This can be understood by evaluating, R, the effective reproductive number for the system in the presence of therapy, that is, the average number of secondary infected cells generated by one primary infected cell in a given population of target cells. The formal derivation of R is presented in S1 Text. Under the simplifying assumption that the CD4 T cell population in the drug sanctuaries (at a given value X^0) is very small compared to that in the main compartment, the effective reproductive number (Eq 5) can be understood by focusing on just the dynamics concerning the drug sanctuaries (Fig 4).