Viral blip dynamics during highly active antiretroviral therapy

Although intermittent episodes of low-level viremia are often observed in well-suppressed highly active antiretroviral therapy (HAART)-treated patients, the timing and amplitude of viral blips have never been examined in detail. We analyze here the dynamics of viral blips, i.e., plasma VL measurements of >50 copies/ml, in 123 HAART-treated patients monitored for a mean of 2.6 years (range, 5 months to 5.3 years). The mean (+/- the standard deviation) blip frequency was 0.09 +/- 0.11/sample, with about one-third of patients showing no viral blips. The mean viral blip amplitude was 158 +/- 132 human immunodeficiency virus type 1 (HIV-1) RNA copies/ml. Analysis of the blip frequency and amplitude distributions suggest that two blips less than 22 days apart have a significant chance of being part of the same episode of viremia. The data are consistent with a hypothetical model in which each episode of viremia consists of a phase of VL rise, followed by two-phase exponential decay. Thus, the term "viral blip" may be a misnomer, since viral replication appears to be occurring over an extended period. Neither the frequency nor the amplitude of viral blips increases with longer periods of observation, but the frequency is inversely correlated with the CD4(+)-T-cell count at the start of therapy, suggesting that host-specific factors but not treatment fatigue are determinants of blip frequency.     

Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection.

Mathematical modeling of viral replication dynamics, based on sequential measurements of levels of virion-associated RNA in plasma during antiretroviral treatment, has led to fundamental new insights into human immunodeficiency virus type 1 pathogenesis. We took advantage of the simian immunodeficiency virus (SIV)-infected macaque model to perform detailed measurements and mathematical modeling during primary infection and during treatment of established infection with the antiretroviral drug (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA). The calculated clearance half-life for productively infected cells during resolution of the peak viremia of primary infection was on the order of 1 day, with slightly shorter clearance half-lives calculated during PMPA treatment. Viral reproduction rates upon discontinuation of PMPA treatment after 2 weeks were approximately twofold greater than those obtained just prior to initiation of treatment in the same animals, likely reflecting accumulation of susceptible target cells during treatment. The basic reproductive ratio (R0) for the spread of SIV infection in vivo, which represents the number of productively infected cells derived from each productively infected cell at the beginning of infection, was also estimated. This parameter quantifies the extent to which antiviral therapy or vaccination must limit the initial spread of virus to prevent establishment of chronic disseminated infection. The results thus provide an important guide for efforts to develop vaccines against SIV and, by extension, human immunodeficiency virus.     

Evidence for polymicrobic flora translocating in peripheral blood of HIV-infected patients with poor immune response to antiretroviral therapy

In advanced HIV infection, the homeostatic balance between gastrointestinal indigenous bacteria and gut immunity fails and microbes are able to overcome the intestinal barrier and gain the systemic circulation. Because microbial translocation is not fully controlled by antiviral therapy and is associated with inefficient CD4+ reconstitution, we investigated the profile of translocating bacteria in peripheral blood of 44 HIV-infected patients starting therapy with advanced CD4+ T-lymphopenia and displaying poor CD4+ recovery on virologically suppressive HAART. According to CD4+ reconstitution at 12-months HAART, patients were considered Partial Immunological Responders, PIRs (CD4+≥250/µl, n = 29) and Immunological non Responders, INRs (CD4+<200/µl, n = 15)). We show that PIRs and INRs present similarly elevated plasma levels of lipopolysaccharide (LPS) and its ligand sCD14 that were not lowered by virologically suppressive therapy. Bacterial 16S rRNA gene amplification and sequencing resulted in a highly polymicrobic peripheral blood microbiota both prior and after 12-month HAART. Several differences in bacterial composition were shown between patients'' groups, mainly the lack of probiotic Lactobacillaceae both prior and after therapy in INRs. Failure to control microbial translocation on HAART is associated with a polymicrobic flora circulating in peripheral blood that is not substantially modified by therapy.     

Bifurcation analysis of the Nowak-Bangham model in CTL dynamics

This paper investigates the local bifurcations of a CTL response model published by Nowak and Bangham [M.A. Nowak, C.R.M. Bangham, Population dynamics of immune responses to persistent viruses, Science 272 (1996) 74]. The Nowak-Bangham model can have three equilibria depending on the basic reproduction number, and generates a Hopf bifurcation through two bifurcations of equilibria. The main result shows a sufficient condition for the interior equilibrium to have a unique bifurcation point at which a simple Hopf bifurcation occurs. For this proof, some new techniques are developed in order to apply the method established by Liu [W.M. Liu, Criterion of Hopf bifurcations without using eigenvalues, J. Math. Anal. Appl. 182 (1) (1994) 250]. In addition, to demonstrate the result obtained theoretically, some bifurcation diagrams are presented with numerical examples.     

Model with two types of CTL regulation and experiments on CTL dynamics

Recently, we developed a mathematical model of interaction between the HIV and the immune system to match various dynamic experiments carried out in HIV-infected humans and SIV-infected macaques. The model includes helper cell-dependent and helper cell-independent cytotoxic lymphocytes (CTLs) and predicts two stable steady states, a state with a high virus load and few helper cells, and another state with a low virus load and many helper cells. Here we upgrade the model to take into account recent reports on the link between the activation status of infected cells and their ability to produce virus, the effect of helper cells at the time of priming on CTL differentiation, and virus dynamics in unvaccinated macaques with a broad genetic background acutely infected with SIVmac251. We also discuss in detail the experimental justification of the CTL block and the robustness of model predictions with respect to the hypothesis of two CTL subtypes.     

The stationary distribution and extinction of a double thresholds HTLV-I infection model with nonlinear CTL immune response disturbed by white noise

This paper investigates the stochastic HTLV-I infection model with CTL immune response,and the corresponding deterministic model has two basic reproduction numbers.We consider the nonlinear CTL immune response for the interaction between the virus and the CTL immune cells.Firstly,for the theoretical needs of system dynamical behavior,we prove that the stochastic model solution is positive and global.In atldition,we obtain the existence of ergodic stationary distribution by stochastic Lyapunov functions.Meanwhile,sufficient condition for the extinction of the stochastic system is acquired.Reasonably,the dynamical behavior of deterministic model is included in our result of stochastic model when the white noise disappears.     

A Cayley tree immune network model with antibody dynamics

A Cayley tree model of idiotypic networks that includes both B cell and antibody dynamics is formulated and analysed. As in models with B cells only, localized states exist in the network with limited numbers of activated clones surrounded by virgin or near-virgin clones. The existence and stability of these localized network states are explored as a function of model parameters. As in previous models that have included antibody, the stability of immune and tolerant localized states are shown to depend on the ratio of antibody to B cell lifetimes as well as the rate of antibody complex removal. As model parameters are varied, localized steady-states can break down via two routes: dynamically, into chaotic attractors, or structurally into percolation attractors. For a given set of parameters percolation and chaotic attractors can coexist with localized attractors, and thus there do not exist clear cut boundaries in parameter space that separate regions of localized attractors from regions of percolation and chaotic attractors. Stable limit cycles, which are frequent in the two-clone antibody B cell (AB) model, are only observed in highly connected networks. Also found in highly connected networks are localized chaotic attractors. As in experiments by Lundkvistet al. (1989.Proc. natn. Acad. Sci. U.S.A. 86, 5074–5078), injection ofAb ₁ antibodies into a system operating in the chaotic regime can cause a cessation of fluctuations ofAb ₁ andAb ₂ antibodies, a phenomenon already observed in the two-clone AB model. Interestingly, chaotic fluctuations continue at higher levels of the tree, a phenomenon observed by Lundkvistet al. but not accounted for previously.     

Competition between CTL narrows the immune response induced by prime-boost vaccination protocols

Recombinant vaccines encoding strings of virus- or tumor-derived peptides and/or proteins are currently being designed for use against both cancer and infectious diseases. These vaccines aim to induce cytotoxic immune responses against several Ags simultaneously. We developed a novel tetramer-based technique, based on chimeric HLA A2/H-2K(b) H chains, to directly monitor the CTL response to such vaccines in HLA-A2 transgenic mice. We found that priming and boosting with the same polyepitope construct induced immune responses that were dominated by CTL of a single specificity. When a mixture of viruses encoding single proteins was used to boost the polyepitope primed response, CTL of multiple specificities were simultaneously expanded to highly effective levels in vivo. In addition, we show that a preexisting response to one of the epitopes encoded within a polyepitope construct significantly impaired the ability of the vaccine to expand CTL of other specificities. Our findings define a novel vaccination strategy optimized for the induction of an effective polyvalent cytotoxic response.     

Global properties of nested network model with application to multi-epitope HIV/CTL dynamics

Mathematical modeling and analysis can provide insight on the dynamics of ecosystems which maintain biodiversity in the face of competitive and prey–predator interactions. Of primary interests are the underlying structure and features which stabilize diverse ecological networks. Recently Korytowski and Smith (Theor Ecol 8(1):111–120, 2015) proved that a perfectly nested infection network, along with appropriate life history trade-offs, leads to coexistence and persistence of bacteria-phage communities in a chemostat model. In this article, we generalize their model in order to apply it to the within-host dynamics virus and immune response, in particular HIV and CTL (Cytotoxic T Lymphocyte) cells. Our model can describe sequential viral escape from dominant immune responses and rise in subdominant immune responses, consistent with observed patterns of HIV/CTL evolution. We find a Lyapunov function for the system which leads to rigorous characterization of persistent viral and immune variants, along with informing upon equilibria stability and global dynamics. Results are interpreted in the context of within-host HIV/CTL evolution and numerical simulations are provided.

     

Dual pressure from antiretroviral therapy and cell-mediated immune response on the human immunodeficiency virus type 1 protease gene

Human immunodeficiency virus (HIV)-specific CD8(+) T-lymphocyte pressure can lead to the development of viral escape mutants, with consequent loss of immune control. Antiretroviral drugs also exert selection pressures on HIV, leading to the emergence of drug resistance mutations and increased levels of viral replication. We have determined a minimal epitope of HIV protease, amino acids 76 to 84, towards which a CD8(+) T-lymphocyte response is directed. This epitope, which is HLA-A2 restricted, includes two amino acids that commonly mutate (V82A and I84V) in the face of protease inhibitor therapy. Among 29 HIV-infected patients who were treated with protease inhibitors and who had developed resistance to these drugs, we show that the wild-type PR82V(76-84) epitope is commonly recognized by cytotoxic T lymphocytes (CTL) in HLA-A2-positive patients and that the CTL directed to this epitope are of high avidity. In contrast, the mutant PR82A(76-84) epitope is generally not recognized by wild-type-specific CTL, or when recognized it is of low to moderate avidity, suggesting that the protease inhibitor-selected V82A mutation acts both as a CTL and protease inhibitor escape mutant. Paradoxically, the absence of a mutation at position 82 was associated with the presence of a high-avidity CD8(+) T-cell response to the wild-type virus sequence. Our results indicate that both HIV type 1-specific CD8(+) T cells and antiretroviral drugs provide complex pressures on the same amino acid sequence of the HIV protease gene and, thus, can influence viral sequence evolution.     

HIV-1 dynamics at different time scales under antiretroviral therapy

We exploit a model that considers three compartments: blood plasma (BP), lymphoid tissue-interstitial spaces (LT-IS), and follicular dendritic cells (FDC), for the HIV-1 dynamics under the application of highly active antiretroviral therapy (HAART) which allowed us to unravel distinct viral dynamics occurring in short- (2 days), middle- (21 days), and long-term (183 days) time scales. The different time scales are determined by the viral clearance rate, the ratio of productively infected CD4⁺ T cells to chronically infected cells, and the dissociation rate of HIV-1 complexes from FDC. This generates a scenario in which, after an initial transient stage, the viral BP dynamics decouples and becomes governed by the lymphoid tissue (LT) dynamics; in a later stage, a new decoupling occurs in which the LT-IS dynamics is slaved to that of the FDC dynamics. We observed an initial increase in the viremia after HAART in a patient who did not receive protease inhibitors (PI). By means of the above-mentioned model we were able to highlight the relevant parameters which need to be estimated at three different time scales after HAART.     

Multi-way flow cytometric immune monitoring of antiretroviral therapy in HIV-infected children

In 40 HIV-infected children, 8-10 years old, belonging to the category A state of infection, the following flow-cytometric parameters were scored: percentage levels of different blood lymphocytes; surface expression of some activation and memory markers in CD4+ cells; switch to Th1 or Th2 of in vitro -stimulated CD4+ cell, tested by intracellular production of interleukin-2 or interleukin-4. Each investigation was carried out both before and 3 months after antiretroviral therapy (AZT and ddC). Some post-therapy changes concerning blood lymphocyte percentages were noticed, not only within CD4+ subpopulation, but also within CD8+, HLA-DR+/CD3 (T-activated) and CD16+CD56+ cells, respectively. On the other hand, following antiretroviral treatment, in HIV- originated CD4+ fresh cells, an improvement of pre-therapy increased values of surface activation (CD69, CD25) markers on memory (CD45RO+) cells, as well as of pre-therapy reduced rate of switching to Th1, revealed by intracellular interleukin-2 synthesis, was found. The significance of data obtained in the multi-way immune monitoring of antiretroviral therapy, in pediatric AIDS, as an additional investigation panel, is discussed.     

Approximate solution of a model of biological immune responses incorporating delay

A model of the humoral immune response, proposed by Dibrov, Livshits and Volkenstein (1977b), in which the antibody production by a constant target cell population depends on the antigenic stimulation at earlier times, is considered from an analytic standpoint. A method of approximation based on a consideration of the asymptotic limit of large delay in the antibody response is shown to be applicable, and to give results similar to those obtained numerically by the above authors. The relevance of this type of approximation to other systems exhibiting outbreak phenomena is discussed.     

A shift in the phenotype of melan-A-specific CTL identifies melanoma patients with an active tumor-specific immune response

In a significant proportion of melanoma patients, CTL specific for the melan-A(26/7-35) epitope can be detected in peripheral blood using HLA-A2/peptide tetramers. However, the functional capacity of these CTL has been controversial, since although they prove to be effective killers after in vitro expansion, in some patients they have blunted activation responses ex vivo. We used phenotypic markers to characterize melan-A tetramer(+) cells in both normal individuals and melanoma patients, and correlated these markers with ex vivo assays of CTL function. Melanoma patients with detectable melan-A tetramer(+) cells in peripheral blood fell into two groups. Seven of thirteen patients had a CCR7(+) CD45R0(-) CD45RA(+) phenotype, the same as that found in some healthy controls, and this phenotype was associated with a lack of response to melan-A peptide ex vivo. In the remaining six patients, melan-A tetramer(+) cells were shifted toward a CCR7(-) CD45R0(+) CD45RA(-) phenotype, and responses to melan-A peptide could be readily demonstrated ex vivo. When lymph nodes infiltrated by melan-A-expressing melanoma cells were examined, a similar dichotomy emerged. These findings demonstrate that activation of melan-A-specific CTL occurs in only some patients with malignant melanoma, and that only patients with such active immune responses are capable of responding to Ag in ex vivo assays.     

Cellular immune response of patients with chromoblastomycosis undergoing antifungal therapy

One of the most characteristic features of the chromoblastomycosis is its unresponsiveness to treatment. In order to analyzed whether during therapy could be observed a change of cellular immune response pattern, we evaluated the production of IL-10, TNF-α and IFN-γ, as well as proliferation of peripheral blood mononuclear cell (PBMC) from patients in different periods of chemotherapy treatment. Our results showed that after 6 months of treatment cells from patients proliferated to fungal antigens and produced a significant level of IFN-γ. However, after 1 year of treatment a low proliferation of T cells and production of IFN-γ accompanied by an increase of IL-10 were observed when compared with 6 months of treatment.     

A monte carlo approach to population dynamics of cells in a HIV immune response model

Summary Using a direct Monte Carlo simulation, population growth of helper T-cells (N _H) and viral cells (N _v) is studied for an immune response model with an enhanced spatial inter-cellular interaction relevant to HIV as a function of viral mutation. In the absence of cellular mobility (P _mob=0), the helper T-cells grow nonmonotonically before reaching saturation and the viral population grows monotonically before reaching a constant equilibrium. Cellular mobility (P _mob=1) enhances the viral growth and reduces the stimulative T-cell growth. Below a mutation threshold (P _c), the steady-state density of helper T-cell (p _H) is larger than that of the Virus (p _v); the density difference Δp _o(=pV−pH) remains a constant at P _mob=1 while −Δp _o→0 as P _mut→P _c at P _mob=0. Above the mutation threshold, the difference Δp _o in cell density, grows with ΔP=P _mut−P _c monotonically: ΔP _o ∞ (ΔP)^β ≃ with β≈0.574±0.016 in absence of mobility, while Δp _o≈6(ΔP) with P _mob=1.     

The effect of an anti-HLA-B27 immune response on CTL recognition of Chlamydia.

The interplay between triggering bacteria and HLA-B27 in the pathogenesis of the spondyloarthropathies remains one of the most active areas of investigation in the rheumatic diseases. This has proved difficult to study systematically in the clinical setting, and in this study we utilized a rat model to address the influence that B27-related immunity may have on the process of generating anti-Chlamydia immunity. When splenocytes from HLA-B27 DNA-immunized Lewis (LEW) animals received restimulation in vitro with Chlamydia-treated cells from B27-transgenic LEW rats, we observed that in addition to the expected CTL recognition of HLA-B27, there was also anti-Chlamydia CTL killing of Chlamydia-sensitized syngeneic fibroblast targets. This was not seen when responding cells in vitro were naive LEW splenocytes. To confirm the existence of CTLs recognizing both HLA-B27 and Chlamydia, LEW rats were immunized with B27-transgenic LEW cells, instead of the B27 DNA construct. Splenocytes from the immune rats were restimulated in vitro with Chlamydia-treated B27-transgenic LEW cells. In this instance, the CTLs retained the allele-specific recognition of HLA-B27, as well as recognition of Chlamydia-sensitized syngeneic fibroblasts. Thus, if there is prior expansion of an immune response against HLA-B27, then the resulting splenocytes demonstrate a reduced threshold for generating a primary anti-Chlamydia CTL response. These studies implicate a dynamic interrelationship between recognition of HLA-B27 and Chlamydia trachomatis. The results may have implications for deciphering the cellular basis of Chlamydia-induced reactive arthritis.     

Pregnancy and virologic response to antiretroviral therapy in South Africa

Background

Although women of reproductive age are the largest group of HIV-infected individuals in sub-Saharan Africa, little is known about the impact of pregnancy on response to highly active antiretroviral therapy (HAART) in that setting. We examined the effect of incident pregnancy after HAART initiation on virologic response to HAART.

Methods and Findings

We evaluated a prospective clinical cohort of adult women who initiated HAART in Johannesburg, South Africa between 1 April 2004 and 30 September 2009, and followed up until an event, death, transfer, drop-out, or administrative end of follow-up on 31 March 2010. Women over age 45 and women who were pregnant at HAART initiation were excluded from the study; final sample size for analysis was 5,494 women. Main exposure was incident pregnancy, experienced by 541 women; main outcome was virologic failure, defined as a failure to suppress virus to ≤400 copies/ml by six months or virologic rebound >400 copies/ml thereafter. We calculated adjusted hazard ratios using marginal structural Cox proportional hazards models and weighted lifetable analysis to calculate adjusted five-year risk differences. The weighted hazard ratio for the effect of pregnancy on time to virologic failure was 1.34 (95% confidence limit [CL] 1.02, 1.78). Sensitivity analyses generally confirmed these main results.

Conclusions

Incident pregnancy after HAART initiation was associated with modest increases in both relative and absolute risks of virologic failure, although uncontrolled confounding cannot be ruled out. Nonetheless, these results reinforce that family planning is an essential part of care for HIV-positive women in sub-Saharan Africa. More work is needed to confirm these findings and to explore specific etiologic pathways by which such effects may operate.     

Stochastic optimal therapy for enhanced immune response

Therapeutic enhancement of humoral immune response to microbial attack is addressed as the stochastic optimal control of a dynamic system. Without therapy, the modeled immune response depends upon the initial concentration of pathogens in a simulated attack. Immune response can be augmented by agents that kill the pathogen directly, that stimulate the production of plasma cells or antibodies, or that enhance organ health. Using a generic mathematical model of immune response to the infection (i.e., of the dynamic state of the system), previous papers demonstrated optimal (open-loop) and neighboring-optimal (closed-loop) control solutions that defeat the pathogen and preserve organ health, given initial conditions that otherwise would be lethal [Optimal Contr. Appl. Methods 23 (2002) 91, Bioinformatics 18 (2002) 1227]. Therapies based on separate and combined application of the agents were derived by minimizing a quadratic cost function that weighted both system response and drug usage, providing implicit control over harmful side effects. Here, we focus on the effects that corrupted or incomplete measurements of the dynamic state may have on neighboring-optimal feedback control. Imperfect measurements degrade the precision of feedback adjustments to therapy; however, optimal state estimation allows the feedback strategy to be implemented with incomplete measurements and minimizes the expected effects of measurement error. Complete observability of the perturbed state for this four state example is provided by measurement of four of the six possible pairs of two variables, either set of three variables, or all four variables. The inclusion of state estimation extends the applicability of optimal control theory for developing new therapeutic protocols to enhance immune response.