Expansion of HIV-1 infected cells and the possible influence on tropism dynamics in individuals on antiretroviral therapy & adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia

For cellular infection HIV-1 interacts with the CD4 receptor and a chemokine receptor, either CCR5 or CXCR4. In the early phase of infection, the virus almost exclusively uses the CCR5-receptor. Only later during disease progression up to 50% of infected individuals without therapy experience a shift to a dominance of CXCR4-tropic viruses, associated with higher CD4 cell depletion rates and an accelerated disease progression. In contrast, under successful therapy a majority of patients show a decrease of CXCR4-tropic variants and only in a few an increase of CXCR4-tropic viruses is observed. As the increase of CXCR4-tropic viruses in patients under therapy was observed to be caused by the outgrowth of a single variant, this study aimed to investigate the possibility of clonal expansion of HIV-1 infected cells by integration site analysis. Although the results confirmed clonal expansion, aberrant cell proliferation due to HIV integration was not observed.
An additional study was performed to validate the popular HIV-1 genotyping tool, Geno2Pheno[coreceptor], for clinical samples of subtype CRF01_AE. The algorithm was shown to have a significant overcalling of X4 variants in this subtype, and by combining phenotypic results with genotypic predictions an adjusted false positive rate (FPR) cut-off was identified to provide more accurate tropism predictions. Included in this work was also the development of a cloning cassette optimized for phenotypic analysis of subtype CRF01_AE samples.