Modeling the short-, middle- and long-term viral load responses for comparing estimated dynamic parameters

A virologic marker, the number of HIV RNA copies or viral load, is currently used to evaluate antiviral therapies in AIDS clinical trials. This marker can be used to assess the antiviral potency of therapies, but is easily affected by drug exposures, drug resistance and other factors during the long-term treatment evaluation process. The study of HIV dynamics is one of the most important development in recent AIDS research for understanding the pathogenesis of HIV-1 infection and antiviral treatment strategies. Although many HIV dynamic models have been proposed by AIDS researchers in the last decade, they have only been used to quantify short-term viral dynamics and do not correctly describe long-term virologic responses to antiretroviral treatment. In other words, these simple viral dynamic models can only be used to fit short-term viral load data for estimating dynamic parameters. In this paper, a mechanism-based differential equation models is introduced for characterizing the long-term viral dynamics with antiretroviral therapy. We applied this model to fit different segments of the viral load trajectory data from a simulation experiment and an AIDS clinical trial study, and found that the estimates of dynamic parameters from our modeling approach are very consistent. We may conclude that our model can not only characterize long-term viral dynamics, but can also quantify short- and middle-term viral dynamics. It suggests that if there are enough data in the early stage of the treatment, the results from our modeling based on short-term information can be used to capture the performance of long-term care with HIV-1 infected patients.     

Design of Viral Dynamic Studies for Efficiently Assessing Potency of Anti‐HIV Therapies in AIDS Clinical Trials

The study of HIV dynamics is one of the most important developments in recent AIDS research. It greatly improves our understanding of the pathogenesis of HIV infection. Recently it has been proposed to use HIV dynamics to evaluate the efficacy of antiviral treatments. Currently a large number of AIDS clinical trials on HIV dynamics are in development worldwide. However, many design issues that arise from HIV dynamic studies have not been addressed. In this paper, we study these problems using intensive Monte Carlo simulations and analytic methods. We evaluate a finite number of feasible candidate designs, which are currently used and proposed in AIDS clinical trials from different perspectives. We compare the viral dynamic marker and classical viral load change markers in terms of power for identifying treatment difference, asymptotic relative efficiency, and sensitivity. Finally we propose some useful suggestions for practitioners based on our results.     

Hierarchical Bayesian inference for HIV dynamic differential equation models incorporating multiple treatment factors

Studies on HIV dynamics in AIDS research are very important in understanding the pathogenesis of HIV‐1 infection and also in assessing the effectiveness of antiretroviral (ARV) treatment. Viral dynamic models can be formulated through a system of nonlinear ordinary differential equations (ODE), but there has been only limited development of statistical methodologies for inference. This article, motivated by an AIDS clinical study, discusses a hierarchical Bayesian nonlinear mixed‐effects modeling approach to dynamic ODE models without a closed‐form solution. In this model, we fully integrate viral load, medication adherence, drug resistance, pharmacokinetics, baseline covariates and time‐dependent drug efficacy into the data analysis for characterizing long‐term virologic responses. Our method is implemented by a data set from an AIDS clinical study. The results suggest that modeling HIV dynamics and virologic responses with consideration of time‐varying clinical factors as well as baseline characteristics may be important for HIV/AIDS studies in providing quantitative guidance to better understand the virologic responses to ARV treatment and to help the evaluation of clinical trial design in response to existing therapies.     

Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics

MOTIVATION: Functional mapping has proven to be powerful for characterizing quantitative trait loci (QTL) that control complex dynamic traits. More recently, functional mapping has been extended to identify the host QTL responsible for HIV dynamics by incorporating a parametric bi-exponential function for earlier stages of viral load trajectories. However, existing functional mapping cannot be used to map long-term HIV dynamics because no mathematical functions are available for later stages of HIV dynamic changes. RESULTS: We derived a statistical model for functional mapping of dynamic QTL through characterizing HIV load trajectories during a long-term period semiparametrically. The new model was constructed within the maximum likelihood framework and implemented with the EM-simplex algorithm. It allows for the test of differences in the genetic control of short- and long-term HIV dynamics and the characterization of the effects of viral-host genome interaction. Extensive simulation studies have been performed to test the statistical behavior of this model. The new model will provide an important tool for genetic and genomic studies of human complex diseases like HIV/AIDS and their pathological progression. AVAILABILITY: Available on request from the corresponding author.     

HIV感染动力学模型概述

自1981年美国首次发现艾滋病以来,艾滋病在世界范围内广泛传播,引起医学专家、生物学家、数学家和物理学家等的极大关注。近年来,HIV动力学模型成为HIV治疗领域的研究热点。HIV基本动力学模型的研究有助于实现对未来疾病发展状况的描述与预测,HIV感染控制模型的研究有助于改善HIV病毒患者的治疗方案,对控制模型的优化有利于发现对HIV患者的有效治疗策略。本文概述了几种基本的HIV感染动力学模型,分析比较了它们的性能差异和各自存在的优缺点,介绍了HIV控制模型及其优化控制模型的计算机Matlab/simulink模拟。     

Designer antiviruses for HIV

Potentially, antiviruses that interfere with HIV propagation could be used as AIDS therapy. If problems associated with HIV recombination and the dynamics of the interactions between HIV and antivirus can be resolved by an appropriate design, an antivirus might defer or prevent the development of AIDS, and might benefit AIDS patients.     

Modeling the Genetic Control of HIV-1 Dynamics After Highly Active Antiretroviral Therapy

The progression of HIV disease has been markedly slowed by the use of highly active antiretroviral therapy (HAART). However, substantial genetic variation was observed to occur among different people in the decay rate of viral loads caused by HAART. The characterization of specific genes involved in HIV dynamics is central to design personalized drugs for the prevention of this disease, but usually cannot be addressed by experimental methods alone rather than require the help of mathematical and statistical methods. A novel statistical model has been recently developed to detect genetic variants that are responsible for the shape of HAART-induced viral decay curves. This model was employed to an HIV/AIDS trial, which led to the identification of a major genetic determinant that triggers an effect on HIV dynamics. This detected major genetic determinant also affects several clinically important parameters, such as half-lives of infected cells and HIV eradication times.Key Words: Hardy-weinberg equilibrium, bi-exponential function, quantitative trait loci, HIV dynamics, functional mapping.     

The use of operational modeling of HIV/AIDS in a systems approach to public health decision making.

Compartmental models of infectious diseases readily represent known biological and epidemiological processes, are easily understood in flow-chart form by administrators, are simple to adjust to new information, and lend themselves to routine statistical analysis such as parameter estimation and model fitting. Technical results are immediately interpretable in epidemiological and public health terms. Deterministic models are easily stochasticized where this is important for practical purposes. With HIV/AIDS, serial data on both HIV prevalence and AIDS morbidity have been available from San Francisco. Assuming the distribution of the incubation period to be biologically stable, statistical analysis is quite feasible in other regions, even those with no reliable HIV data. Transmission rates must be estimated locally. It is also often possible to estimate the effective size of a population subgroup at risk, from population data on AIDS morbidity only. Computer simulation provides estimates of the evolving pattern of both HIV prevalence and AIDS morbidity. Some public health questions can be answered only by appropriately formulated stochastic models.     

AIDS猕猴模型在HIV疫苗研究中的应用

对HIV疫苗的研究一直是国际上艾滋病方面研究的热点和难点。动物模型则为疫苗研究必不可缺少的重要工具,缺乏合适的动物模型很大程度上制约了AIDS疫苗的研究。目前在国际上SIV或SHIV感染的猕猴模型为最常用的AIDS研究模型,受猕猴背景及病毒特性等多种因素的影响,使得以上两种模型在HIV疫苗研究中仍存在一定的局限性。为了更好地发挥猕猴模型在HIV疫苗研究中的巨大潜力,开发理想的AIDS猕猴模型已成为目前HIV疫苗研究的首要任务。本文简要介绍了AIDS疫苗的研发策略、研发概况以及SIV/SHIV猕猴模型在HIV疫苗中的应用,并对其中存在的问题及其应用前景进行了探讨。     

猕猴模型在HIV疫苗研究中的应用

对HIV疫苗的研究一直是国际上艾滋病方面研究的热点和难点。动物模型则为疫苗研究必不可缺少的重要工具,缺乏合适的动物模型很大程度上制约了AIDS疫苗的研究。目前在国际上SIV或SHIV感染的猕猴模型为最常用的AIDS研究模型,受猕猴背景及病毒特性等多种因素的影响,使得以上两种模型在HIV疫苗研究中仍存在一定的局限性。为了更好地发挥猕猴模型在HIV疫苗研究中的巨大潜力,开发理想的AIDS猕猴模型已成为目前HIV疫苗研究的首要任务。本文简要介绍了AIDS疫苗的研发策略、研发概况以及SIV/SHIV猕猴模型在HIV疫苗中的应用,并对其中存在的问题及其应用前景进行了探讨。     

When Did HIV Incidence Peak in Harare,Zimbabwe? Back-Calculation from Mortality Statistics

HIV prevalence has recently begun to decline in Zimbabwe, a result of both high levels of AIDS mortality and a reduction in incident infections. An important component in understanding the dynamics in HIV prevalence is knowledge of past trends in incidence, such as when incidence peaked and at what level. However, empirical measurements of incidence over an extended time period are not available from Zimbabwe or elsewhere in sub-Saharan Africa. Using mortality data, we use a back-calculation technique to reconstruct historic trends in incidence. From AIDS mortality data, extracted from death registration in Harare, together with an estimate of survival post-infection, HIV incidence trends were reconstructed that would give rise to the observed patterns of AIDS mortality. Models were fitted assuming three parametric forms of the incidence curve and under nine different assumptions regarding combinations of trends in non-AIDS mortality and patterns of survival post-infection with HIV. HIV prevalence was forward-projected from the fitted incidence and mortality curves. Models that constrained the incidence pattern to a cubic spline function were flexible and produced well-fitting, realistic patterns of incidence. In models assuming constant levels of non-AIDS mortality, annual incidence peaked between 4 and 5% between 1988 and 1990. Under other assumptions the peak level ranged from 3 to 8% per annum. However, scenarios assuming increasing levels of non-AIDS mortality resulted in implausibly low estimates of peak prevalence (11%), whereas models with decreasing underlying crude mortality could be consistent with the prevalence and mortality data. HIV incidence is most likely to have peaked in Harare between 1988 and 1990, which may have preceded the peak elsewhere in Zimbabwe. This finding, considered alongside the timing and location of HIV prevention activities, will give insight into the decline of HIV prevalence in Zimbabwe.     

Prevention of Parent to Child Transmission (PPTCT) Program Data in India: An Emerging Data Set for Appraising the HIV Epidemic

Background

Evidence based resource allocation and decentralized planning of an effective HIV/AIDS response requires reliable information on levels and trends of HIV at national and sub-national geographic levels. HIV sentinel surveillance data from antenatal clinics (HSS-ANC) has been an important data source to assess the HIV/AIDS epidemic in India, but has a number of limitations. We assess the value of Prevention of Parent to Child Transmission (PPTCT) programme data to appraise the HIV epidemic in India.

Methods/Findings

HIV data from PPTCT sites were compared to HSS-ANC and general population level surveys at various geographic levels in the states of Karnataka, Maharashtra and Andhra Pradesh. Chi-square tests were used to ascertain statistical significance. PPTCT HIV prevalence was significantly lower than HSS-ANC HIV prevalence (0.92% vs. 1.22% in Andhra Pradesh, 0.65% vs. 0.89% in Karnataka, 0.52% vs. 0.60% in Maharashtra, p<0.001 for all three states). In all three states, HIV prevalence from PPTCT centres that were part of the sentinel surveillance was comparable to HSS-ANC prevalence but significantly higher than PPTCT centres that were not part of the sentinel surveillance. HIV prevalence from PPTCT data was comparable to that from general population surveys. In all three states, significant declines in HIV prevalence between 2007 and 2010 were observed with the PPTCT data set. District level analyses of HIV trends and sub-district level analysis of HIV prevalence were possible using the PPTCT and not the HSS-ANC data sets.

Conclusion

HIV prevalence from PPTCT may be a better proxy for general population prevalence than HSS-ANC. PPTCT data allow for analysis of HIV prevalence and trends at smaller geographic units, which is important for decentralized planning of HIV/AIDS programming. With further improvements to the system, India could replace its HSS-ANC with PPTCT programme data for surveillance.     

Design of long-term HIV dynamic studies using semiparametric mixed-effects models

Studies of HIV dynamics in AIDS research are very important in understanding the pathogenesis of HIV-1 infection and also in assessing the effectiveness of antiviral therapies. There are many AIDS clinical trials on HIV dynamics currently in development worldwide, giving rise to many design issues yet to be addressed. For example, most studies are focused on short-term viral dynamics and the existing models may not be applicable to describe long-term virologic response. In this paper, we use a simulation-based approach to study the designs of long-term viral dynamics under semiparametric nonlinear mixed-effects models. These models not only can preserve the meaningful interpretation of the short-term HIV dynamics, but also characterize the long-term virologic responses to antiretroviral (ARV) treatment. We investigate a number of feasible clinical protocol designs similar to those currently used in AIDS clinical trials. In particular, we evaluate whether earlier samplings can result in more useful information about the viral response trajectory; we also evaluate the effectiveness of two strategies: more frequent samplings per subject with fewer subjects versus fewer samplings per subject with more subjects while keeping the total number of samplings constant. The results of our investigation provide quantitative guidance for designing and selecting ARV therapy.     

Mining HIV dynamics using independent component analysis

MOTIVATION: We implement a data mining technique based on the method of Independent Component Analysis (ICA) to generate reliable independent data sets for different HIV therapies. We show that this technique takes advantage of the ICA power to eliminate the noise generated by artificial interaction of HIV system dynamics. Moreover, the incorporation of the actual laboratory data sets into the analysis phase offers a powerful advantage when compared with other mathematical procedures that consider the general behavior of HIV dynamics. RESULTS: The ICA algorithm has been used to generate different patterns of the HIV dynamics under different therapy conditions. The Kohonen Map has been used to eliminate redundant noise in each pattern to produce a reliable data set for the simulation phase. We show that under potent antiretroviral drugs, the value of the CD4+ cells in infected persons decreases gradually by about 11% every 100 days and the levels of the CD8+ cells increase gradually by about 2% every 100 days. AVAILABILITY: Executable code and data libraries are available by contacting the corresponding author. IMPLEMENTATION: Mathematica 4 has been used to simulate the suggested model. A Pentium III or higher platform is recommended.     

HIV/AIDS epidemic in Eastern Europe: Recent developments in the Russian Federation and Ukraine among women

Background: The Russian Federation and the Ukraine are among the Eastern European countries with the fastest growing number of cases of HIV. According to data from the Joint United Nations Program on HIV/AIDS, nearly 90% of newly reported HIV diagnoses in Eastern Europe in 2006 were from the Russian Federation (66%) and the Ukraine (21%). A growing number of women are infected with HIV. The impact of gender on HIV/AIDS is an important factor in understanding the development and evolution of the HIV/AIDS epidemic in Eastern Europe.Objective: The aim of this study was to assess the importance of integrating gender consideration into the creation of HIV programs and to examine the effect of gender on HIV/AIDS.Methods: Reported HIV/AIDS cases from the official epidemiological register of the Ukrainian Centre for AIDS Prevention alongside data from the Russian Federal AIDS Center were analyzed. Joint United Nations Program on HIV/AIDS country fact sheets were reviewed and analyzed, and this information was supplemented with published HIV prevalence and sexually transmitted disease case reporting information, unpublished reports, and expert evaluations.Results: Of the newly registered cases of HIV, the proportion of women rose from 13.0% in 1995 to 44.0% in 2006 in the Russian Federation, and from 37.2% in 1995 to 41.9% in 2006 in the Ukraine. There has also been a considerable increase in mother-to-child transmission of HIV since 1995. Between 1987 and 1994, the proportion of children among the people newly infected with HIV in the Ukraine was 2.2%; in 2006 it was 17.6%. In 2006, 16,078 new HIV cases were registered in the Ukraine and 39,652 new HIV cases in the Russian Federation. Large increases in the number of HIV-infected women were reported from both countries.Conclusions: The data examined in this study suggest subregional differences in the magnitude of the HIV/AIDS epidemic in the Russian Federation and the Ukraine and the importance of the impact of gender on the rapid spread of the HIV/AIDS epidemic among women and women of child-bearing age. To protect women from HIV infection, it is important to find ways to empower them by implementing policies and specific prevention measures that increase their access to knowledge about HIV/AIDS; the empowerment of women is vital to reversing the HIV/AIDS epidemic.     

HIV/AIDS in Asia： The Shape of Epidemics and Their Molecular Epidemiology

The Asia-Pacific region is a home to 60% of the population in the world and to approximately one quarter of people with HIV/AIDS. Close to a million of people has been infected and a half million people died of AIDS annually in Asia,becoming the second largest epicenter of global AIDS epidemic. Molecular epidemiology has been useful tool to track a course of HIV spread. In-depth knowledge from the studies on molecular epidemiology elucidates the dynamics of HIV spread and the interrelationship of epidemics in the different regions in Asia.     

A strategy for testing established human plasma protein manufacturing procedures for their ability to inactivate or eliminate human immunodeficiency virus

The manufacturing procedures used for the preparation of human plasma proteins that were established before AIDS was first described may reasonably be expected to provide AIDS safe products. Such manufacturing procedures are heat treatment at 60 degrees C in solution for ten hours, described as pasteurization, preparation of human immunoglobulins by ethanol precipitation, pepsin treatment, and sulfonation. To test whether these methods effectively inactivated and/or eliminated the AIDS causing human immunodeficiency virus (HIV), nine volumes or more of plasma or a plasma fraction taken from a production lot were spiked with HIV using one volume of a HIV concentrate and were then subjected to exactly the same procedure as that specified for the manufacturing process. HIV infectivity titres of the initial HIV/plasma protein mixtures and of the resulting products after treatment were determined by the H9 cell assay. In all cases studied complete inactivation/elimination of the added HIV was achieved. We therefore conclude that pasteurization of human plasma proteins or the manufacturing procedure used for the isolation of immunoglobulins from plasma pools result in final products which do not contain any infectious HIV and which are thus safe in that they cannot be vehicles for the transmission of AIDS.