The effective reproductive number can be understood by focusing on just the dynamics concerning infected cell numbers in the drug sanctuaries (Y0) when the drug sanctuaries hold only a small fraction of the body’s CD4 T cells. Under this assumption the net traffic of infected cells out of the drug sanctuaries is approximately κτ0Y0 day-1 (see S1 Text for details). The dynamics of infected cells in the drug sanctuaries will therefore be governed by a single influx rate (new infections at rate βX^0(1−z0)/u0 day-1) and two efflux rates (cell clearance at rate δ0 Y0 day-1 and cell egress at rate κτ0Y0 day-1).