No evidence for competition between cytotoxic T-lymphocyte responses in HIV-1 infection

Defining Kinetic Properties of HIV-Specific CD8⁺ T-Cell Responses in Acute Infection

Multiple lines of evidence indicate that CD8 + T cells are important in the control of HIV-1 (HIV) replication. However, CD8 + T cells induced by natural infection cannot eliminate the virus or reduce viral loads to acceptably low levels in most infected individuals. Understanding the basic quantitative features of CD8 + T-cell responses induced during HIV infection may therefore inform us about the limits that HIV vaccines, which aim to induce protective CD8 + T-cell responses, must exceed. Using previously published experimental data from a cohort of HIV-infected individuals with sampling times from acute to chronic infection we defined the quantitative properties of CD8 + T-cell responses to the whole HIV proteome. In contrast with a commonly held view, we found that the relative number of HIV-specific CD8 + T-cell responses (response breadth) changed little over the course of infection (first 400 days post-infection), with moderate but statistically significant changes occurring only during the first 35 symptomatic days. This challenges the idea that a change in the T-cell response breadth over time is responsible for the slow speed of viral escape from CD8 + T cells in the chronic infection. The breadth of HIV-specific CD8 + T-cell responses was not correlated with the average viral load for our small cohort of patients. Metrics of relative immunodominance of HIV-specific CD8 + T-cell responses such as Shannon entropy or the Evenness index were also not significantly correlated with the average viral load. Our mathematical-model-driven analysis suggested extremely slow expansion kinetics for the majority of HIV-specific CD8 + T-cell responses and the presence of intra- and interclonal competition between multiple CD8 + T-cell responses; such competition may limit the magnitude of CD8 + T-cell responses, specific to different epitopes, and the overall number of T-cell responses induced by vaccination. Further understanding of mechanisms underlying interactions between the virus and virus-specific CD8 + T-cell response will be instrumental in determining which T-cell-based vaccines will induce T-cell responses providing durable protection against HIV infection.

Evolutionary dynamics of HIV at multiple spatial and temporal scales

Infectious diseases remain a formidable challenge to human health, and understanding pathogen evolution is crucial to designing effective therapeutics and control strategies. Here, we review important evolutionary aspects of HIV infection, highlighting the concept of selection at multiple spatial and temporal scales. At the smallest scale, a single cell may be infected by multiple virions competing for intracellular resources. Recombination and phenotypic mixing introduce novel evolutionary dynamics. As the virus spreads between cells in an infected individual, it continually evolves to circumvent the immune system. We discuss evolutionary mechanisms of HIV pathogenesis and progression to AIDS. Viral spread throughout the human population can lead to changes in virulence and the transmission of immune-evading variation. HIV emerged as a human pathogen due to selection occurring between different species, adapting from related viruses of primates. HIV also evolves resistance to antiretroviral drugs within a single infected host, and we explore the possibility for the spread of these strains between hosts, leading to a drug-resistant epidemic. We investigate the role of latency, drug-protected compartments, and direct cell-to-cell transmission on viral evolution. The introduction of an HIV vaccine may select for viral variants that escape vaccine control, both within an individual and throughout the population. Due to the strong selective pressure exerted by HIV-induced morbidity and mortality in many parts of the world, the human population itself may be co-evolving in response to the HIV pandemic. Throughout the paper, we focus on trade-offs between costs and benefits that constrain viral evolution and accentuate how selection pressures differ at different levels of selection.

Infection of HIV-specific CD4 T helper cells and the clonal composition of the response

A hallmark of human immunodeficiency virus is its ability to infect CD4+ T helper cells, thus impairing helper cell responses and consequently effector responses whose maintenance depends on help (such as killer T cells and B cells). In particular, the virus has been shown to infect HIV-specific helper cells preferentially. Using mathematical models, we investigate the consequence of this assumption for the basic dynamics between HIV and its target cells, assuming the existence of two independently regulated helper cell clones, directed against different epitopes of the virus. In contrast to previous studies, we examine a relatively simple scenario, only concentrating on the interactions between the virus and its target cells, not taking into account any helper-dependent effector responses. Further, there is no direct competition for space or antigenic stimulation in the model. Yet, a set of interesting outcomes is observed that provide further insights into factors that shape helper cell responses. Despite the absence of competition, a stronger helper cell clone can still exclude a weaker one because the two clones are infected by the same pathogen, an ecological concept called "apparent competition". Moreover, we also observe "facilitation": if one of the helper cell clones is too weak to become established in isolation, the presence of a stronger clone can provide enhanced antigenic stimulation, thus allowing the weaker clone to persist. The dependencies of these outcomes on parameters is explored. Factors that reduce viral infectivity and increase the death rate of infected cells promote coexistence, which is in agreement with the observation that stronger immunity correlates with broader helper cell responses. The basic model is extended to explicitly take into account helper-dependent CTL responses and direct competition. This study sheds further light onto the factors that can influence the clonal composition of HIV-specific helper cell responses, which has implications for the overall pattern of disease progression.

Modelling the spread of HIV immune escape mutants in a vaccinated population

Because cytotoxic T-lymphocytes (CTLs) have been shown to play a role in controlling human immunodeficiency virus (HIV) infection and because CTL-based simian immunodeficiency virus (SIV) vaccines have proved effective in non-human primates, one goal of HIV vaccine design is to elicit effective CTL responses in humans. Such a vaccine could improve viral control in patients who later become infected, thereby reducing onwards transmission and enhancing life expectancy in the absence of treatment. The ability of HIV to evolve mutations that evade CTLs and the ability of these ‘escape mutants’ to spread amongst the population poses a challenge to the development of an effective and robust vaccine. We present a mathematical model of within-host evolution and between-host transmission of CTL escape mutants amongst a population receiving a vaccine that elicits CTL responses to multiple epitopes. Within-host evolution at each epitope is represented by the outgrowth of escape mutants in hosts who restrict the epitope and their reversion in hosts who do not restrict the epitope. We use this model to investigate how the evolution and spread of escape mutants could affect the impact of a vaccine. We show that in the absence of escape, such a vaccine could markedly reduce the prevalence of both infection and disease in the population. However the impact of such a vaccine could be significantly abated by CTL escape mutants, especially if their selection in hosts who restrict the epitope is rapid and their reversion in hosts who do not restrict the epitope is slow. We also use the model to address whether a vaccine should span a broad or narrow range of CTL epitopes and target epitopes restricted by rare or common HLA types. We discuss the implications and limitations of our findings.

The evolution and spread of HIV strains that evade the immune response poses a major challenge to the development of an effective and robust HIV vaccine. We present a new mathematical tool that we use to dissect the drivers of the spread of these ‘immune escape mutants’ in a vaccinated population. Our study focuses on a vaccine that can reduce infectiousness and enhance longevity but does not provide sterilizing immunity. We show that in the absence of escape such a vaccine could reduce the prevalence of both infection and disease in the population. However, vaccine impact could be significantly abated by immune escape mutants, especially if they emerge rapidly and revert very slowly after transmission to hosts in whom the original selection pressure is absent. We also discuss the effect that vaccine breadth and the frequency with which different epitopes are targeted have upon vaccine impact.

Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection

HIV-1 often evades cytotoxic T cell (CTL) responses by generating variants that are not recognized by CTLs. We used single-genome amplification and sequencing of complete HIV genomes to identify longitudinal changes in the transmitted/founder virus from the establishment of infection to the viral set point at 1 year after the infection. We found that the rate of viral escape from CTL responses in a given patient decreases dramatically from acute infection to the viral set point. Using a novel mathematical model that tracks the dynamics of viral escape at multiple epitopes, we show that a number of factors could potentially contribute to a slower escape in the chronic phase of infection, such as a decreased magnitude of epitope-specific CTL responses, an increased fitness cost of escape mutations, or an increased diversity of the CTL response. In the model, an increase in the number of epitope-specific CTL responses can reduce the rate of viral escape from a given epitope-specific CTL response, particularly if CD8+ T cells compete for killing of infected cells or control virus replication nonlytically. Our mathematical framework of viral escape from multiple CTL responses can be used to predict the breadth and magnitude of HIV-specific CTL responses that need to be induced by vaccination to reduce (or even prevent) viral escape following HIV infection.