Infected Cell Density Research Articles

Viral infection dynamics with immune chemokines and CTL mobility modulated by the infected cell density.

We study a viral infection model incorporating both cell-to-cell infection and immune chemokines. Based on experimental results in the literature, we make a standing assumption that the cytotoxic T lymphocytes (CTL) will move toward the location with more infected cells, while the diffusion rate of CTL is a decreasing function of the density of infected cells. We first establish the global existence and ultimate boundedness of the solution via a priori energy estimates. We then define the basic reproduction number of viral infection and prove (by the uniform persistence theory, Lyapunov function technique and LaSalle invariance principle) that the infection-free steady state is globally asymptotically stable if . When , then becomes unstable, and another basic reproduction number of CTL response becomes the dynamic threshold in the sense that if , then the CTL-inactivated steady state is globally asymptotically stable; and if , then the immune response is uniform persistent and, under an additional technical condition the CTL-activated steady state is globally asymptotically stable. To establish the global stability results, we need to prove point dissipativity, obtain uniform persistence, construct suitable Lyapunov functions, and apply the LaSalle invariance principle.

Identification of optimal flow rate for culture media, cell density, and oxygen toward maximization of virus production in a fed-batch baculovirus-insect cell system.

In recent times, it has been realized that novel vaccines are required to combat emerging disease outbreaks, and faster optimization is required to respond to global vaccine demands. Although, fed-batch operations offer better productivity, experiment-based optimization of a new fed-batch process remains expensive and time-consuming. In this context, we propose a novel computational framework that can be used for process optimization and control of a fed-batch baculovirus-insect cell system. Since the baculovirus expression vector system (BEVS) is known to be widely used platforms for recombinant protein/vaccine production, we chose this system to demonstrate the identification of optimal profile. Toward this, first, we constructed a mathematical model that captures the time course of cell and virus growth in a baculovirus-insect cell system. Second, the proposed model was used for numerical analysis to determine the optimal operating profiles of control variables such as culture media, cell density, and oxygen based on a multiobjective optimal control formulation. Third, a detailed comparison between batch and fed-batch culture was perfromed along with a comparison between various alternatives of fed-batch operation. Finally, we demonstrate that a model-based quantification of controlled feed addition in fed-batch culture is capable of providing better productivity as compared to a batch culture. The proposed framework can be utilized for the estimation of optimal operating regions of different control variables to achieve maximum infected cell density and virus yield while minimizing the substrate/media, uninfected cell, and oxygen consumption.

Toward Performance Improvement of a Baculovirus–Insect Cell System under Uncertain Environment: A Robust Multiobjective Dynamic Optimization Approach for Semibatch Suspension Culture

The baculovirus expression vector system (BEVS) is one of the well-known versatile platforms for the recombinant protein/vaccine production. Mathematical modeling and optimization of a baculovirus–insect cell system can have significant industrial relevance as this reduces the number of expensive experiments and time involved in the experiment-based optimization. However, modeling and control of such a nonlinear system remains challenging due to the presence of uncertainties in the model. In this context, we propose a novel computational framework combining the principles of systems biology and dynamic optimization under uncertainty for optimizing a semibatch baculovirus–insect cell system. Toward this, first, a mathematical model replicating the dynamic experimental data on cell and virus growth was identified. Next, the proposed model was used for deterministic multiobjective dynamic optimization of the control variables, substrate, and multiplicity of infection (MOI) to achieve the conflicting objectives of productivity maximization and substrate minimization, simultaneously. Finally, based on the sensitivity analysis, six of the most influential parameters depicting model uncertainties have been considered for the robust multiobjective optimal control of the system. A comprehensive comparison displays up to 114% and 76% increases in the cell densities for the deterministic and stochastic semibatch processes, respectively, compared to the batch process. Semibatch operation also favors a minimum 40% reduction in MOI required to achieve the same level of infected cell density compared to the batch operation. This study provides a generic methodology for exhibiting a proof of concept that a semibatch suspension culture considering uncertainty in model parameters can give better productivity compared to a batch suspension culture for a BEVS.

Development of an In Vivo Probe to Track SARS-CoV-2 Infection in Rhesus Macaques.

Infection with the novel coronavirus, SARS-CoV-2, results in pneumonia and other respiratory symptoms as well as pathologies at diverse anatomical sites. An outstanding question is whether these diverse pathologies are due to replication of the virus in these anatomical compartments and how and when the virus reaches those sites. To answer these outstanding questions and study the spatiotemporal dynamics of SARS-CoV-2 infection a method for tracking viral spread in vivo is needed. We developed a novel, fluorescently labeled, antibody-based in vivo probe system using the anti-spike monoclonal antibody CR3022 and demonstrated that it could successfully identify sites of SARS-CoV-2 infection in a rhesus macaque model of COVID-19. Our results showed that the fluorescent signal from our antibody-based probe could differentiate whole lungs of macaques infected for 9 days from those infected for 2 or 3 days. Additionally, the probe signal corroborated the frequency and density of infected cells in individual tissue blocks from infected macaques. These results provide proof of concept for the use of in vivo antibody-based probes to study SARS-CoV-2 infection dynamics in rhesus macaques.

Global Existence of a Virus Infection Model with Saturated Chemotaxis

In this paper, a virus infection model with saturated chemotaxis is formulated and analyzed, where the chemotactic sensitivity for chemotactic movements of the cells is described. This model contains three state variables namely the population density of uninfected cells, the population density of infected cells and the concentration of virus particles, respectively. By virtue of regularized approximation technique and fixed point theorem, the local solvability of the regularized system corresponding to the original system is established. Then by extracting a suitable sequence along which the respective approximate solutions approach a limit in convenient topologies, with addition of Gagliardo-Nirenberg interpolation inequality as well as Lp-estimate techniques, we show that the original system describing the virus infection model exists at least one global weak solution. To illustrate the application of our theoretical results, an optimal control problem of the epidemic system is considered, where the admissible control domain is assumed to be a bounded closed convex subset. With the help of Aubin compactness theorem and lower semicontinuous of the cost functional, the existence of the optimal pair is proved. Our results generalize and improve partial previously known ones, and moreover, we first prove that the optimal control problem has at least one optimal pair.

Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium.

Neurological complications are common in patients with COVID-19. Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal pathogen of COVID-19, has been detected in some patient brains, its ability to infect brain cells and impact their function is not well understood. Here, we investigated the susceptibility of human induced pluripotent stem cell (hiPSC)-derived monolayer brain cells and region-specific brain organoids to SARS-CoV-2 infection. We found that neurons and astrocytes were sparsely infected, but choroid plexus epithelial cells underwent robust infection. We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. Together, our findings provide evidence for selective SARS-CoV-2 neurotropism and support the use of hiPSC-derived brain organoids as a platform to investigate SARS-CoV-2 infection susceptibility of brain cells, mechanisms of virus-induced brain dysfunction, and treatment strategies.

HIV-1 infection dynamics and optimal control with Crowley-Martin function response

Background and Objective: As we all know, mathematical models provide very important information for the study of the human immunodeficiency virus type. Mathematical model of human immunodeficiency virus type-1 (HIV-1) infection with contact rate represented by Crowley-Martin function response is taken into account. The aims of this novel study is to checkthe local and global stability of the disease and also prevent the outbreak from the community. Methods: The mathematical model as well as optimal system of nonlinear differential equations are tackled numerically by Runge-Kutta fourth-order method. For global stability we use Lyapunov-LaSalle invariance principle and for the description of optimal control, Pontryagin’s maximum principle is used. Results: Graphical results are depicted and examined with different parameters values versus the basic reproductive number R0 and also the plots with and without control. The density of infected cells continued to increase without treatment, but the concentration of these cells decreased after treatment. The intensity of the pathogenic virus before and after the optimal treatment. This indicates a sharp drop in the rate of pathogenic viruses after treatment. It prevents the production of viruses by preventing cell infection and minimizing side effects. Conclusions: We analysed the model by defining the basic reproductive number, showing the boundedness, positivity and permanence of the solution, and proving the local and global stability of the infection-free state. We show that the threshold quantity R0 < 1, the elimination of HIV-1 infection from the T cell population, is eradicated; while for the threshold quantity R0 > 1, HIV-1 infection remains in the host. When the threshold quantity R0 > 1, then it shows that the steady-state of chronic disease is globally stable. Optimal control strategies are developed with the optimal control pair for the description of optimal control. To reduce the density of infected cells and viruses as well as maximize the density of healthy cells is determined by the objective functional.

The Nonlinear Relations that Predict Influenza Viral Dynamics, Host Response, Pathology, and Disease Severity

Abstract Influenza A viruses cause a significant amount of morbidity and mortality. Understanding how the infection is controlled by host immune responses and how different factors influence severity are critical to combat the infection. During infection, virus increases exponentially, peaks, then declines until resolution. The viral decline is often biphasic, which we previously determined is a consequence of density-dependent infected cell clearance. The second, rapid clearance phase corresponds with the infiltration of CD8 T cells, but how the rate changes with infected cell density and CD8 density is unclear. Further, neither of these kinetics directly correlate to disease severity. Thus, we investigated these relations by infecting mice with influenza A/PR8, simultaneously measuring virus and CD8s, and developing/calibrating a kinetic model. The model predicts that virus resolution is sensitive to T cell expansion, that there is a critical CD8 magnitude below which the infection is significantly prolonged, and that the efficiency of CD8-mediated clearance is dependent on infected cell density. To further examine this finding and validate the model, we quantified infected cells kinetics using histomorphometry. These data showed that the area of lung infected reflects the predicted infected cell dynamics, and that the infection resolution dynamics parallel the relative CD8 magnitude. Our analysis further revealed a nonlinear relation between disease severity and the percent damaged lung. Establishing these critical connections that map the kinetics of virus, infected cells, T cells, lung pathology, and disease severity aids our ability to predict the course of infection, disease progression, and potential complications.

An analysis of functional curability on HIV infection models with Michaelis-Menten-type immune response and its generalization

Let HIV infection be modeled by a dynamical system with a Michaelis-Mente-type immune response. A functional cure refers to driving the system from a stable high-viral-load state to a stable low-viral-load state. This may occur only when at least two stable equilibrium states coexist in the system. This paper analyzes how the number of biologically meaningful equilibrium states varies with system parameters. Meanwhile, it investigates how patients' profiles of immune responses determine their clinical outcomes, with focus on functional curability. The analysis provides a criterion that a functional cure is possible only if the capability of immune stimulation starts to attenuate when the density of infected cells is below a threshold. From treatment viewpoints, such a criterion is crucial because it identifies which patients cannot use a low-viral-load state as a treatment endpoint. The deriving process also provides a method to study functional curability problems with a wider class of immune response functions and functional curability problems of similar virus infections such as chronic hepatitis B virus infection.

Persistence of low levels of plasma viremia and of the latent reservoir in patients under ART: A fractional-order approach

Low levels of viral load are found in HIV-infected patients, after many years under successful suppressive anti-retroviral therapy (ART). The factors leading to this persistence are still under debate, but it is now more or less accepted that the latent reservoir may be crucial to the maintenance of this residual viremia. In this paper, we study the role of the latent reservoir in the persistence of the latent reservoir and of the plasma viremia in a fractional-order (FO) model for HIV infection. Our model assumes that (i) the latently infected cells may undergo bystander proliferation, without active viral production, (ii) the latent cell activation rate decreases with time on ART, (iii) the productively infected cells’ death rate is a function of the infected cell density. The proposed model provides new insights on the role of the latent reservoir in the persistence of the latent reservoir and of the plasma virus. Moreover, the fractional-order derivative distinguishes distinct velocities in the dynamics of the latent reservoir and of plasma virus. The later may be used to better approximations of HIV-infected patients data. To our best knowledge, this is the first FO model that deals with the role of the latent reservoir in the persistence of low levels of viremia and of the latent reservoir.

A diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis

From a biological perspective, a diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis is proposed. In the model, the diffusion of virus consists of two parts, the random diffusion and the chemotactic movement. The chemotaxis flux of virus depends not only on their own density, but also on the density of infected cells, and the density gradient of infected cells. The well posedness of the proposed model is deeply investigated. For the proposed model, the linear stabilities of the infection-free steady state E0 and the infection steady state E* are extensively performed. We show that the threshold dynamics can be expressed by the basic reproduction number R0 of the model without chemotaxis. That is, the infection-free steady state E0 is globally asymptotically stable if R0 < 1, and the virus is uniformly persistent if R0 > 1. In addition, we use the cross iteration method and the Schauder’s fixed point theorem to prove the existence of travelling wave solutions connecting the infection-free steady state E0 and the infection steady state E* by constructing a pair of upper-lower solutions. At last, numerical simulations are presented to confirm theoretical findings.

A NECESSARY CONDITON ON THE FUNCTIONAL CURABILITY OF HIV INFECTION

Let the Human Immunodeficiency Virus (HIV) infection be mod- eled by a dynamical system. A classical result shows that if the basic reproduc- tion number is less than one, the system eventually reaches the virus eradication state. If it is greater than one, the virus population sustains within hosts. In the latter case, treatments are required for patients with persistent high vi- ral load. However, in the treatment of this infection, it is usually difficult to completely eliminate the within-host viruses for infected patients. Recently, a treatment goal set up by the medical society is to achieve a functional cure for patients. A functional cure in the treatment of HIV infection is to permanently suppress the virus replication or to lead to patients' long-term remission state without completely eliminating the within-host viruses. In our previous study, we extend the classical result and show that a functional cure is possible only if the capability of patients' immune stimulation starts to attenuate when the density of infected cells is below a threshold. In this study, we show that the conclusion is still valid in a more accurate model proposed by Adams, Banks et al. This finding implies that the reached conclusion is robust under different accuracy in modeling HIV infection and suggests that it is the fundamental principle in governing the the phenomenon of a functional cure.

Decline in Helicoverpa armigera nucleopolyhedrovirus occlusion body yields with increasing infection cell density in vitro is strongly correlated with viral DNA levels.

The phenomenon of the reduction in the cell-specific yield with increasing infection cell density (ICD), the cell density effect, is one of the main hurdles for improving virus yields in vitro. In the current study, the reduction in cell-specific yields (viral DNA [vDNA], polyhedrin mRNA and occlusion body [OB]) with increasing ICD for Helicoverpa armigera nucleopolyhedrovirus (HearNPV)-infected HzAM1 (Helicoverpa zea) insect cells has been investigated. HzAM1 cells were propagated in Sf900™ III serum-free medium and synchronously infected with wild-type HearNPV at various ICDs of 0.5-5×10(6)cells/mL at an MOI of 5PFU/cell. Infection was conducted either in the original medium or in fresh medium. As found previously for Sf9 and High Five cells, there were negative correlations between the three key virus infection indicators (vDNA, mRNA and OB) and the peak cell density (PCD). Generally, the yield decline with increasing PCD was most pronounced for OB, followed by mRNA, and was more moderate for vDNA. The decline was significantly reduced, but not totally arrested, when fresh medium was used. There were also strong correlations between OB and mRNA, mRNA and vDNA, and OB and vDNA levels. These results suggest that the reduction in baculovirus yield (OB) at high PCDs is associated with limitations during the upstream processes of replication and transcription together with limitations during protein translation. Furthermore, the peak protein productivity per unit of cell volume in the HzAM1/HearNPV system was shown to be higher than that of the Sf9/rAcMNPV system, but lower than that of the High Five/rAcMNPV system.

Effect of the peak cell density of recombinant AcMNPV-infected Hi5 cells on baculovirus yields.

The phenomenon of the cell density effect is not readily explained by an obvious nutrient limitation, and a recent study has suggested that for recombinant Autographa californica multiple nucleopolyhedrovirus (rAcMNPV)-infected Sf9 cells, a drop in messenger RNA (mRNA) levels may be sufficient to explain the cell density effect for this system. The current study aims to investigate the response in cell-specific yields (viral DNA (vDNA), LacZ mRNA and β-galactosidase (β-Gal) protein) with increasing infection cell density (ICD) for rAcMNPV-infected Hi5 cells, where the rAcMNPV expresses the β-Gal gene under control of the polyhedral promoter. Hi5 cells in suspension culture of Express Five® medium were synchronously infected with a rAcMNPV at multiple ICDs between 0.5 and 6 × 10(6) cells/mL and a multiplicity of infection of 10 plaque-forming units (PFU)/cell either in the original or fresh medium conditions. There were negative correlations between the three key virus infection indicators (vDNA, mRNA and β-Gal) and the peak cell density (PCD). However, unlike infected Sf9 cells, the yield decline started at the lowest PCD investigated (0.6 × 10(6) cells/mL). Generally, the yield decline with increasing PCD was most pronounced for β-Gal followed by mRNA and was more moderate for vDNA. The decline was significantly reduced but not totally arrested when fresh medium replacement was used. The results suggest that the reduction in recombinant protein-specific yields at high PCDs is associated with limitations during the up-stream processes of replication and transcription rather than entirely caused by limitations during translation. In addition, low production rates at late infection stages of moderate to high ICDs are a probable cause of the cell density effect.

Complex dynamic behavior in a viral model with state feedback control strategies.

With the consideration of mechanism of prevention and control for the spread of viral diseases, in this paper, we propose two novel virus dynamics models where state feedback control strategies are introduced. The first model incorporates the density of infected cells (or free virus) as control threshold value; we analytically show the existence and orbit stability of positive periodic solution. Theoretical results imply that the density of infected cells (or free virus) can be controlled within an adequate level. The other model determines the control strategies by monitoring the density of uninfected cells when it reaches a risk threshold value. We analytically prove the existence and orbit stability of semi-trivial periodic solution, which show that the viral disease dies out. Numerical simulations are carried out to illustrate the main results.

Metabolic and Kinetic analyses of influenza production in perfusion HEK293 cell culture

BackgroundCell culture-based production of influenza vaccine remains an attractive alternative to egg-based production. Short response time and high production yields are the key success factors for the broader adoption of cell culture technology for industrial manufacturing of pandemic and seasonal influenza vaccines. Recently, HEK293SF cells have been successfully used to produce influenza viruses, achieving hemagglutinin (HA) and infectious viral particle (IVP) titers in the highest ranges reported to date. In the same study, it was suggested that beyond 4 × 106 cells/mL, viral production was limited by a lack of nutrients or an accumulation of toxic products.ResultsTo further improve viral titers at high cell densities, perfusion culture mode was evaluated. Productivities of both perfusion and batch culture modes were compared at an infection cell density of 6 × 106 cells/mL. The metabolism, including glycolysis, glutaminolysis and amino acids utilization as well as physiological indicators such as viability and apoptosis were extensively documented for the two modes of culture before and after viral infection to identify potential metabolic limitations. A 3 L bioreactor with a perfusion rate of 0.5 vol/day allowed us to reach maximal titers of 3.3 × 1011 IVP/mL and 4.0 logHA units/mL, corresponding to a total production of 1.0 × 1015 IVP and 7.8 logHA units after 3 days post-infection. Overall, perfusion mode titers were higher by almost one order of magnitude over the batch culture mode of production. This improvement was associated with an activation of the cell metabolism as seen by a 1.5-fold and 4-fold higher consumption rates of glucose and glutamine respectively. A shift in the viral production kinetics was also observed leading to an accumulation of more viable cells with a higher specific production and causing an increase in the total volumetric production of infectious influenza particles.ConclusionsThese results confirm that the HEK293SF cell is an excellent substrate for high yield production of influenza virus. Furthermore, there is great potential in further improving the production yields through better control of the cell culture environment and viral production kinetics. Once accomplished, this cell line can be promoted as an industrial platform for cost-effective manufacturing of the influenza seasonal vaccine as well as for periods of peak demand during pandemics.

A PARABOLIC–HYPERBOLIC FREE BOUNDARY PROBLEM MODELLING TUMOR TREATMENT WITH VIRUS

We consider a procedure for cancer therapy which consists of injecting replication-competent viruses into the tumor. The viruses infect tumor cells, replicate inside them, and eventually cause their death. As infected cells die, the viruses inside them are released and then proceed to infect adjacent tumor cells. However, a major factor influencing the efficacy of virus agents is the immune response that may limit the replication and spread of the replication-competent virus. The competition between tumor cells, a replication-competent virus and an immune response is modelled as a free boundary problem for a nonlinear system of partial differential equations, where the free boundary is the surface of the tumor. In this model, the immune response equation is a semilinear parabolic equation, including a chemotaxis term which is used to describe the movement of the immune response induced by gradients of the infected cell density. Under the assumption that the chemotactic sensitivity coefficient is small compared with the diffusion coefficient of the immune response, we prove the global existence and uniqueness of the solution of this free boundary problem. For large chemotactic coefficient, the global existence is still open.

The biopesticide market for global agricultural use

The biopesticide market for global agricultural use

HIV-1 Infection and Low Steady State Viral Loads

Highly active antiretroviral therapy (HAART) reduces the viral burden in human immunodeficiency virus type 1 (HIV-1) infected patients below the threshold of detectability. However, substantial evidence indicates that viral replication persists in these individuals. In this paper we examine the ability of several biologically motivated models of HIV-1 dynamics to explain sustained low viral loads. At or near drug efficacies that result in steady state viral loads below detectability, most models are extremely sensitive to small changes in drug efficacy. We argue that if these models reflect reality many patients should have cleared the virus, contrary to observation. We find that a model in which the infected cell death rate is dependent on the infected cell density does not suffer this shortcoming. The shortcoming is also overcome in two more conventional models that include small populations of cells in which the drug is less effective than in the main population, suggesting that difficulties with drug penetrance and maintenance of effective intracellular drug concentrations in all cells susceptible to HIV infection may underlie ongoing viral replication.

Rational scale-up of a baculovirus-insect cell batch process based on medium nutritional depth

We have developed a serum-free cell culture process utilizing a recombinant baculovirus (AcNPV) expression vector to infect Trichoplusia ni insect cells for the production of the human lysosomal enzyme, glucocerebrosidase. The enzyme, which is harvested as a secreted protein in this process, can serve as a replacement therapy for the genetic deficiency Gaucher disease. In the course of pilot scale-up of a batch glucocerebrosidase process from 25-mL working volume shaker flask units to 25-L working volume stirred bioreactor units, a semi-empirical model was developed for the rational determination of scaleable process parameters, including host cell density at infection, multiplicity of infection (MOI), and harvest time. A key assumption of the model is that maximum protein production is limited by the serum-free medium's nutritional capacity, which can, in turn, be determined from the growth of uninfected cells. For the host cell/medium combination used in this study, the nutritional limit was determined to be 1.3 x 10(7) to 1.7 x 10(7) viable-cell-days/mL. Based on this, the model predicts that optimal protein expression is consistent with a 4-day batch process where the host cell density at the time of infection is 1.5 x 10(6) to 2.0 x 10(6) cells/mL and the MOI is 0.09-0.3. These parameters were empirically confirmed to give the highest achievable batch product yield, first in shaker flasks and then at larger scales. The low MOI allows at least one population doubling to take place post viral addition, so that the effective infected cell density producing product generally exceeds 4 x 10(6) cells/mL. It was also interesting to note that this process consistently achieved the same level of maximum protein production at the 25-L bioreactor scale in 4 days compared to 5 days at the shaker flask scale. This may be attributable to better control of the culture environment in the bioreactor. Unlike some other lepidopteran insect cells, such as Sf-9, T. ni cells were found to produce significant levels of the inhibitory metabolites ammonia and lactate. Our results suggest that reduction and/or removal of inhibitory metabolites might be beneficial for infection of high-density cultures of these cells and might also facilitate application of more sophisticated culture strategies, including fed-batch. (c) 1996 John Wiley & Sons, Inc.