Figure 2

Histogram of the observed number of mutant sequences sampled at more than one time point, N _m . At day 6, 12, 18, and 24 post infection, 30 nef sequences were sampled. The observed number of mutant sequences which were present at more than one time point was counted from the total of 120 sequences sampled sequentially over 4 time points. For example, N _m = 0 denotes that no mutant sequence from the founder gene appeared at more than one time point. The histogram of N _m with 95% CIs was constructed by repeating 10² asynchronous MC infection simulations. While the founder nef gene remains as the majority of the sampled sequences, loss of mutant sequences in the serial samples was frequently observed.