A mathematical model of vaccination against HIV to prevent the development of AIDS.

Vaccination and post-exposure immunization against the human immunodeficiency viruses (HIV-1 and HIV-2) faces the problem of the extensive genetic and antigenic variability of these viruses. This raises the question of what fraction of all possible antigen strains of the virus must be recognized by the immune response to a vaccine to prevent development of acquired immunodeficiency disease (AIDS). The success of a vaccine can depend on the variability of the target epitopes. The different HIV variants must be suppressed faster than new escape mutants can be produced. In this paper the antigenic variation of HIV during an individual infection is described by a stochastic process. The central assumption is that antigenic drift is important for the virus to survive immunological attack and to establish a persistent infection that leads to the development of AIDS after a long incubation period. The mathematical analysis reveals that the fraction of antigenic variants recognized by the immune response, that is induced by a successful immunogen, must exceed 1-1/R, where R is the diversification rate of the virus population. This means that if each HIV strain can produce, on average, five new escape mutants, then more than 80% of the possible variants must be covered by the immunogen. A generic result of the model is that, no matter how immunogenic a vaccine is, it will fail if it does not enhance immune attack against a sufficiently large fraction of strains. Furthermore, it is shown that the timing of the application of post-exposure immunization is important.     

Variability of HIV infections.

Genetic variation is the hallmark of infections with lentiviruses in general and the human immunodeficiency viruses (HIV-1, HIV-2) in particular. This article reviews both experimental evidence for the variability of the HIV genome during the course of an individual infection and mathematical models that outline the potential importance of antigenic variation as a major factor to drive disease progression. The essential idea is that the virus evades immune pressure by the continuous production of new mutants resistant to current immunological attack. This results in the accumulation of antigenic diversity during the asymptomatic period. The existence of an antigenic diversity threshold is derived from the asymmetric interaction between the virus quasispecies and the CD4 cell population: CD4 cells mount immune responses some of which are directed against specific HIV variants, but each virus strain can induce depletion of all CD4 cells and therefore impair immune responses regardless of their specificity. Therefore, increasing HIV diversity enables the virus population to escape from control by the immune system. In this context the observed genetic variability is responsible for the fact that the virus establishes a persistent infection without being cleared by the immune response and induces immunodeficiency disease after a long and variable incubation period. Mathematical biology has revealed a novel mechanism for viral pathogenesis.     

From HIV infection to AIDS: a dynamically induced percolation transition?

The origin of the unusual incubation period distribution in the development of AIDS is largely unresolved. A key factor in understanding the observed distribution of latency periods, as well as the occurrence of infected individuals not developing AIDS at all, is the dynamics of the long-lasting struggle between HIV and the immune system. Using a computer simulation, we study the diversification of viral genomes under mutation and the selective pressure of the immune system. In non-HIV infections, vast spreading of viral genomes in genome space usually does not take place. In the case of an HIV infection, this may occur, as the virus successively weakens the immune system by the depletion of CD4+ cells. In a sequence space framework, this leads to a dynamically induced percolation transition, corresponding to the onset of AIDS. As a result, we obtain a prolonged shape of the incubation period distribution, as well as a finite fraction of non-progressors that do not develop AIDS, comparing well with results from recent clinical research.     

Estimation of the incidence of HIV infection

The aim of the method of 'back projection' is to provide estimates of the number of new infections with the human immunodeficiency virus (HIV) as a function of time, by using the numbers of diagnoses of the acquired immune deficiency syndrome (AIDS) together with information on the distribution of the incubation period between infection and diagnosis. Here, the method is investigated with particular reference to cases of HIV infection and AIDS in the United Kingdom.     

Do endogenous cannabinoids contribute to HIV-mediated immune failure?

The failure of the immune system to mount a successful attack on the human immunodeficiency virus (HIV) is an old enigma for AIDS research. The high mutational capacity of HIV, which unremittingly confuses the immune system, is a major factor in immune failure. But this alone cannot fully explain the certain and inescapable failure of the immune system, leading to full-blown AIDS. Here, we propose the hypothesis that endogenous cannabinoids, derived mostly from macrophages, might participate in the general failure of the immune system in HIV-infected individuals.     

HIV persistence in monocytes leads to pathogenesis and AIDS

An hypothesis of the pathogenic mechanism leading to acquired immunodeficiency syndrome (AIDS) that places special emphasis on the potential for infected monocytes to act as the reservoir of a persistent human immunodeficiency virus (HIV) infection has been developed. Monocytes may mediate directly the infection and ultimate destruction of helper T cells; this establishes a direct relationship between antigen presentation and HIV dissemination, thus accounting for the cytopathogenic effects and immune system debilitation associated commonly with AIDS. The possibility that this mode of virus dissemination can account for the depletion of helper-T-cell subsets based on their antigen specificity is considered and may explain why the cellular immune response to the virus is ineffective. This concept and may also elucidate the role of intercurrent infections in the development of disease and it suggests mechanistic explanations for the conversion from prodromal to fulminant AIDS.     

Does apoptosis contribute to CD4 T cell depletion in human immunodeficiency virus infection ?

Despite an extensive knowledge of the molecular characteristics of the human immunodeficiency virus (HIV) identified more than ten years ago as the cause of AIDS (acquired immune deficiency syndrome) (Barre-Sinoussi et al. 1983) some critical questions have not been answered yet: Is the progressive disappearance of CD4+ helper T lymphocytes, the hallmark of AIDS, directly related to the killing of infected cells by the virus? If not, how do CD4+T cells die? Is HIV using its viral factory to kill uninfected bystander cells? What causes the immune system collapse in HIV infection? In the past three years some important studies have provided stimulating clues suggesting that AIDS is not only related to the killing of host cells by HIV but is also a consequence of mechanisms of misactivation of the immune system, leading to anergy or apoptosis of non-infected effector cells. We discuss some of the in vivo and in vitro models providing evidence that HIV is able to kill and cripple the immune system either by acting directly on its targets or indirectly in bystander T cells keeping in mind that HIV disease must be considered as a multifactorial process.     

Fold recognition of the human immunodeficiency virus type 1 V3 loop and flexibility of its crown structure during the course of adaptation to a host

The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of the virus, which is an important determinant of HIV pathogenesis. Hence, the information about preferred conformations of the V3-loop region and its flexibility could be a crucial tool for understanding the mechanisms of progression from an initial infection to AIDS. Taking into account the uncertainty of the loop structure, we predicted the structural flexibility, diversity, and sequence fitness to the V3-loop structure for each of the sequences serially sampled during an asymptomatic period. Structural diversity correlated with sequence diversity. The predicted crown structure usage implied that structural flexibility depended on the patient and that the antigenic character of the virus might be almost uniform in a patient whose immune system is strong. Furthermore, the predicted structural ensemble suggested that toward the end of the asymptomatic period there was a change in the V3-loop structure or in the environment surrounding the V3 loop, possibly because of its proximity to the gp120 core.     

On transient effects in the HIV/AIDS epidemic

During the initially exponential spread of the human immunodeficiency virus (HIV—the causative agent of AIDS) the growth rate of the number of AIDS cases decreases from plus infinity to the growth rate of HIV infections. A sensitivity analysis shows that for all reasonable values of the parameters of the HIV epidemic (incubation period, initial doubling time, etc.) the effect of this positive transient becomes negligible when the annual number of AIDS cases reaches a few dozen. Necessary and sufficient conditions are given for the growth rate of the number of AIDS cases to be monotonically decreasing during the positive transient. A mildly pathological density function for the incubation period of AIDS provides an example of a growth rate of AIDS that does not decrease monotonically, even though HIV is spreading exponentially. A negative transient occurs when the growth rate of HIV begins to decrease. In this context a somewhat surprising result emerges under the assumption that the growth rate of HIV is non-increasing: the growth rate of AIDS is at all times larger than the growth rate of HIV. A logistic HIV epidemic illustrates this result, and implications for the growth of the HIV epidemic in the United States and Europe are discussed. In particular, it is shown that the positive transient must have passed by 1982 in the United States and by 1986 or 1987 for the five European countries with the largest caseloads.     

Why is HIV a pathogen?

The pathogenesis of HIV begins with a profound depletion of CD4+ T cells in the gut followed by a long period of clinically silent but dynamic virus replication and diversification with high host cell turnover before the onset of AIDS. The AIDS-defining opportunistic infections and tumors mark the end-point of a long balancing act between virus and host that occurs when CD4+ T cell numbers fall below a level that can sustain immunity. Comparative studies of lentivirus infections in other species show that AIDS is not an inevitable outcome of infection because simian immunodeficiency virus in natural hosts seldom causes disease. What distinguishes pathogenic from 'passenger' infection is a systemic activation of immune responses followed by destruction of the integrity of lymphoid follicles. Macrophage and dendritic cell infection also contribute to pathogenesis. Maedi-Visna virus infection in sheep, which targets these cells but not T lymphocytes, also leads to progressive disease and death that resembles the wasting and brain diseases of HIV without the T cell immunodeficiency. Thus, lessons from pathogenic and nonpathogenic lentivirus infections provide insight into the complex syndrome called AIDS.     

Cytokines and HIV infection

Infection with the human immunodeficiency virus (HIV) results in the production of cytokines by cells that comprise the immune system. Such cytokines regulate both immune function and viral replication, and thereby complicate their contribution to the progression to AIDS. Certain cytokines that regulate immune function exert opposing effects, such that some promote mainly cellular immune function, whereas others enhance antibody production. It has been suggested that an imbalance in cytokine production is responsible in part for the immune dysregulation characteristic of progression to AIDS. Different cytokines can also have different effects on HIV expression and replication. Cytokine-based therapy has been suggested for preventing or delaying progression to AIDS. If such therapy is to be successful, it will be necessary to identify the correlate of immune protection, as well as to determine which cytokines enhance or suppress protective immunity, and the effects of these cytokines on viral replication.     

Epidemiological and statistical aspects of the AIDS epidemic: introduction

In 1988, a government working party studied estimates of incidence and prevalence of numbers of acquired immunodeficiency syndrome (AIDS) cases. They investigated a series of epidemiological, statistical and mathematical problems associated with predicting trends in incidences of AIDS. This paper introduces a series of papers that give a fuller and more technical exposition of the appendixes of that working party report. The papers provide a brief background to the current state of knowledge on the epidemiology of the infection and the disease; a deterministic model for human immunodeficiency virus (HIV) transmission in the male homosexual community in England and Wales is introduced. Back-projection methods are studied in two papers, following the distribution of the incubation period of the disease. The concept of minimum size of the epidemic is introduced. Mathematical functions to describe the spread of HIV infection are refined by using past trends in the incidence of AIDS to estimate values for some parameters. Survival times for AIDS patients from the point of diagnosis are considered and evidence for changes in male homosexual sexual behaviour is studied; lag-time from the point of diagnosis to the report of the case is also examined. There is a comparative analysis of the AIDS epidemic in various European countries. The incubation period of HIV in patients with haemophilia A and B infections and the problems associated with making predictions for different at-risk groups or small subgroups based on geographical area are discussed. Reasons for fluctuation between the number of reported cases from month to month are provided.     

Adenosine signaling and adenosine deaminase regulation of immune responses: impact on the immunopathogenesis of HIV infection

Infection by human immunodeficiency virus (HIV) causes the acquired immune deficiency syndrome (AIDS), which has devastating effects on the host immune system. HIV entry into host cells and subsequent viral replication induce a proinflammatory response, hyperactivating immune cells and leading them to death, disfunction, and exhaustion. Adenosine is an immunomodulatory molecule that suppresses immune cell function to protect tissue integrity. The anti-inflammatory properties of adenosine modulate the chronic inflammation and immune activation caused by HIV. Lack of adenosine contributes to pathogenic events in HIV infection. However, immunosuppression by adenosine has its shortcomings, such as impairing the immune response, hindering the elimination of the virus and control of viral replication. By attempting to control inflammation, adenosine feeds a pathogenic cycle affecting immune cells. Deamination of adenosine by ADA (adenosine deaminase) counteracts the negative effects of adenosine in immune cells, boosting the immune response. This review comprises the connection between adenosinergic system and HIV immunopathogenesis, exploring defects in immune cell function and the role of ADA in protecting these cells against damage.     

Sequence divergence and open regions of RNA secondary structures in the envelope regions of the 17 human immunodeficiency virus isolates.

Genetic variation during the course of infection of an individual is a remarkable feature of the acquired immune deficiency syndrome (AIDS) disease. This variation has been studied for the envelope protein encoding regions of seventeen different sequences from various isolates of human immunodeficiency virus (HIV) using multiple sequence comparison and calculation of variability. The open regions with little intramolecular base pairing in these envelope sequences are predicted by a recently developed statistical method. The minimum length L for a run of hypervariable sites, conserved sites, or open regions that gives significance at the 1% (or 0.1%) level is then determined by a scan statistical method. The results show that significant clusters of open regions predicted at the RNA levels correlate with significant clusters of hypervariable sites in the HIV envelope gene. Those significant genomic variations in HIVs seem to be manifested mainly in the extracellular portion of the envelope protein. Twelve potential antigenic determinants are predicted using an antigenic index method. Interestingly, the majority of the significant hypervariable regions in the exterior envelope protein (gp120) were predicted potential epitopes.     

Determination of the spread of HIV from the AIDS incidence history

The relation between the incidence of HIV in the general population, the number of AIDS cases, and the incubation period for the disease is examined. The number of AIDS cases can be expressed in terms of a convolution integral over the incubation period distribution and the temporal history of HIV incidence. In order to determine the level of HIV incidence it is necessary to invert the convolution. In this manner, it is possible to determine the spread of HIV up to the present time from knowledge of the AIDS incidence history and the incubation period. We describe the inversion of the convolution in terms of a Laplace transform technique that is applicable for any given incubation period distribution. Substantial simplifications in the technique are found in the case of an Erlang distribution for the probability density. The spread of HIV infections in the United States is charted through 1988 using AIDS incidence data that are corrected for both the revised AIDS case definition and reporting time delays. The results are consistent with current estimates of the HIV incidence in the United States and show no evidence of saturation in the rate of new infections. Indeed, the rate of new infections still appears to be climbing as of that date. While the technique is unable to predict the future course of the epidemic, it may provide a useful benchmark for comparison with mathematical models of the epidemic. The techniques are conceptually applicable to diseases other than AIDS.     

HIV病毒潜伏库的形成机制和对策挑战

长期以来,病毒潜伏库(latent viral reservoir,LVR)的存在严重阻碍了AIDS的有效治疗,LVR无法被人体免疫系统识别,高效抗逆转录病毒疗法(highly active antiretroviral therapy, HAART)对其无效,一旦中断抗病毒治疗,患者会出现快速耐药和病毒血症反弹.截至...     

Structural features of T-cell recognition: applications to vaccine design

T lymphocytes, in contrast to antibodies, appear to recognize primarily a limited number of antigenic sites on any given antigenic protein. We find that a single site can so dominate the T-cell repertoire that the presence or absence of a response to one immunodominant site can make the difference between a high responder and a low responder, even though low responders respond to other sites almost as well as high responders. Besides interaction with major histocompatibility complex (MHC) molecules, the mode by which the antigen is processed into fragments for T-cell recognition also determines which sites are seen. The products of natural processing of the protein appear to be larger than the synthetic peptides and contain structures which hinder binding to certain MHC molecules or to the T-cell receptor. A third factor in immunodominance is the intrinsic structure of the antigenic site. We have shown that amphipathic helices have a higher than random chance of being immunodominant, and have developed a computer program to locate such structures in protein amino acid sequences. We prospectively predicted sites in the malaria circumsporozoite protein and found that the four most widely recognized sites in an endemic area of West Africa were all predicted. Similarly, we identified two helper T-cell sites from the HIV (AIDS virus) envelope, and have now shown that immunization with these elicits enhanced antibody responses to the whole envelope when injected into monkeys. These sites are also recognized by human T cells from volunteers who had been immunized with a recombinant vaccinia virus expressing the HIV envelope. Also, because cytotoxic T lymphocytes (CTLS) may play a critical role in defence against AIDS, we have used a recombinant vaccinia virus and transfectants expressing the HIV envelope gene to induce specific CTLS against the HIV envelope. Using synthetic peptides, we were able to identify the first CTL recognition site in the AIDS virus. These results may contribute to the rational design of vaccines.     

Structure and design of broadly-neutralizing antibodies against HIV

Since the discovery more than 30 years ago of human immunodeficiency virus (HIV) as the causative agent of the deadly disease, acquired immune deficiency disease (AIDS), there have been no efficient vaccines against the virus. For the infection of the virus, the HIV surface glycoprotein gp120 first recognizes the CD4 receptor on the target helper T-cell, which initiates HIV fusion with the target cell and, if unchecked, leads to destruction of the patient's immune system. Despite the difficulty of developing appropriate immune responses in HIV-infected individuals, patient sera often contain antibodies that have broad neutralization activity, indicating the possibility of immunological treatment and prevention. Recently, through extensive structural studies of neutralizing antibodies of HIV in complex with gp120, the critical mechanisms of broad neutralization against HIV have been elucidated. Based on these discoveries, the structure-aided designs of antibodies and novel scaffolds were performed to create extremely potent neutralizing antibodies against HIV. These new discoveries and advances shed light on the road to development of efficient immunological therapies against AIDS.     

Microdevices for examining immunological responses of single cells to HIV

More than 60 million people in the world have been diagnosed with HIV infections since the virus was recognized as the causative agent of AIDS in the 1980s. Even though more than half of the infected patients have died, effective disease treatment and prevention measures have not been established. ART (antiretroviral therapy) is the only proven HIV treatment that sustains the suppression of patient viraemia. Current routine approaches to treat HIV infections are targeted at developing vaccines that will induce humoral or cell memory immune responses. However, developing an effective vaccine has been challenging because the HIV mutates rapidly, which allows the virus to evade immune surveillances established against the previous strain. In addition, the virus is able to quickly establish a reservoir and treatment is difficult because of the general lack of knowledge about HIV immune response mechanisms. This review introduces common disease symptoms and the progression of HIV infection with a brief summary of the current treatment approaches. Different cellular immune responses against HIV are also discussed, with emphasis on a nanotechnology research that has focused on probing T-cell response to HIV infection. Furthermore, we discuss recent noteworthy nanotechnology updates on T-cell response screening that is focused on HIV infection. Finally, we review potential future treatment strategies based on the correlations between T-cell response and HIV infection.     

SHIV89.6P pathogenicity in cynomolgus monkeys and control of viral replication and disease onset by human immunodeficiency virus type 1 Tat vaccine

The Tat protein of human immunodeficiency virus (HIV) is produced very early after infection, plays a key role in the virus life cycle and in acquired immunodeficiency syndrome (AIDS) pathogenesis, is immunogenic and well conserved among all virus clades. Notably, a Tat-specific immune response correlates with non-progression to AIDS. Here, we show that a vaccine based on the Tat protein of HIV blocks primary infection with the simian/human immunodeficiency virus (SHIV)89.6P and prevents the CD4 T cell decline and disease onset in cynomolgus monkeys. No signs of virus replication were found in five out of seven vaccinated macaques for almost 1 year of follow-up. Since the inoculated virus (derived from rhesus or from cynomolgus macaques) is shown to be highly pathogenic in cynomolgus macaques, the results indicate efficacy of Tat vaccination in protection against highly pathogenic virus challenge. Finally, the studies of the Tat-specific immunological responses indicate a correlation of protection with a cytotoxic T cell response. Thus, a Tat-based vaccine is a promising candidate for preventive and therapeutic vaccination in humans.