Model of HIV-1 disease progression based on virus-induced lymph node homing and homing-induced apoptosis of CD4+ lymphocytes

An Integrated Spatial Dynamics-Pharmacokinetic Model Explaining Poor Penetration of Anti-retroviral Drugs in Lymph Nodes

Although combined anti-retroviral therapy (cART) suppresses plasma HIV viremia below the limit of detection in a majority of HIV patients, evidence is emerging that the distribution of the anti-retroviral drugs is heterogeneous in tissue. Clinical studies measuring antiretroviral drug concentrations in lymph nodes (LNs) revealed lower concentrations compared to peripheral blood levels suggesting poor drug penetration properties. Our current study is an attempt to understand this poor anti-retroviral drug penetration inside lymph node lobules through integrating known pharmacokinetic and pharmacodynamic (PK/PD) parameters of the anti-retroviral drugs into a spatial model of reaction and transport dynamics within a solid lymph node lobule. Simulated drug penetration values were compared against experimental results whenever available or matched with data that is available for other drugs in a similar class. Our integrated spatial dynamics pharmacokinetic model reproduced the experimentally observed exclusion of antivirals from lymphoid sites. The strongest predictor of drug exclusion from the lymphoid lobule, independent of drug class, was lobule size; large lobules (high inflammation) exhibited high levels of drug exclusion. PK/PD characteristics associated with poor lymphoid penetration include high cellular uptake rates and low intracellular half-lives. To determine whether this exclusion might lead to ongoing replication, target CD4+ T cell, infected CD4+ T cell, free virus, and intracellular IC50 values of anti-retroviral drugs were incorporated into the model. Notably, for median estimates of PK/PD parameters and lobule diameters consistent with low to moderate inflammation, the model predicts no ongoing viral replication, despite substantial exclusion of the drugs from the lymphoid site. Monte-Carlo studies drawn from the prior distributions of the PK/PD parameters predicts increases in site-specific HIV replication in a small fraction of the patient population for lobule diameters greater than 0.2 mm; this fraction increases as the site diameter/ inflammation level increases. The model shows that cART consisting of two nRTIs and one PI is the most likely treatment combination to support formation of a sanctuary site, a finding that is consistent with clinical observations.

Positive feedback through inflammation creates bistable behavior in HIV tissue sanctuaries

Combination Antiretroviral Therapy (cART) consists of a cocktail of drugs administered to HIV-infected patients that can suppress the amount of HIV in the patient's blood plasma to an undetectable level. Our previous work has suggested that some HIV-infected patients, despite being placed on cART, can still have ongoing viral replication occurring in self-sustaining inflamed lymph node follicle sanctuary sites. Spatial models of the putative sites show that inflammation is a necessary condition for ongoing HIV replication. In this study, we model the hypothesis that ongoing HIV replication may provide a sufficiently strong pro-inflammatory signal to maintain inflammation levels consistent with continued HIV replication. A system of ordinary differential equations integrated with a reactive-diffusion system is used to model the HIV dynamics and the diameter of a lymph node follicle as a function of time and external influence. The estimates of the parameters in our model come from prior data when available. The results of our study show that these dynamics have two stable steady-state solutions, one with low inflammation and no ongoing HIV replication in the site, and one with high inflammation and high levels of ongoing HIV replication in the site. We furthermore show that the system can transition between the two outcomes in response to a transient exogenous addition of pro-inflammatory signaling, consistent with the antigenic stimulus of a secondary infection. The spatial isolation of the sites results in a low viral load in the blood plasma for both conditions.

Modeling the immune response to HIV infection

The interplay between immune response and HIV is intensely studied via mathematical modeling, with significant insights but few direct answers. In this short review, we highlight advances and knowledge gaps across different aspects of immunity. In particular, we identify the innate immune response and its role in priming the adaptive response as ripe for modeling. The latter have been the focus of most modeling studies, but we also synthesize key outstanding questions regarding effector mechanisms of cellular immunity and development of broadly neutralizing antibodies. Thus far, most modeling studies aimed to infer general immune mechanisms; we foresee that significant progress will be made next by detailed quantitative fitting of models to data, and prediction of immune responses.

The Role of Immune Response in Optimal HIV Treatment Interventions

A mathematical model for the transmission dynamics of human immunodeficiency virus (HIV) within a host is developed. Our model focuses on the roles of immune response cells or cytotoxic lymphocytes (CTLs). The model includes active and inactive cytotoxic immune cells. The basic reproduction number and the global stability of the virus free equilibrium is carried out. The model is modified to include anti-retroviral treatment interventions and the controlled reproduction number is explored. Their effects on the HIV infection dynamics are investigated. Two different disease stage scenarios are assessed: early-stage and advanced-stage of the disease. Furthermore, optimal control theory is employed to enhance healthy CD4+ T cells, active cytotoxic immune cells and minimize the total cost of anti-retroviral treatment interventions. Two different anti-retroviral treatment interventions (RTI and PI) are incorporated. The results highlight the key roles of cytotoxic immune response in the HIV infection dynamics and corresponding optimal treatment strategies. It turns out that the combined control (both RTI and PI) and stronger immune response is the best intervention to maximize healthy CD4+ T cells at a minimal cost of treatments.

Late presentation to HIV/AIDS care at the Douala general hospital, Cameroon: its associated factors, and consequences

Background

The introduction of anti-retroviral treatment (ART) has significantly reduced mortality and morbidity associated with HIV/AIDS. While treatment at early stages of the disease is related to a better prognosis, late presentation (LP) to care is harmful to the infected person, the society and is more costly. We aimed to describe late presentation to HIV care, its associated factors and consequences in patients followed up in a tertiary hospital in Cameroon.

Methods

We retrospectively assessed patients’ files between 1996 and 2014 at the Douala general hospital (DGH) HIV treatment centre. Late presentation (LP) to HIV care was defined as a CD4+ T cell count< 350 cells/mm3 or advanced clinical stages of the disease (WHO stages 3/4) at first presentation for care. We used logistic regression to study factors associated with late presentation and assessed occurrence of opportunistic infections and mortality at 3, 6 and 12 months after presentation to care.

Results

Of 1866 files studied, mean age was 40 (SD: 10) years, median CD4+ T cell count was 147 (IQR: 63–270) cells/mm3, 58.2% were at HIV clinical stages 3 and 4. The prevalence of late presentation to HIV care was 89.7% (95% CI: 88.2–91.0%) and remained above 80% from 1996 to 2014. Circumstances of diagnosis: prevention of mother to child transmission program/blood donation (OR = 0.16, 95% CI 0.10–0.29), having a positive partner (OR = 0.16, 95%CI = 0.10–0.26), and routine screening (OR = 0.13, 95%CI = 0.10–0.19) reduced the odds of presenting late compared to clinical suspicion. Students had lower odds of presenting late compared to people who had an employment (OR = 0.50, 95%CI = 0.26–0.98). Calendar time OR = 1.64, 95% CI = 1.08–2.48 for ≥2010 vs. < 2005) increased the odds of late presentation. Mortality and opportunistic infections prevalence remained significantly higher in late presenters at 3, 6 and 12 months than in early presenters.

Conclusion

Late presentation to HIV care is very high at the DGH and is related to poor outcome. More screening and sensitization campaigns should be carried out in the population to diagnose the disease at an earlier stage.

Mathematical analysis and dynamic active subspaces for a long term model of HIV

a long-term model of HIV infection dynamics [8] was developed to describe the entire time course of the disease. It consists of a large system of ODEs with many parameters, and is expensive to simulate. In the current paper, this model is analyzed by determining all infection-free steady states and studying the local stability properties of the unique biologically-relevant equilibrium. Active subspace methods are then used to perform a global sensitivity analysis and study the dependence of an infected individual's T-cell count on the parameter space. Building on these results, a global-in-time approximation of the T-cell count is created by constructing dynamic active subspaces and reduced order models are generated, thereby allowing for inexpensive computation.

Late Presentation into Care of HIV Disease and Its Associated Factors in Asia: Results of TAHOD

Many HIV-infected individuals do not enter health care until late in the infection course. Despite encouraging earlier testing, this situation has continued for several years. We investigated the prevalence of late presenters and factors associated with late presentation among HIV-infected patients in an Asian regional cohort. This cohort study included HIV-infected patients with their first positive HIV test during 2003-2012 and CD4 count and clinical status data within 3 months of that test. Factors associated with late presentation into care (CD4 count <200 cells/μl or an AIDS-defining event within ±3 months of first positive HIV test) were analyzed in a random effects logistic regression model. Among 3,744 patients, 2,681 (72%) were late presenters. In the multivariable model, older patients were more likely to be late presenters than younger (≤30 years) patients [31-40, 41-50, and ≥51 years: odds ratio (OR) = 1.57, 95% confidence interval (CI) 1.31-1.88; OR = 2.01, 95% CI 1.58-2.56; and OR = 1.69, 95% CI 1.23-2.31, respectively; all p ≤ 0.001]. Injecting drug users (IDU) were more likely (OR = 2.15, 95% CI 1.42-3.27, p < 0.001) and those with homosexual HIV exposure were less likely (OR = 0.45, 95% CI 0.35-0.58, p < 0.001) to be late presenters compared to those with heterosexual HIV exposure. Females were less likely to be late presenters (OR = 0.44, 95% CI 0.36-0.53, p < 0.001). The year of first positive HIV test was not associated with late presentation. Efforts to reduce the patients who first seek HIV care at the late stage are needed. The identified risk factors associated with late presentation should be utilized in formulating targeted public health intervention to improve earlier entry into HIV care.

Modeling the Slow CD4+ T Cell Decline in HIV-Infected Individuals

The progressive loss of CD4+ T cell population is the hallmark of HIV-1 infection but the mechanism underlying the slow T cell decline remains unclear. Some recent studies suggested that pyroptosis, a form of programmed cell death triggered during abortive HIV infection, is associated with the release of inflammatory cytokines, which can attract more CD4+ T cells to be infected. In this paper, we developed mathematical models to study whether this mechanism can explain the time scale of CD4+ T cell decline during HIV infection. Simulations of the models showed that cytokine induced T cell movement can explain the very slow decline of CD4+ T cells within untreated patients. The long-term CD4+ T cell dynamics predicted by the models were shown to be consistent with available data from patients in Rio de Janeiro, Brazil. Highly active antiretroviral therapy has the potential to restore the CD4+ T cell population but CD4+ response depends on the effectiveness of the therapy, when the therapy is initiated, and whether there are drug sanctuary sites. The model also showed that chronic inflammation induced by pyroptosis may facilitate persistence of the HIV latent reservoir by promoting homeostatic proliferation of memory CD4+ cells. These results improve our understanding of the long-term T cell dynamics in HIV-1 infection, and support that new treatment strategies, such as the use of caspase-1 inhibitors that inhibit pyroptosis, may maintain the CD4+ T cell population and reduce the latent reservoir size.

The CD4+ T cell population within HIV-infected individuals declines slowly as disease progresses. When CD4+ cells drop to below 200 cells/ul, the infection is usually considered to enter the late stage, i.e., acquired immune deficiency syndrome (AIDS). CD4+ T cell depletion can take many years but the biological events underlying such slow decline are not well understood. Some studies showed that the majority of infected T cells in lymph nodes die by pyroptosis, a form of programmed cell death, which can release inflammatory signals attracting more CD4+ T cells to be infected. We developed mathematical models to describe this process and explored whether they can generate the long-term CD4+ T cell decline. We showed that pyroptosis induced cell movement can explain the slow time scale of CD4+ T cell depletion and that pyroptosis may also contribute to the persistence of latently infected cells, which represent a major obstacle to HIV eradication. The modeling prediction agrees with patient data in Rio de Janeiro, Brazil. These results suggest that a combination of current treatment regimens and caspase-1 inhibitor that can inhibit pyroptosis might provide a new way to maintain the CD4+ T cell population and eradicate the HIV latent reservoir.

Dynamics of HIV infection in lymphoid tissue network

Human immunodeficiency virus (HIV) is a fast replicating ribonucleic acid virus, which can easily mutate in order to escape the effects of drug administration. Hence, understanding the basic mechanisms underlying HIV persistence in the body is essential in the development of new therapies that could eradicate HIV infection. Lymphoid tissues are the primary sites of HIV infection. Despite the recent progress in real-time monitoring technology, HIV infection dynamics in a whole body is unknown. Mathematical modeling and simulations provide speculations on global behavior of HIV infection in the lymphatic system. We propose a new mathematical model that describes the spread of HIV infection throughout the lymphoid tissue network. In order to represent the volume difference between lymphoid tissues, we propose the proportionality of several kinetic parameters to the lymphoid tissues' volume distribution. Under this assumption, we perform extensive numerical computations in order to simulate the spread of HIV infection in the lymphoid tissue network. Numerical computations simulate single drug treatments of an HIV infection. One of the important biological speculations derived from this study is a drug saturation effect generated by lymphoid network connection. This implies that a portion of reservoir lymphoid tissues to which drug is not sufficiently delivered would inhibit HIV eradication despite of extensive drug injection.

Predictors of Late HIV Diagnosis among Adult People Living with HIV/AIDS Who Undertake an Initial CD4 T Cell Evaluation, Northern Ethiopia: A Case-Control Study

Introduction

Early HIV testing and timely initiation of ART is critical for the improved quality of life of PLWHIV. Having identified a higher rates of Late HIV diagnosis, this study was aimed to determine Determinants of late diagnosis of HIV among adult HIV patients in Bahir Dar, Northern Ethiopia.

Methods

A case control study was conducted between January 2010 to December 2011 at Bahir Dar Felege Hiwot Referral Hospital. The study subjects consisted of 267 cases and 267 controls. Cases were adult people living with HIV/AIDS whose initial CD₄ T cell count was < 200/μl of blood. Controls were those with a CD₄ T cell count of greater than 200/ μl. Trained staff nurses were involved in data collection using a semi-structured questionnaire. Data was entered and analyzed using SPSS version 20. Descriptive statistics and Binary logistic regression were performed.

Results

Subjects who hold a certificate and above (AOR = 0.26; 95% CI = 0.13. 0.54), being initiated by friends, families and other socials to undertake HIV testing (AOR = 0.65; 95% CI = 0.29, 1.48), who reported a medium and high knowledge score about HIV/AIDS and who undertake HIV testing while visiting a clinic for ANC (AOR = 0.40; 95% CI = 0.19, 0.83) were less likely to be diagnosed late. Subjects who undertake HIV testing due to providers’ initiation (AOR = 1.70; 95%CI = 1.08, 2.68), who reported a medium internalized stigma (AOR = 4.94; 95% CI = 3.13, 7.80) and who reported a high internalized stigma score towards HIV/AIDS (AOR = 16.64; 95% CI = 8.29, 33.4) had a high odds of being diagnosed late compared to their counterparts.

Conclusion

Internalized stigma, low knowledge level about HIV/AIDS, not to have attended formal education and failure to undertake HIV testing by own initiation were significant determinant factors associated with Late HIV diagnosis. Education about HIV/AIDS, promotion of general education, and encouraging people to motivate their social mates to undertake HIV testing are highly recommended.

Opportunities for earlier HIV diagnosis in a pediatric ED

OBJECTIVES

Emergency department (ED) HIV screening is recommended but challenging to implement and of uncertain effectiveness in pediatric EDs (PEDs). We sought to determine whether there were opportunities for earlier HIV diagnosis in the PED for a cohort of young adults diagnosed with HIV.

METHODS

This retrospective cohort study reviewed PED records of a group of young adults receiving HIV care in an urban hospital setting. Pediatric ED visits were selected for review if they took place after the patient's estimated time of HIV acquisition and before their eventual diagnosis. Charts were reviewed to determine whether HIV infection was suspected and whether testing was offered.

RESULTS

Among a cohort of HIV-positive young adults, only 3 (3.6%; 95% confidence interval, 0.9-10.8) of 84 were seen in the PED during the time they were undiagnosed but likely to be infected with HIV. Among these subjects, there was no documentation that HIV testing was offered or refused nor was there documented suspicion of HIV.

CONCLUSIONS

There are opportunities for earlier diagnosis of HIV in PEDs, affirming the importance of HIV screening implementation in these settings. However, PEDs are unlikely to have the same frequency of contact with undiagnosed individuals as do adult EDs. Alternative methods of accessing at-risk adolescent populations must be identified.

Computational study to determine when to initiate and alternate therapy in HIV infection

HIV is a widespread viral infection without cure. Drug treatment has transformed HIV disease into a treatable long-term infection. However, the appearance of mutations within the viral genome reduces the susceptibility of HIV to drugs. Therefore, a key goal is to extend the time until patients exhibit resistance to all existing drugs. Current HIV treatment guidelines seem poorly supported as practitioners have not achieved a consensus on the optimal time to initiate and to switch antiretroviral treatments. We contribute to this discussion with predictions derived from a mathematical model of HIV dynamics. Our results indicate that early therapy initiation (within 2 years postinfection) is critical to delay AIDS progression. For patients who have not received any therapy during the first 3 years postinfection, switch in response to virological failure may outperform proactive switching strategies. In case that proactive switching is opted, the switching time between therapies should not be larger than 100 days. Further clinical trials are needed to either confirm or falsify these predictions.

Slow turnover of HIV-1 receptors on quiescent CD4+ T cells causes prolonged surface retention of gp120 immune complexes in vivo

Peripheral blood CD4(+) T cells in HIV-1(+) patients are coated with Ig. However, the causes and consequences of the presence of Ig(+) CD4(+) T cells remain unknown. Previous studies have demonstrated the rapid turnover of viral receptors (VRs) on lymphoma and tumor cells. The present study investigates the turnover of VRs on peripheral quiescent CD4(+) T cells (qCD4s), which are the most abundant peripheral blood CD4(+) T cells. Utilizing pharmacological and immunological approaches, we found that the turnover of VRs on qCD4s is extremely slow. As a result, exposure to gp120 or HIV-1 virions in vitro causes gp120 to remain on the surface for a long period of time. It requires approximately three days for cell-bound gp120 on the surface to be reduced by 50%. In the presence of patient serum, gp120 forms surface immune complexes (ICs) that are also retained for a long time. Indeed, when examining the percentages of Ig(+) CD4(+) T cells at different stages of HIV-1 infection, approximately 70% of peripheral resting CD4(+) T cells (rCD4s) were coated with surface VRs bound to slow-turnover gp120-Ig. The levels of circulating ICs in patient serum were insufficient to form surface ICs on qCD4s, suggesting that surface ICs on qCD4s require much higher concentrations of HIV-1 exposure such as might be found in lymph nodes. In the presence of macrophages, Ig(+) CD4(+) T cells generated in vitro or directly isolated from HIV-1(+) patients were ultimately phagocytosed. Similarly, the frequencies and percentages of Ig(+) rCD4s were significantly increased in an HIV-1(+) patient after splenectomy, indicating that Ig(+) rCD4s might be removed from circulation and that non-neutralizing anti-envelope antibodies could play a detrimental role in HIV-1 pathogenesis. These findings provide novel insights for vaccine development and a rationale for using Ig(+) rCD4 levels as an independent clinical marker.

Role of active and inactive cytotoxic immune response in human immunodeficiency virus dynamics

Objectives

Mathematical models can be helpful to understand the complex dynamics of human immunodeficiency virus infection within a host. Most of work has studied the interactions of host responses and virus in the presence of active cytotoxic immune cells, which decay to zero when there is no virus. However, recent research highlights that cytotoxic immune cells can be inactive but never be depleted.

Methods

We propose a mathematical model to investigate the human immunodeficiency virus dynamics in the presence of both active and inactive cytotoxic immune cells within a host. We explore the impact of the immune responses on the dynamics of human immunodeficiency virus infection under different disease stages.

Results

Standard mathematical and numerical analyses are presented for this new model. Specifically, the basic reproduction number is computed and local and global stability analyses are discussed.

Conclusion

Our results can give helpful insights when designing more effective drug schedules in the presence of active and inactive immune responses.

Spatial modeling of HIV cryptic viremia and 2-LTR formation during raltegravir intensification

Combination Antiretroviral Therapy (cART) can suppress plasma HIV below the limit of detection in normal assays. Recently reported results suggest that viral replication may continue in some patients, despite undetectable levels in the blood. It has been suggested that the appearance of the circularized episomal HIV DNA artifact 2-LTR following treatment intensification with the integrase inhibitor raltegravir is a marker of ongoing viral replication. Other work has suggested that lymphoid organs may be a site of reduced antiviral penetration and increased viral production. In this study we model the hypothesis that this ongoing replication occurs in lymphoid follicle sanctuary sites and investigate the patterns of 2-LTR formation expected after raltegravir application. Experimental data is used to estimate the reaction and diffusion parameters in the model, and Monte-Carlo simulations are used to explore model behavior subject to variation in these rates. The results suggest that conditions for the formation of an observed transient peak in 2-LTR formation following raltegravir intensification include a sanctuary site diameter larger than 0.2mm, a viral basic reproductive ratio within the site larger than 1, and a total volume of active sanctuary sites above 20mL. Significant levels of uncontrolled replication can occur in the sanctuary sites without measurable changes in the plasma viral load. By contrast, subcritical replication (where the basic reproductive ratio of the virus is less than 1 in all sites) always results in monotonic increases of measured 2-LTR following raltegravir intensification, occurring at levels below the limit of detection.

Modelling the course of an HIV infection: insights from ecology and evolution

The Human Immunodeficiency Virus (HIV) is one of the most threatening viral agents. This virus infects approximately 33 million people, many of whom are unaware of their status because, except for flu-like symptoms right at the beginning of the infection during the acute phase, the disease progresses more or less symptom-free for 5 to 10 years. During this asymptomatic phase, the virus slowly destroys the immune system until the onset of AIDS when opportunistic infections like pneumonia or Kaposi’s sarcoma can overcome immune defenses. Mathematical models have played a decisive role in estimating important parameters (e.g., virion clearance rate or life-span of infected cells). However, most models only account for the acute and asymptomatic latency phase and cannot explain the progression to AIDS. Models that account for the whole course of the infection rely on different hypotheses to explain the progression to AIDS. The aim of this study is to review these models, present their technical approaches and discuss the robustness of their biological hypotheses. Among the few models capturing all three phases of an HIV infection, we can distinguish between those that mainly rely on population dynamics and those that involve virus evolution. Overall, the modeling quest to capture the dynamics of an HIV infection has improved our understanding of the progression to AIDS but, more generally, it has also led to the insight that population dynamics and evolutionary processes can be necessary to explain the course of an infection.

Modeling of HIV-1 infection: insights to the role of monocytes/macrophages, latently infected T4 cells, and HAART regimes

A novel dynamic model covering five types of cells and three connected compartments, peripheral blood (PB), lymph nodes (LNs), and the central nervous system (CNS), is here proposed. It is based on assessment of the biological principles underlying the interactions between the human immunodeficiency virus type I (HIV-1) and the human immune system. The simulated results of this model matched the three well-documented phases of HIV-1 infection very closely and successfully described the three stages of LN destruction that occur during HIV-1 infection. The model also showed that LNs are the major location of viral replication, creating a pool of latently infected T4 cells during the latency period. A detailed discussion of the role of monocytes/macrophages is made, and the results indicated that infected monocytes/macrophages could determine the progression of HIV-1 infection. The effects of typical highly active antiretroviral therapy (HAART) drugs on HIV-1 infection were analyzed and the results showed that efficiency of each drug but not the time of the treatment start contributed to the change of the turnover of the disease greatly. An incremental count of latently infected T4 cells was made under therapeutic simulation, and patients were found to fail to respond to HAART therapy in the presence of certain stimuli, such as opportunistic infections. In general, the dynamics of the model qualitatively matched clinical observations very closely, indicating that the model may have benefits in evaluating the efficacy of different drug therapy regimens and in the discovery of new monitoring markers and therapeutic schemes for the treatment of HIV-1 infection.

A simple method for estimating the prevalence of undiagnosed HIV infection in an emergency department

OBJECTIVES

Estimating the prevalence of undiagnosed HIV in emergency departments (EDs) is not straightforward. Regional epidemiologic data are unlikely to translate directly to a single ED setting, and the prevalence of undiagnosed HIV likely differs between EDs within a region. We propose a simple method for estimating the prevalence of undiagnosed HIV in individual EDs.

METHODS

First, incident cases are grouped by zip codes and combined with census data to calculate zip code-specific case rates. Second, the proportion of ED patients living in each zip code is determined. Third, the prevalence of undiagnosed disease is estimated as the mean zip code case rate, weighted by the proportion of ED patients living in each zip code, multiplied by the estimated time from infection to diagnosis. We applied this method to 3 EDs in a metropolitan region with an annual HIV/AIDS case rate of 6.2 per 100,000.

RESULTS

From 1999 through 2003, the annual HIV case rate was estimated to range from 6.4 to 12.7 at an urban academic ED, 5.9 to 10.2 at an urban community ED, and 2.1 to 4.9 at a suburban community ED. The estimated prevalence of undiagnosed disease was 0.05% (urban academic), 0.04% (urban community), and 0.02% (suburban community).

CONCLUSION

Publicly reported regional AIDS or HIV statistics do not reflect ED-specific HIV epidemiology, but ED-specific case rates can be crudely estimated from readily available data. This method promises to be a valuable aid for translating HIV screening to ED settings.

Tuberculosis: global approaches to a global disease

Mycobacterium tuberculosis is a remarkably successful human pathogen. The interaction with the human host is complex and much remains unknown. Recent advances in systems biology have allowed the integration of data from humans and animal models into computational approaches. For example, mathematical models provide a platform for in silico manipulation of host-pathogen interactions to gain insight into this infection across temporal and biologic scales. Here, we review recent studies on global approaches toward identifying comprehensive responses of both host and bacillus during infection, and the potential for incorporation of these data into many types of useful computational systems. Systems biology approaches provide a unique opportunity to study interventions that may improve therapy and vaccines against this major killer.

Late presenters to HIV care and treatment, identification of associated risk factors in HIV-1 infected Indian population

Background

Timely access to antiretroviral therapy is a key to controlling HIV infection. Late diagnosis and presentation to care diminish the benefits of antiretrovirals and increase risk of transmission. We aimed to identify late presenters in patients sent for first CD4 T cell count after HIV diagnosis, for therapy initiation evaluation. Further we aimed at identifying patient factors associated with higher risk of late presentation.

Methods

Retrospective data collection and analysis was done for 3680 subjects visiting the laboratory for CD4 T cell counts between 2001 and 2007. We segregated the patients on basis of their CD4 T cell counts after first HIV diagnosis. Factors associated with risk of late presentation to CD4 T cell counts after HIV diagnosis were identified using univariate analysis, and the strength of association of individual factor was assessed by calculation of odds ratios.

Results

Of 3680 subjects, 2936 (83.37%) were defined as late presenters. Late testing varied among age groups, transmission categories, and gender. Males were twice as likely to present late as compared to females. We found significant positive association of heterosexual transmission route (p < 0.001), and older age groups of 45 years and above (p = 0.0004) to late presentation. Female sex, children below 14 years of age and sexual contact with HIV positive spouse were associated with significantly lower risks to presenting late. Intravenous drug users were also associated with lower risks of late presentation, in comparison to heterosexual transmission route.

Conclusions

The study identifies HIV infected population groups at a higher risk of late presentation to care and treatment. The risk factors identified to be associated with late presentation should be utilised in formulating targeted public health interventions in order to improve early HIV diagnosis.

Antiretroviral therapy restores diversity in the T-cell receptor Vbeta repertoire of CD4 T-cell subpopulations among human immunodeficiency virus type 1-infected children and adolescents

Human immunodeficiency virus (HIV) type 1 infection perturbs the T-cell receptor (TCR) Vbeta repertoire. The TCR CDR3 length diversity of individual Vbeta families was examined within CD45RA and CD45RO CD4 T cells to assess the impact of the virus on clonality throughout CD4 T-cell activation and differentiation. A cross-sectional and longitudinal cohort study of 13 HIV-infected and 8 age-matched healthy children and adolescents examined the Vbeta CDR3 length profiles within CD4 T-cell subsets by the use of spectratyping. HIV-infected subjects demonstrated higher numbers of perturbations in CD4 CD45RA T cells (5.8 +/- 4.9 Vbeta families) than healthy individuals (1.6 +/- 1.8 Vbeta families) (P = 0.04). Surprisingly, CD4 CD45RO central memory T cells from infected subjects showed no increased perturbations compared to the perturbations for the same cells from healthy subjects (2.9 +/- 3.1 and 1.1 +/- 1.8 Vbeta families, respectively; P = 0.11). CD4 CD45RA TCR perturbations were higher among infected subjects with >25% CD4 cells than healthy subjects (mean number of perturbed Vbeta families, 6.6 +/- 5.4; P = 0.04). No correlations between perturbations in CD4 subsets and pretherapy age or viral load were evident. In contrast to CD8 T cells, HIV induces TCR disruptions within CD45RA but not CD45RO CD4 T cells. Therapy-induced viral suppression resulted in increases in thymic output and the normalization of the diversity of TCR within CD45RA CD4 T cells after 2 months of treatment. Perturbations occur prior to CD4 T-cell attrition and normalize with effective antiretroviral therapy. The impact of HIV on the diversity of TCR within naïve, central memory, and effector memory CD4 T cells is distinctly different from that in CD8 T cells.

HIV care and treatment factors associated with improved survival during TB treatment in Thailand: an observational study

Background

In Southeast Asia, HIV-infected patients frequently die during TB treatment. Many physicians are reluctant to treat HIV-infected TB patients with anti-retroviral therapy (ART) and have questions about the added value of opportunistic infection prophylaxis to ART, the optimum ART regimen, and the benefit of initiating ART early during TB treatment.

Methods

We conducted a multi-center observational study of HIV-infected patients newly diagnosed with TB in Thailand. Clinical data was collected from the beginning to the end of TB treatment. We conducted multivariable proportional hazards analysis to identify factors associated with death.

Results

Of 667 HIV-infected TB patients enrolled, 450 (68%) were smear and/or culture positive. Death during TB treatment occurred in 112 (17%). In proportional hazards analysis, factors strongly associated with reduced risk of death were ART use (Hazard Ratio [HR] 0.16; 95% confidence interval [CI] 0.07–0.36), fluconazole use (HR 0.34; CI 0.18–0.64), and co-trimoxazole use (HR 0.41; CI 0.20–0.83). Among 126 patients that initiated ART after TB diagnosis, the risk of death increased the longer that ART was delayed during TB treatment. Efavirenz- and nevirapine-containing ART regimens were associated with similar rates of adverse events and death.

Conclusion

Among HIV-infected patients living in Thailand, the single most important determinant of survival during TB treatment was use of ART. Controlled clinical trials are needed to confirm our findings that early ART initiation improves survival and that the choice of non-nucleoside reverse transcriptase inhibitor does not.

Contributions to early HIV diagnosis among patients linked to care vary by testing venue

OBJECTIVE

Early HIV diagnosis reduces transmission and improves health outcomes; screening in non-traditional settings is increasingly advocated. We compared test venues by the number of new diagnoses successfully linked to the regional HIV treatment center and disease stage at diagnosis.

METHODS

We conducted a retrospective cohort study using structured chart review of newly diagnosed HIV patients successfully referred to the region's only HIV treatment center from 1998 to 2003. Demographics, testing indication, risk profile, and initial CD4 count were recorded.

RESULTS

There were 277 newly diagnosed patients meeting study criteria. Mean age was 33 years, 77% were male, and 46% were African-American. Median CD4 at diagnosis was 324. Diagnoses were earlier via partner testing at the HIV treatment center (N = 8, median CD4 648, p = 0.008) and with universal screening by the blood bank, military, and insurance companies (N = 13, median CD4 483, p = 0.05) than at other venues. Targeted testing by health care and public health entities based on patient request, risk profile, or patient condition lead to later diagnosis.

CONCLUSION

Test venues varied by the number of new diagnoses made and the stage of illness at diagnosis. To improve the rate of early diagnosis, scarce resources should be allocated to maximize the number of new diagnoses at screening venues where diagnoses are more likely to be early or alter testing strategies at test venues where diagnoses are traditionally made late. Efforts to improve early diagnosis should be coordinated longitudinally on a regional basis according to this conceptual paradigm.

Toward a multiscale model of antigen presentation in immunity

A functioning immune system and the process of antigen presentation in particular encompass events that occur at multiple length and time scales. Despite a wealth of information in the biological literature regarding each of these scales, no single representation synthesizing this information into a model of the overall immune response as it depends on antigen presentation is available. In this article, we outline an approach for integrating information over relevant biological and temporal scales to generate such a representation for major histocompatibility complex class II-mediated antigen presentation. In addition, we begin to address how such models can be used to answer questions about mechanisms of infection and new strategies for treatment and vaccines.

Natural variation in HIV infection: Monte Carlo estimates that include CD8 effector cells

Viral load and CD4 T-cell counts in patients infected with the human immunodeficiency virus (HIV) are commonly used to guide clinical decisions regarding drug therapy or to assess therapeutic outcomes in clinical trials. However, random fluctuations in these markers of infection can obscure clinically significant change. We employ a Monte Carlo simulation to investigate contributing factors in the expected variability in CD4 T-cell count and viral load due solely to the stochastic nature of HIV infection. The simulation includes processes that contribute to the variability in HIV infection including CD4 and CD8 T-cell population dynamics as well as T-cell activation and proliferation. The simulation results may reconcile the wide range of variabilities in viral load observed in clinical studies, by quantifying correlations between viral load measurements taken days or weeks apart. The sensitivity of variability in T-cell count and viral load to changes in the lifetimes of CD4 and CD8 T-cells is investigated, as well as the effects of drug therapy.

Factors associated with delayed initiation of HIV medical care among infected persons attending a southern HIV/AIDS clinic

BACKGROUND

Despite the proven benefits conferred by early human immunodeficiency virus (HIV) diagnosis and presentation to care, delays in HIV medical care are common; these delays are not fully understood, especially in the southern United States.

METHODS

We evaluated the extent of, and characteristics associated with, delayed presentation to HIV care among 1,209 patients at an HIV/AIDS Outpatient Clinic in Birmingham, Alabama between 1996 and 2005.

RESULTS

Two out of five (41.2%) patients first engaged care only after they had progressed to CDC-defined AIDS. Among these, 53.6% were diagnosed with HIV in the year preceding entry to care. Recent presentation (2002 - 2005), male sex, age > or = 25, Medicare or Medicaid insurance coverage, and presentation within six months of HIV diagnosis were independently associated with initiating care after progression to AIDS.

CONCLUSIONS

A high proportion of patients entered clinical care after experiencing substantial disease progression. Interventions that effectively improve the timing of HIV diagnosis and presentation to care are needed.

A modeling approach to the impact of HIV mutations on the immune system

A dynamical system modeling the HIV infection, including a mutation occurrence process, is used, after simplifications, to show the impact of the viral diversity on the immune response and disease dynamics, by introducing an indicator of the immune system behavior, the immunological recognition efficacy (IRE) index. The existence, the expression and the stability of the endemically infected steady state of the IRE index-based model, as function of this index, are mathematically analyzed. The monotony of the steady state with respect to the IRE index is studied and an asymptotic analysis of the dynamical system performed. It is shown that the IRE index-based model provides a bound to the responses of the initial complex dynamical system. The biological interpretation of these mathematical results is the exhaustion of the immune system as a consequence of the continuous generation of viral mutants.

Optimal HIV treatment by maximising immune response

We present an optimal control model of drug treatment of the human immunodeficiency virus (HIV). Our model is based upon ordinary differential equations that describe the interaction between HIV and the specific immune response as measured by levels of natural killer cells. We establish stability results for the model. We approach the treatment problem by posing it as an optimal control problem in which we maximise the benefit based on levels of healthy CD4+ T cells and immune response cells, less the systemic cost of chemotherapy. We completely characterise the optimal control and compute a numerical solution of the optimality system via analytic continuation.

T cell dynamics in HIV-1 infection

In the absence of antiretroviral treatment, HIV-1 establishes a chronic, progressive infection of the human immune system that invariably, over the course of years, leads to its destruction and fatal immunodeficiency. Paradoxically, while viral replication is extensive throughout the course of infection, deterioration of conventional measures of immunity is slow, including the characteristic loss of CD4(+) T cells that is thought to play a key role in the development of immunodeficiency. This conundrum suggests that CD4(+) T cell-directed viral cytopathicity alone cannot explain the course of disease. Indeed, recent advances now indicate that HIV-1 pathogenesis is likely to result from a complex interplay between the virus and the immune system, particularly the mechanisms responsible for T cell homeostasis and regeneration. We review these data and present a model of HIV-1 pathogenesis in which the protracted loss of CD4(+) T cells results from early viral destruction of selected memory T cell populations, followed by a combination of profound increases in overall memory T cell turnover, damage to the thymus and other lymphoid tissues, and physiological limitations in peripheral CD4(+) T cell renewal.

Comparison of three kinetic models of HIV-1 infection: implications for optimization of treatment

Clinical markers in the peripheral blood guide the treatment of human immunodeficiency virus type 1 (HIV-1). Likewise, many of the theoretical models developed to simulate infection only incorporate variables in the blood. To test the suitability of blood-only models, three distinct models of HIV infection kinetics are compared: "full model" including latently and actively infected cells and virus in the peripheral blood and lymphoid tissue (LT); "reduced model", including peripheral blood and LT without latent cells; and "blood model" including only actively infected cells and virus in the peripheral blood. Using the same parameter values for all three, qualitative differences are demonstrated between the blood model and its more inclusive counterparts. Additionally, optimization studies show that the reduced and blood models generate progressively lower optimal treatment levels relative to the full model when constant-level treatment is considered. These findings indicate that including the lymphoid tissue and latently infected cells into kinetic models may lead to differing conclusions with regard to optimal treatment and could be useful in guiding therapy even when plasma viral levels are below detectable limits.

Review of medical encounters in the 5 years before a diagnosis of HIV-1 infection: implications for early detection

Early detection of HIV infection improves prognosis and reduces transmission, but 30%-40% of cases are diagnosed late. A comprehensive and systematic review of medical encounters before diagnosis has not been done. This study reviews 5 years of medical encounters before the diagnosis of HIV infection in members of a large managed care organization where access to care is reasonably good. Patient characteristics, HIV risk factors, and clinical events preceding diagnosis were examined and tested for association with late diagnosis (CD4 cell count of <200/microL at diagnosis). Of 440 HIV-infected patients, 62% had CD4 cell counts of <350/microL, 43% had CD4 cell counts of <200/microL, and 18% had CD4 cell counts of <50/microL at diagnosis. Twenty-six percent of all patients had risks documented >1 year before diagnosis. Only 22% of patients had one of eight clinical indicators suggested in the literature as reasons to test for HIV >1 year before diagnosis. In multiple logistic regression, older age, male sex, race, risk group, no prior HIV testing, physician-initiated testing, and having any of eight clinical indicators before diagnosis were each associated with late diagnosis (p <or=.05). Late diagnosis remains a challenge despite good access to care. In our setting, effective risk assessment before symptoms arise offers greater potential for raising the mean CD4 cell count at diagnosis than does increased awareness of selected HIV-associated clinical prompts.

Molecular virology and immunology of HIV infection

Great progress has been made with respect to our understanding of the immunopathogenesis of AIDS and the infectious agent, HIV, that causes the disease. HIV, a human retrovirus with tropism for CD4(+) T cells and monocytes, induces a decrease of T-cell counts, T-cell dysfunction, and, ultimately, immunodeficiency. HIV also causes B-cell dysfunction characterized by polyclonal activation, hypergammaglobulinemia, and lack of specific antibody responses. Chemokine receptors-mainly CCR5 and CXCR4-have been found to be necessary for viral entry into the host cell, a step that can be inhibited by chemokine-related molecules that are ligands for those receptors. After HIV infection, a strong cellular immunity develops and partially controls viral replication. It can take several years for HIV infection to become clinically evident. Studies in long-term nonprogressors have shown the determinant roles of both helper and cytotoxic T cells in the control of HIV disease. Advances in HIV immunology research are currently being applied in the development of prophylactic and therapeutic vaccines.

Dynamics of naive and memory CD4+ T lymphocytes in HIV-1 disease progression

Understanding the dynamics of naive and memory CD4+ T cells in the immune response to HIV-1 infection can help elucidate typical disease progression patterns observed in HIV-1 patients. Although infection markers such as CD4+ T-cell count and viral load are monitored in patient blood, the lymphatic tissues (LT) have been shown to be an important viral reservoir. Here, we introduce the first comprehensive theoretical model of disease progression based on T-cell subsets and virus circulating between the two compartments of LT and blood. We use this model to predict several trademarks observed in adult HIV-1 disease progression such as the establishment of a setpoint in the asymptomatic stage. Our model predicts that both host and viral elements play a role in determining different disease progression patterns. Viral factors include viral infectivity and production rates, whereas host factors include elements of specific immunity. We also predict the effect of highly active antiretroviral therapy and treatment cessation on cellular and viral dynamics in both blood and LT.

Increased expression of the inflammatory chemokine CXC chemokine ligand 9/monokine induced by interferon-gamma in lymphoid tissues of rhesus macaques during simian immunodeficiency virus infection and acquired immunodeficiency syndrome

Chemokines are important mediators of cell trafficking during immune inductive and effector activities, and dysregulation of their expression might contribute to the pathogenesis of human immunodeficiency virus type 1 and the related simian immunodeficiency virus (SIV). To understand better the effects of SIV infection on lymphoid tissues in rhesus macaques, we examined chemokine messenger RNA (mRNA) expression patterns by using DNA filter array hybridization. Of the 34 chemokines examined, the interferon gamma (IFN-gamma)-inducible chemokine CXC chemokine ligand 9/monokine induced by interferon-gamma (CXCL9/Mig) was one of the most highly up-regulated chemokines in rhesus macaque spleen tissue early after infection with pathogenic SIV. The relative levels of expression of CXCL9/Mig mRNA in spleen and lymph nodes were significantly increased after infection with SIV in both quantitative image capture and analysis and real-time reverse transcriptase-polymerase chain reaction assays. In addition, in situ hybridization for CXCL9/Mig mRNA revealed that the patterns of expression were altered after SIV infection. Associated with the increased expression of CXCL9/Mig were increased numbers of IFN-gamma mRNA-positive cells in tissues and reduced percentages of CXC chemokine receptor (CXCR) 3(+)/CD3(+) and CXCR3(+)/CD8(+) lymphocytes in peripheral blood. We propose that SIV replication in vivo initiates IFN-gamma-driven positive-feedback loops in lymphoid tissues that disrupt the trafficking of effector T lymphocytes and lead to chronic local inflammation, thereby contributing to immunopathogenesis.

The dynamics of CD4+ T-cell depletion in HIV disease

The size and composition of the CD4+ T-cell population is regulated by balanced proliferation of progenitor cells and death of mature progeny. After infection with the human immunodeficiency virus, this homeostasis is often disturbed and CD4+ T cells are instead depleted. Such depletion cannot result simply from accelerated destruction of mature CD4+ T cells - sources of T-cell production must also fail. Ironically, this failure may be precipitated by physiological mechanisms designed to maintain homeostasis in the face of accelerated T-cell loss.

Release of virus from lymphoid tissue affects human immunodeficiency virus type 1 and hepatitis C virus kinetics in the blood

Kinetic parameters of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infections have been estimated from plasma virus levels following perturbation of the chronically infected (quasi-) steady state. We extend previous models by also considering the large pool of virus localized in the lymphoid tissue (LT) compartment. The results indicate that the fastest time scale of HIV-1 plasma load decay during therapy probably reflects the clearance rate of LT virus and not, as previously supposed, the clearance rate of virus in plasma. This resolves the discrepancy between the clearance rate estimates during therapy and those based on plasma apheresis experiments. In the extended models plasma apheresis measurements are indeed expected to reflect the plasma decay rate. We can reconcile all current HIV-1 estimates with this model when, on average, the clearance rate of virus in plasma is approximately 20 day(-1), that of LT virus is approximately 3 day(-1), and the death rate of virus-producing cells is approximately 0.5 day(-1). The fast clearance in the LT compartment increases current estimates for total daily virus production. Because HCV is produced in the liver, we let virus be produced into the blood compartment of our model. The results suggest that extending current HCV models with an LT compartment is not likely to affect current estimates for kinetic parameters and virus production. Estimates for treatment efficacy might be affected, however.

A model to predict cell-mediated immune regulatory mechanisms during human infection with Mycobacterium tuberculosis

A key issue for the study of tuberculosis infection (TB) is to understand why individuals infected with Mycobacterium tuberculosis experience different clinical outcomes. Elaborating the immune mechanisms that determine whether an infected individual will suffer active TB or latent infection can aid in developing treatment and prevention strategies. To better understand the dynamics of M. tuberculosis infection and immunity, we have developed a virtual human model that qualitatively and quantitatively characterizes the cellular and cytokine control network operational during TB infection. Using this model, we identify key regulatory elements in the host response. In particular, factors affecting cell functions, such as macrophage activation and bactericidal capabilities, and effector T cell functions such as cytotoxicity and cytokine production can each be determinative. The model indicates, however, that even if latency is achieved, it may come at the expense of tissue damage if the response is not properly regulated. A balance in Th1 and Th2 immune responses governed by IFN-gamma, IL-10, and IL-4 facilitate this down-regulation. These results are further explored through virtual deletion and depletion experiments.