Fig 3.
Within-host dynamics for the within-host selection model (panels a-c) and the within-host neutral model (panels d-f), (a,d) in the absence of a reservoir (k = a = 0), (b,e) in the presence of a reservoir, but without homeostatic proliferation in the reservoir (rL = 0.5, k = 5 x 10−3, a = 0.01 per day, ρ = 0 per day), and (c,f) in the presence of a reservoir, with a low level of homeostatic proliferation (rL = 0.5, k = 5 x 10−4, a = 0.01 per day, ρ = 9 x 10−3 per day). The black line indicates the time at which the frequency of the initial strain has declined to 10%. The presence of a latent reservoir delays the within-host dynamics, and this delay becomes even more profound if there is a low level of homeostatic proliferation in the reservoir. The number of strains is n = 16. In the within-host selection model, strains have linearly increasing replication rates between γ1 = 1.0 and γ16 = 1.05 and the infection is initiated with strain 9. In the within-host neutral model, all strains have equal within-host fitness and strains are characterised by the number of neutral mutations they carry compared to the founder strain. In this case the last strain (carrying ≥15 mutations) is absorbing, i.e. there are no mutations out of this bin. All other parameter values are as stated in Table 1.