(A) The rate of CD8E-mediated infected cell clearance () plotted as a function of infected cells () and effector CD8+ T cells (; CD8E). The colored markers (denoted a–g) indicate the infected cell clearance rate that corresponds to different time points during the infection for the best-fit solution. (B) Values of for the indicated time points associated with the markers a–g. (C) Corresponding locations of the various values (markers a–g) on the best-fit solution of the CD8+ T cell model for virus (), infected cells (), and CD8E (). (D) Solutions of the CD8+ T cell model (Equation (1)-(6)) for virus () and total CD8+ T cells () using the best-fit parameters (black line) and when varying the CD8E expansion rate (; magenta lines) to illustrate how different total CD8+ T cell magnitudes alter infection duration. The magenta lines are solutions from when the percent relative to from the best-fit solution was 42% (solid line), 39.2% (dash-dotted line), 39.1% (dashed line), or 37% (dotted line). (E) The time at which infected cells reach the half-saturation constant (; gray circles) and the infection duration (time where ; black diamonds) are shown for the various CD8+ T cell magnitudes. The gray line between these points is the time required to eliminate infected cells and achieve complete resolution of the infection (). (F) Fit of the CD8+ T cell model (Equation (1)-(6)) to viral loads and CD8+ T cells (magenta diamonds) following depletion at −2, 0, 3, and 7 d pi (magenta arrows). The best model (Supplementary file 2) resulted in fewer target cells (), a lower CD8E influx (), and a higher CD8E expansion rate (). All other parameters were fixed to the best-fit value in Table 1. The solid lines are and the dashed lines are for the cases where CD8+ T cells were depleted (magenta) and where they were not depleted (black). (G) Comparison of the log10 ratio of virus to CD69+CD8+ T cells with and without CD8+ T cell depletion (magenta and black, respectively). All data are shown as mean ± standard deviation.