Rapid phenotypic drug susceptibility assays that detect drug resistance in HIV clinical isolates irrespective of the genes containing mutations that lead to drug resistance. The invention provides assays for determining HIV infection and the degree thereof, for determining the efficacy of candidate HIV inhibitors; and for clinically monitoring the progress of HIV therapies. In one embodiment, methods of the invention feature infecting a cell line, expressing CD4, CXCR4 and CCR5 receptors on the cell surface, and a marker gene product, with HIV in the presence of a putative HIV inhibitor, wherein the marker gene product expression increases in response to said cell line infection with HIV; and dynamically counting the number of said cells, e.g., by flow cytometry, expressing the marker gene product and comparing the number of cells expressing the marker gene product to a control value to determine whether the putative HIV inhibitor is an inhibitor of HIV.
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