocytes, one where multiple genomes are acquired one at a time in a series of sequential infectious contacts of a target cell with free virions and infected cells, and the other where cell-to-cell transmission of multiple virions or genomes results from a single infectious contact of a target cell with an infected cell. The two mechanisms imply different genetic diversities of proviruses within an infected cell and therefore different rates of emergence of drug resistance via recombination.

HIV Infections↗
PubMed2004

Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection.

Several primate models indicate that cytotoxic T lymphocyte-inducing vaccines may be unable to prevent human immunodeficiency virus infection but may have a long-term benefit in controlling viral replication and delaying disease progression. Here we show that analysis of the kinetics of antigen-specific CD8+ T-cell expansion suggests a delay in activation following infection that allows unimpeded early viral replication. Viral kinetics do not differ between controls and vaccinees during this delay phase. An increase in virus-specific CD8+ T-cell numbers around day 10 postinfection coincides with a slowing in viral replication in vaccinees and reduces peak viral loads by around 1 log. However, this response is too little too late to prevent establishment of persistent infection.

AIDS Vaccines↗