Synchronous versus asynchronous oscillations for antigenically varying Plasmodium falciparum with host immune response

We consider a deterministic intra-host model for Plasmodium falciparum (Pf) malaria infection, which accounts for antigenic variation between n clonal variants of PfEMP1 and the corresponding host immune response (IR). Specifically, the model separates the IR into two components, specific and cross-reactive, respectively, in order to demonstrate that the latter can be a mechanism for the sequential appearance of variants observed in actual Pf infections. We show that a strong variant-specific IR relative to the cross-reactive IR favours the asynchronous oscillations (sequential dominance) over the synchronous oscillations in a number of ways. The decay rate of asynchronous oscillations is smaller than that for the synchronous oscillations, allowing for the parasite to survive longer. With the introduction of a delay in the stimulation of the IR, we show that only a small delay is necessary to cause persistent asynchronous oscillations and that a strong variant-specific IR increases the amplitude of the asynchronous oscillations.     

Immune response to a malaria infection: properties of a mathematical model

We establish some properties of a within host mathematical model of malaria proposed by Recker et al. [M. Recker et al., Transient cross-reactive immune responses can orchestrate antigenic variation in malaria, Lett. Nature 429 (2004), pp. 555-558; M. Recker and S. Gupta, Conflicting immune responses can prolong the length of infection in Plasmodium falciparum malaria, Bull. Math. Biol. 68 (2006), pp. 821-835.], which includes the role of the immune system during the infection. The model accounts for the antigenic variation exhibited by the malaria parasite (Plasmodium falciparum). We show that the model can exhibit a wide variety of dynamical behaviours. We provide criteria for global stability, competitive exclusion and persistence. We also demonstrate that the disease equilibrium can be destabilized by non-symmetric cross-reactive responses.     

Virus load and antigenic diversity

In this paper, we analyse mathematical models for the interaction between virus replication and immune responses. We show that the immune system can provide selection pressure for or against viral diversity. The paper provides new insights into the relationship between virus load (=the abundance of virus in an infected individual) and antigenic diversity. Antigenic variation can increase virus load during infections, but the correlation between load and diversity in comparisons among different infected individuals can be positive or negative, depending on whether individuals differ in their cross-reactive or strain-specific immune responses. We derive two models: our first model applies to any replicating parasite that can escape from immune responses; our second model includes immune function impairment, and specifically describes infections with the human immunodeficiency virus (HIV).     

How do antigenically varying pathogens avoid cross-reactive responses to invariant antigens?

Pathogens such as trypanosomes and malaria use antigenic variation to evade immune responses and prolong the duration of infections. As pathogens typically express more than one antigen, even relatively rare conserved antigens might be expected to trigger cross-reactive immune responses capable of clearing the infection. We use simple mathematical models that explicitly consider the dynamic interplay between the replicating pathogen, immune responses to different antigens and immune exhaustion to explore how pathogens can escape the responses to both variable and invariant (conserved) antigens. Our results suggest two hypotheses. In the first, limited quantities of invariant antigens on each pathogen may lead to saturation in killing by cross-reactive responses. In the second, antigenic variation of the dominant antigens prolongs the duration of infection sufficiently to allow for exhaustion of the cross-reactive responses to subdominant, invariant epitopes prior to their being able to control the infection. These hypotheses make distinct predictions: the former predicts that cross-reactive responses will always be ineffective while the latter predicts that appropriately timed treatment could, by preventing exhaustion, lead to the generation of long-lasting protective cross-reactive immunity and thus act similarly to a vaccine.     

Synchronous versus asynchronous oscillations for antigenically varying Plasmodium falciparum with host immune response

We consider a deterministic intra-host model for Plasmodium falciparum (Pf) malaria infection, which accounts for antigenic variation between n clonal variants of PfEMP1 and the corresponding host immune response (IR). Specifically, the model separates the IR into two components, specific and cross-reactive, respectively, in order to demonstrate that the latter can be a mechanism for the sequential appearance of variants observed in actual Pf infections. We show that a strong variant-specific IR relative to the cross-reactive IR favours the asynchronous oscillations (sequential dominance) over the synchronous oscillations in a number of ways. The decay rate of asynchronous oscillations is smaller than that for the synchronous oscillations, allowing for the parasite to survive longer. With the introduction of a delay in the stimulation of the IR, we show that only a small delay is necessary to cause persistent asynchronous oscillations and that a strong variant-specific IR increases the amplitude of the asynchronous oscillations.     

Inferring Epitopes of a Polymorphic Antigen Amidst Broadly Cross-Reactive Antibodies Using Protein Microarrays: A Study of OspC Proteins of Borrelia burgdorferi

Epitope mapping studies aim to identify the binding sites of antibody-antigen interactions to enhance the development of vaccines, diagnostics and immunotherapeutic compounds. However, mapping is a laborious process employing time- and resource-consuming ‘wet bench’ techniques or epitope prediction software that are still in their infancy. For polymorphic antigens, another challenge is characterizing cross-reactivity between epitopes, teasing out distinctions between broadly cross-reactive responses, limited cross-reactions among variants and the truly type-specific responses. A refined understanding of cross-reactive antibody binding could guide the selection of the most informative subsets of variants for diagnostics and multivalent subunit vaccines. We explored the antibody binding reactivity of sera from human patients and Peromyscus leucopus rodents infected with Borrelia burgdorferi to the polymorphic outer surface protein C (OspC), an attractive candidate antigen for vaccine and improved diagnostics for Lyme disease. We constructed a protein microarray displaying 23 natural variants of OspC and quantified the degree of cross-reactive antibody binding between all pairs of variants, using Pearson correlation calculated on the reactivity values using three independent transforms of the raw data: (1) logarithmic, (2) rank, and (3) binary indicators. We observed that the global amino acid sequence identity between OspC pairs was a poor predictor of cross-reactive antibody binding. Then we asked if specific regions of the protein would better explain the observed cross-reactive binding and performed in silico screening of the linear sequence and 3-dimensional structure of OspC. This analysis pointed to residues 179 through 188 the fifth C-terminal helix of the structure as a major determinant of type-specific cross-reactive antibody binding. We developed bioinformatics methods to systematically analyze the relationship between local sequence/structure variation and cross-reactive antibody binding patterns among variants of a polymorphic antigen, and this method can be applied to other polymorphic antigens for which immune response data is available for multiple variants.     

Antibodies to the strain-specific and cross-reactive determinants of the haemagglutinin of influenza H3N2 virus. 3. Selection of antigenic variations in vitro and in vivo

Antigenic variants of influenza A/Hong Kong/1/68 (H3N2) were obtained in vitro by letting virus multiply in the allantosis-on-shell system in the presence of anti-haemagglutinin antibodies, prepared from immune goat serum to purified haemagglutinin antigen, and in vivo by giving mice antibody intraperitoneally one day before challenge with a sublethal dose of live virus. In both systems it was shown that the most narrowly reacting strain-specific antibodies selected antigenic variants at an apparently higher rate than a more cross-reactive preparation of antibodies.     

A model of the role of natural killer cells in immune surveillance — I

Summary The theory of immune surveillance of Thomas and Burnet stated in part that antigenic differences between neoplastic and normal cells provide the stimulus for their destruction by cells of the immune system. Burnet pointed to the T lymphocyte as the cell which mediated this surveillance. The existence of some form of surveillance in cases of no T lymphocyte functioning presents the possibility that surveillance, if present at all, is mediated by non T cells.Cells identified as naturally cytotoxic killer (NK) cells appear to have properties required of a surveillance effector population. This paper utilizes properties of NK cells and the effects of interferon on this population to construct a mathematical model of the characteristics that an NK cell surveillance would have. A two level theory of immune surveillance is proposed.This research has been supported in part by the National Science Foundation under grant #NSF-Eng. 7904852     

The effects of symmetry on the dynamics of antigenic variation

In the studies of dynamics of pathogens and their interactions with a host immune system, an important role is played by the structure of antigenic variants associated with a pathogen. Using the example of a model of antigenic variation in malaria, we show how many of the observed dynamical regimes can be explained in terms of the symmetry of interactions between different antigenic variants. The results of this analysis are quite generic, and have wider implications for understanding the dynamics of immune escape of other parasites, as well as for the dynamics of multi-strain diseases.     

The effects of host heterogeneity on pathogen population structure.

We have shown that among pathogens, populations may self-organize into strains with non-overlapping repertoires of antigenic variants as a consequence of strong immune selection operating on polymorphic antigens. Recently, we have also demonstrated that over a wide range of intermediate levels of immune selection, pathogens may still be structured into discrete strains, but different sets of non-overlapping pathogen types will replace each other in a cyclical or chaotic manner. These models assume that the ranking of antigens in terms of the strength of the induced immune response is the same for every host. However, host immune responses may be restricted by the genotype of the individual. To explore this issue, a mathematical model was constructed under the assumption that a proportion of the host population responds principally to a variable antigen while the remainder of the population responds principally to a conserved antigen. The results of this analysis indicate that discrete strain structure (DSS) will be maintained even with a high frequency of hosts that do not respond in a variant-specific manner. Furthermore, the range of the immune selection pressure over which DSS prevails is increased (and the region of cyclical or chaotic behaviour reduced) by the inclusion of hosts that respond in a cross-reactive rather than a variant-specific manner.     

Vaccination with SARS-CoV-2 variants of concern protects mice from challenge with wild-type virus

Vaccines against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been highly efficient in protecting against Coronavirus Disease 2019 (COVID-19). However, the emergence of viral variants that are more transmissible and, in some cases, escape from neutralizing antibody responses has raised concerns. Here, we evaluated recombinant protein spike antigens derived from wild-type SARS-CoV-2 and from variants B.1.1.7, B.1.351, and P.1 for their immunogenicity and protective effect in vivo against challenge with wild-type SARS-CoV-2 in the mouse model. All proteins induced high neutralizing antibodies against the respective viruses but also induced high cross-neutralizing antibody responses. The decline in neutralizing titers between variants was moderate, with B.1.1.7-vaccinated animals having a maximum fold reduction of 4.8 against B.1.351 virus. P.1 induced the most cross-reactive antibody responses but was also the least immunogenic in terms of homologous neutralization titers. However, all antigens protected from challenge with wild-type SARS-CoV-2 in a mouse model.

This study explores the immune response induced by wild type and variant SARS-CoV-2 spike proteins, and the protection that these immune responses provide against challenge with wild type virus in the mouse model.     

Cross-reactive neutralization epitopes on VP3 of human rotavirus: analysis with monoclonal antibodies and antigenic variants.

We analyzed cross-reactive neutralization epitopes on protein VP3 of human rotavirus (HRV) by the use of neutralizing monoclonal antibodies (N-MAbs), which showed a variety of interserotypic reactivity patterns when examined in a neutralization test and an enzyme-linked immunosorbent assay against 15 HRV and 2 animal RV strains. Serological study with the six cross-reactive N-MAbs revealed antigenic variations in some HRV strains within the same serotype as well as a marked antigenic difference between serotype 2 strains and serotype 1, 3, and 4 strains. Epitope analysis of the antigenic variants resistant to the six individual cross-reactive N-MAbs suggested the existence of at least three distinct cross-reactive neutralization epitopes on VP3 of HRV.     

Higher homologous and lower cross-reactive Gag-specific T-cell responses in human immunodeficiency virus type 2 (HIV-2) than in HIV-1 infection

Human immunodeficiency virus type 2 (HIV-2) infection results in slower CD4⁺ T-cell decline, lower plasma viral load levels, and hence slower progression of the disease than does HIV-1 infection. Although the reasons for this are not clear, it is possible that HIV-2 replication is more effectively controlled by host responses. We used aligned pools of overlapping HIV-1 and HIV-2 Gag peptides in an enhanced gamma interferon enzyme-linked immunospot assay to compare the levels of homologous and cross-reactive Gag-specific T-cell responses between HIV-1- and HIV-2-infected patients. HIV-2-infected patients showed broader and stronger homologous Gag-specific T-cell responses than HIV-1-infected patients. In contrast, the cross-reactive T-cell responses in HIV-2-infected patients were both narrower and weaker than those in HIV-1-infected patients, in line with overall weaker correlations between homologous and heterologous T-cell responses among HIV-2-infected patients than among HIV-1-infected patients. Cross-reactive responses in HIV-2-infected patients tended to correlate directly with HIV-1/HIV-2 Gag sequence similarities; this was not found in HIV-1-infected patients. The CD4⁺ T-cell counts of HIV-2-infected patients correlated directly with homologous responses and inversely with cross-reactive responses; this was not found in HIV-1-infected patients. Our data support a model whereby high-level HIV-2-specific T-cell responses control the replication of HIV-2, thus limiting viral diversification and priming of HIV-1 cross-reactive T-cell responses over time. However, we cannot exclude the possibility that HIV-2 replication is controlled by other host factors and that HIV-2-specific T-cell responses are better maintained in the context of slow viral divergence and a less damaged immune system. Understanding the nature of immune control of HIV-2 infection could be crucial for HIV vaccine design.     

Mathematical biology of HIV infections: antigenic variation and diversity threshold.

Infection with the human immunodeficiency virus (HIV) results in severe damage to the immune system and consequent disease (AIDS) after a long and variable incubation period (on average 8-10 years). Why the incubation period should be so long is a puzzle. We outline an explanation based on the dynamics of the interplay between the immune response and antigenic variation in the virus population. The essential idea is that AIDS results when the diversity of antigenic variants of HIV in an infected patient exceeds some threshold, beyond which the immune system can no longer cope. The paper develops a simple mathematical model for this process, based on experimental observations, and explores several ramifications.     

Evolution of human immunodeficiency virus type 1 in a patient with cross-reactive neutralizing activity in serum

Analysis of longitudinally obtained HIV-1 env sequences from an individual with reported cross-reactive neutralizing activity revealed that the majority of viral variants obtained from serum between 4 and 7 years after seroconversion were unable to persist in peripheral blood. Here we show that these viral variants were more sensitive to autologous serum neutralization, had shorter envelopes with fewer potential N-linked glycosylation sites, and showed lower replication kinetics than successfully evolving HIV-1 variants. These data reflect the host selection pressures on phenotypic characteristics of HIV-1 and illustrate in detail the dynamic interaction between HIV-1 and its host's humoral immune responses.     

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.     

Structural Allele-Specific Patterns Adopted by Epitopes in the MHC-I Cleft and Reconstruction of MHC:peptide Complexes to Cross-Reactivity Assessment

The immune system is engaged in a constant antigenic surveillance through the Major Histocompatibility Complex (MHC) class I antigen presentation pathway. This is an efficient mechanism for detection of intracellular infections, especially viral ones. In this work we describe conformational patterns shared by epitopes presented by a given MHC allele and use these features to develop a docking approach that simulates the peptide loading into the MHC cleft. Our strategy, to construct in silico MHC:peptide complexes, was successfully tested by reproducing four different crystal structures of MHC-I molecules available at the Protein Data Bank (PDB). An in silico study of cross-reactivity potential was also performed between the wild-type complex HLA-A2-NS31073 and nine MHC:peptide complexes presenting alanine exchange peptides. This indicates that structural similarities among the complexes can give us important clues about cross reactivity. The approach used in this work allows the selection of epitopes with potential to induce cross-reactive immune responses, providing useful tools for studies in autoimmunity and to the development of more comprehensive vaccines.     

Rhythmic patterns in phagocytosis and the production of reactive oxygen species by zebrafish leukocytes

Multiple components of vertebrate immune systems have been shown to exhibit circadian fluctuations. While the zebrafish is currently generating a wealth of information on the molecular pacemakers that may control circadian rhythms, there have been no reports of rhythmic activity in zebrafish leukocytes. In this study, we found that phagocytosis and the production of reactive oxygen species by zebrafish leukocytes varied significantly throughout twenty-four hour periods. A distinct peak in cellular ROS levels occurred before dawn, while the kinetics of respiratory burst responses were least rapid at this time of day. Phagocytosis of E. coli peaked late in the day, whereas there was no daily variation in phagocytosis of S. aureus. As seen in other species, the number of bacteria ingested per cell peaked during the night. These data provide direct evidence of rhythmic immune system activity, and demonstrate that zebrafish can be a valuable model in which to study the relationships between circadian gene expression, systemic pacemakers, and the activity of vertebrate immune system cells.     

Phase variation in Francisella tularensis affecting intracellular growth, lipopolysaccharide antigenicity and nitric oxide production

Many microbial pathogens, such as Mycobacterium spp. and Salmonella spp., use macrophage intracellular growth or antigenic variation as mechanisms for avoiding the host immune system. In this work we present evidence to show that the intracellular pathogen Francisella tularensis uses phase variation to alter antigenicity and the host macrophage nitric oxide response simultaneously, thereby modulating its intracellular growth. The lipopolysaccharide (LPS) and lipid A of F. tularensis fails to stimulate production of significant levels of nitric oxide (NO) by rat macrophages. However, spontaneous variants of F. tularensis expressing an antigenically distinct LPS induce rat macrophages to produce increased levels of NO, thereby suppressing microbial intramacrophage growth. Similarly, lipid A isolated from these variants stimulates increased levels of NO production. A reverse phase shift can occur, which returns the LPS to the original antigenic form, reduces NO production, and restores intramacrophage growth. These findings represent the first demonstration of a phase-variation phenomenon which modulates intracellular growth and an innate immune response. Furthermore, these results suggest that a microbial pathogen can exploit macrophage NO production for its own benefit, perhaps by prolonging the host-pathogen association during the acute phase of disease or during the process of establishing a carrier state.     

The Relation of Agglutinins to Antigenic Variation of Trypanosoma lewisi*

SYNOPSIS. During the course of infection in the rat, Trypanosoma lewisi produces 2 antigenic variants: the 1st represents the initial, reproducing population of cells; and the 2nd the nonreproducing, ablastin-inhibited adult population. The specificities of the agglutinins elicited by the variants were studied by adsorption and agglutination methods and the newer immunoelectroadsorption technic. It was found that the reproducing variant has a surface antigen that reacts with the agglutinin specific for the adult variant, but this antigen does not become immunogenic until transformation to the adult variant occurs. It was also found, with fractions of immune sera obtained by gel filtration, that the agglutinin specific for the reproducing variant is IgG and that specific for the adult variant, IgM. The antigenic variants of pathogenic and nonpathogenic trypanosomes are compared, and the roles of trypanocidal and ablastic antibodies in the induction of antigenic variation are discussed.