The ability to accelerate the accumulation of favorable combinations of mutations renders recombination a potent force underlying the emergence of forms of HIV that escape multi-drug therapy and specific host-immune responses. In this study, a mathematical model is developed that describes the dynamics of the emergence of recombinant forms of HIV following infection with diverse viral genomes. Mimicking recent in vitro experiments, target cells simultaneously exposed to two distinct, homozygous viral populations are considered and dynamical equations are constructed that predict the time-evolution of populations of uninfected, singly infected, and doubly infected cells, and homozygous, heterozygous, and recombinant viruses. Model predictions capture several recent experimental observations quantitatively and provide insights into the role of recombination in HIV dynamics. Comparisons of data from single round infection experiments with model predictions of the probability with which recombination accumulates distinct mutations present on the two genomic strands in a vision, indicates that »8 recombinational strand transfer events occur on average (95% confidence interval: 6-10) during reverse transcription of HIV in T cells. Model predictions of virus and cell dynamics describe the time-evolution and the relative prevalence of various infected cell subpopulations following the onset of infection observed experimentally. Remarkably, model predictions are in quantitative agreement with the experimental scaling relationship that the percentage of cells infected with recombinant genomes is proportional to the percentage of cells co-infected with the two genomes employed at the onset of infection. The model developed thus presents an accurate description of the influence of recombination on HIV dynamics in vitro. When distinctions between different viral genomes are ignored, the model reduces to the standard model of viral dynamics, which successfully predicts viral load changes in HIV patients undergoing therapy. The model developed may thus serve as a useful framework to predict the emergence of multi-drug resistant forms of HIV in infected individuals.

Statistical models have greatly improved our understanding of the pathogenesis of HIV-1 infection and guided for the treatment of AIDS patients and evaluation of antiretroviral (ARV) therapies. Although various statistical modeling and analysis methods have been applied for estimating the parameters of HIV dynamics via mixed-effects models, a common assumption of distribution is normal for random errors and random-effects. This assumption may lack the robustness against departures from normality so may lead misleading or biased inference. Moreover, some covariates such as CD4 cell count may be often measured with substantial errors. Bivariate clustered (correlated) data are also commonly encountered in HIV dynamic studies, in which the data set particularly exhibits skewness and heavy tails. In the literature, there has been considerable interest in, via tangible computation methods, comparing different proposed models related to HIV dynamics, accommodating skewness (in univariate) and covariate measurement errors, or considering skewness in multivariate outcomes observed in longitudinal studies. However, there have been limited studies that address these issues simultaneously. One way to incorporate skewness is to use a more general distribution family that can provide flexibility in distributional assumptions of random-effects and model random errors to produce robust parameter estimates. In this research, we developed Bayesian hierarchical models in which the skewness was incorporated by using skew-elliptical (SE) distribution and all of the inferences were carried out through Bayesian approach via Markov chain Monte Carlo (MCMC). Two real data set from HIV/AIDS clinical trial were used to illustrate the proposed models and methods. This dissertation explored three topics. First, with an SE distribution assumption, we compared models with different time-varying viral decay rate functions. The effect of skewness on the model fitting was also evaluated. The associations between the estimated decay rates based on the best fitted model and clinical related variables such as baseline HIV viral load, CD4 cell count and longterm response status were also evaluated. Second, by jointly modeling via a Bayesian approach, we simultaneously addressed the issues of outcome with skewness and a covariate process with measurement errors. We also investigated how estimated parameters were changed under linear, nonlinear and semiparametric mixed-effects models. Third, in order to accommodate individual clustering within subjects as well as the correlation between bivariate measurements such as CD4 and CD8 cell count measured during the ARV therapies, bivariate linear mixed-effects models with skewed distributions were investigated. Extended underlying normality assumption with SE distribution assumption was proposed. The impacts of different distributions in SE family on the model fit were also evaluated and compared. Real data sets from AIDS clinical trial studies were used to illustrate the proposed methodologies based on the three topics and compare various potential models with different distribution specifications. The results may be important for HIV/AIDS studies in providing guidance to better understand the virologic responses to antiretroviral treatment. Although this research is motivated by HIV/AIDS studies, the basic concepts of the methods developed here can have generally broader applications in other fields as long as the relevant technical specifications are met. In addition, the proposed methods can be easily implemented by using the publicly available WinBUGS package, and this makes our approach quite accessible to practicing statisticians in the fields.