<p>Simulation results of naive T-cell counts (in black) and average TREC contents (in red) for an individual infected by HIV at the age of 30, assuming that the naive T-cell division rate increased according to the constraints described in Supplemental Methods. Left panels show the short-term dynamics while right panels show the long-term dynamics. Panel a shows the results for CD8<sup>+</sup> T cells, Panels b and c for CD4<sup>+</sup> T cells. In panel c, we have modeled the effect of increased turnover during the acute phase of infection, by using a 5-fold higher value of both <i>d</i> and <i>p</i> during the first 6 months of infection compared to the later stage of infection. For CD4<sup>+</sup> T cells (panels b and c) we plotted the upper and lower bounds on the parameter constraints (denoted by the solid lines (<i>k</i><sub><i>p</i></sub> = <i>k</i><sub><i>d</i></sub> and <i>k</i><sub><i>p</i></sub> = <i>d(k</i><sub><i>d</i></sub><i>—1)/p+1</i>, see Supplemental Methods) as well as an intermediate case (denoted by the dashed lines (<i>k</i><sub><i>d</i></sub><<i>k</i><sub><i>p</i></sub>< <i>d(k</i><sub><i>d</i></sub><i>—1)/p+1</i>) assuming that the thymic output and the average number of TREC per RTE are not changed after HIV infection (i.e. <i>k</i><sub><i>s</i></sub> = 1 and <i>k</i><sub>c</sub> = 1). <u>Parameters</u>: Panel a: before infection <i>σ</i><sub><i>0</i></sub> = 1.09×10<sup>10</sup> cells/year, <i>h</i> = 1.5×10<sup>11</sup>cells, <i>d</i> = 0.109/year, <i>c</i> = 0.25 and <i>ν</i> = 0.05/year; after infection: <i>d</i> = 1.314/year and <i>p</i> = 1.300/year. Panels b and c: before infection <i>σ</i><sub><i>0</i></sub> = 3.65×10<sup>10</sup> cells/year, <i>h</i> = 3.2×10<sup>11</sup>, <i>d</i> = 0.183/year, <i>c</i> = 0.25 and <i>ν</i> = 0.05/year; after infection: <i>d</i> = 0.548/year, <i>p</i> = 0.498, 0.510 or 0.532/year. Panel c: <i>d</i> = 2.740/year, <i>p</i> = 2.490, 2.550 or 2.660/year during the first six months of infection.</p
