Fig 4. The impact of trafficking on ongoing replication can be understood by focusing on the dynamics concerning the drug sanctuaries.

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 $\mathrm{\beta }{\widehat{\mathrm{X}}}_0(1-{\mathrm{z}}_0)/{\mathrm{u}}_0$ day^-1) and two efflux rates (cell clearance at rate δ₀ Y₀ day^-1 and cell egress at rate κτ₀Y₀ day^-1).