Processes of viral evolution, and changes in host cell populations, lead to late-infection virological events that impact disease progression and outcome. Understanding the effects of such events is key to comprehending pathogenesis and the ways that post-acute-infection therapy can best benefit patients. The frequent switch of the viral population from the early use of CCR5 (R5) to the later use of CXCR4 (X4) as entry coreceptor may be a critical late event. X4 virus is associated with poor prognosis and faster disease progression, both in the absence of therapy and under HAART. Were this switch prevented, progression could be slowed. Progression is marked by depletion of naive CD4+ T-cells and cells recently produced by the thymus. Loss of these cells may contribute to the failure of T-cell homeostasis that precedes AIDS onset. Naive T-cells preferentially express CXCR4, so that late appearance of X4 virus may lead to immune deficiency. But it is not clear if properties of X4 viruses themselves, such as replicative fitness and cytopathicity, or X4 host cell range per se, mainly define the X4 role in HIV pathogenesis. Viral fitness is the complex result of evolving virus properties in the changing host environment. Fitness, cytopathicity, and disease are related, but not identical. In an effort to clarify the relationship between viral evolution and late-infection pathogenesis, we propose to 1) identify viral genetic changes that characterize progression to AIDS, and clinically relevant genetic predictors of progression and immune reconstitution under HAART; 2) identify viral genetic changes important to coreceptor usage and viral fitness; and, 3) clarify the relationships among cell population biology, viral phenotype and fitness, and disease outcome. To achieve these aims, we will analyze T cell populations, primary viruses and viral sequences obtained from 30 longitudinally-sampled HIV-infected men in the Multicenter AIDS Cohort Study (MACS). Additional patients will be sequenced less extensively, providing data for a study of correlation between baseline genotype and progression. Viral envelope genes will be analyzed using phylogenetic methods, and genotyped for coreceptor usage. Fitness of viruses will be assessed by in vitro competition, and cytopathicity of viruses will be tested using an in vitro apoptosis/caspase assay. Data will be correlated with markers of disease progression, and correlates will be assessed for their ability to predict the critical events leading to disease, by targeted analysis of additional subjects.
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