This invention relates, in part, to methods and compositions for determining the susceptibility of an HIV to an anti-HIV
drug or the replication capacity of an HIV. In certain embodiments, the methods comprise culturing a host
cell in the presence of the anti-HIV
drug, measuring the activity of the indicator
gene in the host
cell; and comparing the activity of the indicator
gene as measured with a reference activity of the indicator
gene. In certain embodiments, the difference between the measured activity of the indicator gene relative to the reference activity correlates with the susceptibility of the HIV to the anti-HIV
drug, thereby determining the susceptibility of the HIV to the anti-HIV drug. In certain embodiments, the difference between the measured activity of the indicator gene relative to the reference activity indicates the replication capacity of the HFV, thereby determining the replication capacity of the HIV. In certain embodiments, the host
cell comprises a patient-derived segment and an indicator gene. In certain embodiments, the patient-derived segment comprises a
nucleic acid sequence that encodes
integrase or
RNAse H.