Fig 3. Experimental measurement of drug effect on R₀ and the initial number of infected cells N₀.

(A) Flow cytometry plots of the fraction of infected cells at different days post infection in the absence of drug or presence of 60 μM TFV or 16 nM ATV. Day 2 is the first time-point after the initial cell-free infection, corresponding to approximately one viral cycle. X-axis is GFP fluorescence, y-axis is autofluorescence, with the fraction of infected cells corresponding to the cells within the area outlined in yellow. Infected cell cultures in the presence of either drug were diluted 1:2 every 2 days. Infected cultures in the absence of drug were diluted 1:100 into uninfected cells every 2 days. (B) Measurement of R₀ in the absence and presence of drug. The number of infected cells at each time-point is normalized by the number of infected cells at day 2 and corrected for the dilution factor used in each infection cycle. 3 independent experiment were performed, with each point denoting the mean ± std of 3 experimental replicates per experiment. Infection in the absence of drug is shown as red circles, TFV as blue triangles, and ATV as green squares. (C) Effect of drug on N₀. For each drug condition N₀ was measured 2 days after cell-free HIV infection and normalized by N₀ for no drug. Mean ± std of 3 independent experiments, where normalization was with N₀ in the absence of drug as measured in the same experiment. Raw numbers of infected cells averaged over all experiments were 1.3 × 10⁴ ± 1.5 × 10³ for no drug infection, 3.4 × 10² ± 1.3 × 10² for TFV and 1.1 × 10⁴ ± 7.4 × 10³ for ATV (mean ± std). The difference between TFV and ATV was significant (p = 6 × 10⁻¹⁴ by t-test).