PATTERNS OF HIV-1 GENETIC VARIATION OVER TIME IN FOUR PATIENTS

Abstract

This thesis presents the longitudinal phylogenetic molecular analysis of the V3 region of the HIV env gene in four hemophiliac participants enrolled in the Hemophilia Growth and Development Study (HGDS). The subjects were selected based on the rate of CD4 T cell decline during the first two years of enrollment in the HGDS. The analysis differs from most previous studies in that plasma HIV viral RNA (not proviral) was analyzed for the extent and character of virion diversity during the latent asymptomatic period through CD4 T cell decline. Major findings were: 1) Individuals with similar clinical courses have distinctively different levels of viral diversity during the period of CD4 decline, suggesting differential immune pressures driving the rate of quasispecies evolution. 2) Two divergent populations of HIV co-existing over multiple timepoints in a single patient; one population of sequences with predominantly macrophage tropic and the other with T cell tropic genotypic features were detected. 3) Positive selection for amino acid substitution within the V3 region correlates well with immune status. In 3 of the 4 patients, there was a general trend towards positive selection for change when CD4 T cell counts were >200, but mutations tended to be silent when immune pressure decreased as CD4 T cell counts fell below 200. 4) Sequences from multiple timepoints within a patient did not cluster in distinct clades. Instead intra-timepoint sequences were found to overlap with sequences from other timepoints. This suggests that early variants persist over time and may represent escape mutants that have evaded immune surveillance.