Figure 2. Estimating the Cost of a CTL Escape Mutation.

(A) Plots the hypothetical changes in the replication rate of the virus during the acute phase of infection. We assume that initially (until time T_r) the virus population expands exponentially at rate r_max, and after t = T_r , the virus replication rate is reduced exponentially at rate λ to a smaller value r_min. Biologically this would correspond to the acute phase of SIV/HIV infection when the replication rate of the virus depends on the availability of target cells, which are depleted by the virus.

(B) Plots changes in the ratio z(t) calculated using Equation 8 with k(t) = 0 for the replication rate r(t) shown by a solid line in (A). For two measurements of the ratio z at t_s = 0 and t_e = 25 d, we obtain a minimal estimate of the cost of the escape mutation assuming exponential virus growth with r_max = 1.5 d⁻¹ (shown by dashed lines), i.e., c_min = 0.065 which is 65% of the actual fitness cost. Other parameters: r_min = 0.5 d⁻¹, T_r = 10 d, λ = 0.5 d⁻¹, z(0) = 0.1, c = 0.1.