Resilience and Bifurcations in Viral Infection Models with Drug Resistance and Time-Varying Dynamics

Therapeutic Vaccination for Hepatitis C: Can Protective T-Cell Responses Be Restored After Prolonged Antigen Exposure?

Previous work has shown that intracellular delay needs to be taken into account to accurately determine the half-life of free virus from drug perturbation experiments (1). The delay also effects the estimated value for the infected T-cell loss rate when we assume that the drug is not completely effective (19). Models of virus infection that include intracellular delay are more accurate representations of the biological data. We analyze a non-linear model of the human immunodeficiency virus (HIV) infection that considers the interaction between a replicating virus, CD4+ T-cell and the cytotoxic-lymphocytes (CTL). We then investigate the intracellular delay effect on the stability of the endemically infected steady state. Criteria are given to ensure that the infected steady state is asymptotically stable for all delays. Model analysis also allows the prediction of a critical delay ?c below which the effector CTL can play a significant role in the immune control mechanism even when the basic reproduction number is high.

Platelet transfusion has been reported to modulate the recipients’ immune system. To date, the precise mechanism(s) driving poor patient outcomes (e.g., increased rate of mortality, morbidity, infectious complications and prolonged hospital stays) following platelet transfusion are largely undefined. To determine the potential for platelet concentrates (PC) to modulate responses of crucial immune regulatory cells, a human in vitro whole blood model of transfusion was established. Maturation and activation of human myeloid dendritic cells (mDC) and the specialized subset blood DC antigen (BDCA)3+ DC were assessed following exposure to buffy-coat derived PC at day (D)2 (fresh) and D5 (date-of-expiry). In parallel, to model recipients with underlying viral or bacterial infection, polyinosinic:polycytidylic acid or lipopolysaccharide was added. Exposure to PC had less of an impact on mDC responses than BDCA3+ DC responses. PC alone downregulated BDCA3+ DC expression of co-stimulatory molecules CD40 and CD80. In the model of viral infection, PC downregulated expression of CD83, and in the bacterial model of infection, PC downregulated CD80, CD83, and CD86. PC alone suppressed mDC production of interleukin (IL)-8, IL-12 and tumor necrosis factor (TNF)-α and BDCA3+ DC production of IL-8, IL-12, and IL-6. In the model of viral infection, production of IL-12 and interferon-gamma inducible protein (IP)-10 was reduced in both DC subsets, and IL-8 was reduced in BDCA3+ DC following PC exposure. When modeling bacterial infection, PC suppressed mDC and BDCA3+ DC production of IL-6 and IL-10 with a reduction in TNF-α evident in mDC. This study assessed the impact of PC “transfusion” on DC surface antigen expression and inflammatory mediator production and provided the first evidence that PC transfusion modulates blood mDC and BDCA3+ DC maturation and activation, particularly in the models of infection. Results of this study suggest that patients who receive PC, particularly those with underlying infectious complications, may fail to establish an appropriate immune response precipitating poor patient outcomes.

The biphasic decay of blood viraemia in patients being treated for human immunodeficiency virus type 1 (HIV-1) infection has been explained as the decay of two distinct populations of cells: the rapid death of productively infected cells followed by the much slower elimination of a second population the identity of which remains unknown. Here we advance an alternative explanation based on the immune response against a single population of infected cells. We show that the biphasic decay can be explained simply, without invoking multiple compartments: viral load falls quickly while cytotoxic T lymphocytes (CTL) are still abundant, and more slowly as CTL disappear. We propose a method to test this idea, and develop a framework that is readily applicable to treatment of other infections.

The rapid occurrence of therapy-resistant mutant strains provides a challenge for anti-viral therapy. An ideal drug target would be a highly conserved molecular feature in the viral life cycle, such as the packaging signals in the genomes of RNA viruses that encode an instruction manual for their efficient assembly. The ubiquity of this assembly code in RNA viruses, including major human pathogens, suggests that it confers selective advantages. However, their impact on viral evolution cannot be assessed in current models of viral infection that lack molecular details of virus assembly. We introduce here a quasispecies-based model of a viral infection that incorporates structural and mechanistic knowledge of packaging signal function in assembly to construct a phenotype-fitness map, capturing the impact of this RNA code on assembly yield and efficiency. Details of viral replication and assembly inside an infected host cell are coupled with a population model of a viral infection, allowing the occurrence of therapy resistance to be assessed in response to drugs inhibiting packaging signal recognition. Stochastic simulations of viral quasispecies evolution in chronic HCV infection under drug action and/or immune clearance reveal that drugs targeting all RNA signals in the assembly code collectively have a high barrier to drug resistance, even though each packaging signal in isolation has a lower barrier than conventional drugs. This suggests that drugs targeting the RNA signals in the assembly code could be promising routes for exploitation in anti-viral drug design.

Respiratory viral infections are strongly associated with asthma exacerbations. Rhinovirus is most frequently-detected pathogen; followed by respiratory syncytial virus; metapneumovirus; parainfluenza virus; enterovirus and coronavirus. In addition; viral infection; in combination with genetics; allergen exposure; microbiome and other pathogens; may play a role in asthma development. In particular; asthma development has been linked to wheezing-associated respiratory viral infections in early life. To understand underlying mechanisms of viral-induced airways disease; investigators have studied respiratory viral infections in small animals. This report reviews animal models of human respiratory viral infection employing mice; rats; guinea pigs; hamsters and ferrets. Investigators have modeled asthma exacerbations by infecting mice with allergic airways disease. Asthma development has been modeled by administration of virus to immature animals. Small animal models of respiratory viral infection will identify cell and molecular targets for the treatment of asthma.

In 1996 Nowak and his colleagues proposed a differential equation virus infection model, which has been widely applied in the study for the dynamics of hepatitis B virus (HBV) infection. Biological dynamics may be described more practically by discrete events rather than continuous ones. Using discrete systems to describe biological dynamics should be reasonable. Based on one revised Nowak et al's virus infection model, this study introduces a discrete virus infection model (DVIM). Two equilibriums of this model, E1 and E2, represents infection free and infection persistent, respectively. Similar to the case of the basic virus infection model, this study deduces a basic virus reproductive number R0 independing on the number of total cells of an infected target organ. A proposed theorem proves that if the basic virus reproductive number R0<1 then the virus free equilibrium E1 is locally stable. The DVIM is more reasonable than an abstract discrete susceptible-infected-recovered model (SIRS) whose basic virus reproductive number R0 is relevant to the number of total cells of the infected target organ. As an application, this study models the clinic HBV DNA data of a patient who was accepted via anti-HBV infection therapy with drug lamivudine. The results show that the numerical simulation is good in agreement with the clinic data.

The dynamics of T cell responses have been extensively studied during single virus infection of naive mice. During a viral infection, viral antigen is presented in the context of MHC class I molecules on the surface of infected cells. Activated CD8 T cells that recognized viral antigens mediate clearance of virus through lysis of these infected cells. We hypothesize that the balance between the replicating speed of the virus and the efficiency at which the T cell response clears the virus is key in determining the disease outcome of the host. Lower T cell efficiency and delayed viral clearance can lead to extensive T cellmediated immunopathology and death in some circumstances. To examine how the efficiency of the immune response would impact immunopathology we studied several viral infection models where T cell responses were predicted to be less than optimal: 1. a model of co-infection with two viruses that contain a crossreactive epitope, 2. a viral infection model where a high dose infection is known to induce clonal exhaustion of the CD8 T cell response, 3. a neonatal virus infection model where the immune system is immature and 4. A model of beneficial heterologous immunity and T cell crossreactivity where mice are immunized as neonates when the T cell pool is still developing. Model 1 . Simultaneous co-infections are common and can occur from mosquito bites, contaminated needle sticks, combination vaccines and the simultaneous administration of multiple vaccines. Using two distantly related arenaviruses, lymphocytic choriomeningitis virus (LCMV) and Pichinde virus (PICV), we questioned if immunological T cell memory and subsequent protection would be altered following a simultaneous co-infection, where two immune responses are generated within the same host at the same time. Coinfection with these two viruses, which require CD8 T cell responses to clear, resulted in decreased immune protection and enhanced immunopathology after challenge with either virus. After primary co-infection, each virus-specific immune response impacted the other as they competed within the same host and resulted in several significant differences in the CD8 T cell responses compared to mice infected with a single virus. Co-infected mice had a dramatic decrease in the overall size of the LCMV-specific CD8 T cell response and variability in which virus-specific response dominated, along with skewing in the immunodominance hierarchies from the normal responses found in single virus infected mice. The reduction in the number of LCMV-specific CD8 memory T cells, specifically cells with an effector memory-like phenotype, was associated with higher viral loads and increased liver pathology in co-infected mice upon LCMV challenge. The variability in the immunodominance hierarchies of co-infected mice resulted in an enhanced cross-reactive response in some mice that mediated enhanced immune-mediated fat pad pathology during PICV challenge. In both viral challenge models, an ineffective memory T cell response in…

The purpose of a forecast, in making an estimate about the future, is to give people information to act on. In the case of a coupled human system, a change in human behavior caused by the forecast can alter the course of events that were the subject of the forecast. In this context, the forecast is an integral part of the coupled human system, with two-way feedback between forecast output and human behavior. However, forecasting programs generally do not examine how the forecast might affect the system in question. This study examines how such a coupled system works using a model of viral infection—the susceptible-infected-removed (SIR) model—when the model is used in a forecasting context. Human behavior is modified by making the contact rate responsive to other dynamics, including forecasts, of the SIR system. This modification creates two-way feedback between the forecast and the infection dynamics. Results show that a faster rate of response by a population to system dynamics or forecasts leads to a significant decline in peak infections. Responding to a forecast leads to a lower infection peak than responding to current infection levels. Inaccurate forecasts can lead to either higher or lower peak infections depending on whether the forecast under-or over-estimates the peak. The direction of inaccuracy in a forecast determines whether the outcome is better or worse for the population. While work is still needed to constrain model functional forms, forecast feedback can be an important component of epidemic dynamics that should be considered in response planning.

Recent studies in mouse models of cancer and chronic viral infection applied genomic assays to profile various states of impaired T cell function and demonstrated that T cell dysfunction is epigenetically imprinted. However, comprehensive characterization of T cell dysfunction across models based on their epigenetic and transcriptional profiles is lacking. We reanalyzed a large collection of recently published chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data sets. After batch effect correction, we observed that epigenetic profiles of dysfunctional tumor-infiltrating T cells and exhausted T cells in chronic viral infection were surprisingly extremely similar. Furthermore, we observed that temporal progression towards dysfunction in chronic infection resembles that in tumorigenesis, and found that T cells committed to becoming dysfunctional early after activation. Motif analysis using generalized linear modeling allowed us to find candidate transcription factors associated with development of dysfunction in both immune settings. This analysis provides a better systematic understanding of cell-intrinsic mechanisms driving different functional states of CD8 T cells and demonstrates the power of systems biology approaches in cancer immunology. Citation Format: Yuri Pritykin, Christina Leslie. Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3384.

Preclinical studies in virological research are pivotal to comprehend mechanisms of viral virulence and pathogenesis and evaluate antiviral therapies or vaccines. Mouse models, through access to various genetic strains and amenable reagents, along with their ease of implementation and cost-effectiveness, remain the gold standard for establishing go/no-go thresholds before advancing to non-human primate or clinical studies. In preclinical mouse studies, standardized weight loss thresholds (WLTs)—which correspond to an established percentage of weight change at which animals are humanely euthanized—are a routine metric to quantitatively evaluate the lethality of a viral pathogen and the effectiveness of antiviral countermeasures in preventing fatal viral disease. While it is recognized that WLTs can significantly impact the assessment of viral virulence, they are often established to meet existing ethical or methodological requirements, rather than being based on a specific scientific rationale. Here, we examine how various experimental variables—including mouse and viral strains and the sex ratio within a mouse cohort—influence the ability of a WLT to support the generation of robust mouse models of fatal viral infection. Using various mouse strains and viral pathogens, we report that variations in experimental conditions in mouse preclinical studies can significantly compromise the performance of a non-adjusted WLT to yield an accurate estimate of viral virulence. Our findings advocate for a robust adjustment of WLT to each experimental framework and associated variables to establish mouse models of fatal viral infection that can generate high-resolution data acquisition while upholding ethical standards. Overall, our study provides methodological insights to enhance the unbiased acquisition and benchmarking of viral virulence and antiviral efficacy data in mouse models.

Interferon-$alpha; for hepatitis C: antiviral or immunotherapy?

In this paper, a class of virus infection models with CTLs response is considered. We incorporate an immune delay and two intracellular delays into the virus infection model. It is found that only incorporating two intracellular delays almost does not change the dynamics of the system, but incorporating an immune delay changes the dynamics of the system very greatly, namely, a Hopf bifurcation and oscillations can appear. Those results show immune delay dominates intracellular delays in some viral infection models, which indicates the human immune system has a special effect in virus infection models with CTLs response, and the human immune system itself is very complicated. In fact, people are aware of the complexity of the human immune system in medical science, which coincides with our investigating. We also investigate the global Hopf bifurcation of the system with the immune delay as a bifurcation parameter.

This paper presents two viral infection models that describe dynamics of the virus under the effect of two distinct types of antibodies. The first model considers the population of five compartments, target cells, infected cells, free virus particles, antibodies type-1 and antibodies type-2. The presence of two types of antibodies can be a result of secondary viral infection. In the second model, we incorporate the latently infected cells. We assume that the antibody responsiveness is given by a combination of the self-regulating antibody response and the predator–prey-like antibody response. For both models, we verify the nonnegativity and boundedness of their solutions, then we outline all possible equilibria and prove the global stability by constructing proper Lyapunov functions. The stability of the uninfected equilibrium EQ0 and infected equilibrium EQ* is determined by the basic reproduction number R0. The theoretical findings are verified through numerical simulations. According to the outcomes, the trajectories of the solutions approach EQ0 and EQ* when R0≤1 and R0&gt;1, respectively. We study the sensitivity analysis to show how the values of all the parameters of the suggested model affect R0 under the given data. The impact of including the self-regulating antibody response and latently infected cells in the viral infection model is discussed. We showed that the presence of the self-regulating antibody response reduces R0 and makes the system more stabilizable around EQ0. Moreover, we established that neglecting the latently infected cells in the viral infection modeling leads to the design of an overflow of antiviral drug therapy.

The exacerbation of asthma during viral infections is mainly explained by neutrophils infiltrating into the airways. However, enhanced functions of eosinophils are also observed. The aim of this study was to reveal the mechanism of how eosinophils are activated during and after viral infection of the airways, using a model of viral infection. A synthetic double-stranded RNA, poly inosinic-cytidyric acid (poly(IC)), was transfected to a human airway epithelial cell line (BEAS-2B) and the primary bronchial epithelial cells, to mimic a viral infection. The production of chemokines from the cells was investigated. The transfection of poly(IC), alone, marginally affected the eotaxin-3 production of the cells. However, the transfection of poly(IC) prior to interleukin (IL)-4 stimulation enhanced eotaxin-3 production. Poly(IC) transfection increased mRNA and protein expressions of IL-4 receptor (R)alpha and IL-2Rgamma, components of the IL-4R. In BEAS-2B cells, IL-4-mediated phosphorylation of signal transducer and activator of transcription six was enhanced in poly(IC) transfected cells. This was reversed by the addition of anti-IL-4Ralpha antibody, suggesting the role of an increased number of IL-4 receptors in enhanced IL-4-induced eotaxin-3 production. Poly(IC)-induced upregulation of IL-4Ralpha was inhibited by treatment with cycloheximide or dexamethasone. In conclusion, these results suggest that viral airway infection may enhance interleukin-4-induced eotaxin-3 production through upregulation of the interleukin-4 receptor in airway epithelial cells.