Fig 2 illustrates the threshold for ongoing replication as a function of the rate at which CD4 T cells move between compartments and the effectiveness of antiretroviral therapy in the drug sanctuaries (see S1 Text for derivation). Here, antiretroviral drug therapy is assumed to be highly effective in the main compartment (z1 = 0.97) and the drug sanctuaries are small in size compared to the main compartment (see S1 Fig for threshold analysis for larger sanctuaries). There is a negative relationship between the effectiveness of antiretroviral therapy in the drug sanctuaries and the rate of cell trafficking between compartments at the threshold for ongoing replication. Even perfect drug sanctuaries (z0 = 0) can only support ongoing replication provided the rate that CD4 T cells traffic through them is below a critical threshold. When immune control in the sanctuary is boosted, the critical threshold for trafficking is lower, that is, stopping ongoing replication in drug sanctuaries becomes easier.