Fig. 2.

Individual HIV-1 diversity dynamics. Each of the 15 subjects’ diversity dynamics as a function of time over 2 years since the first sample. The dotted line of each panel indicates the neutral diversification rate, $2.16\times {10}^{-5}$ per site per day [33–35], and the solid curve denotes the best-fit of the mixed effects model. All 15 subjects show a statistically significant linear increase in diversity over time; subjects CH077, CH131, CH159 and CH505’s quadratic increases are statistically significant. The linear diversification rate for the first 150 days of each individual is listed in Table 1 and the linear and quadratic diversification rates over 2 years are listed in Additional file 1: Table S1