Relationship between HIV-1 fitness with protease inhibitor-associated compensatory mutations and (A) CD4 cell counts or (B) viral loads. For a population of recently diagnosed drug-naïve patients, a fitness landscape was used to estimate in vivo HIV fitness under protease inhibitor drug selective pressure. Estimated viral fitness was discretized into 10 groups, and the distribution of viral load and CD4 cell count was plotted using boxplots. The widths of boxplot are proportional to the number of samples used. The proportion of patients with indications of recent (acute) infection within each fitness group is shown in red.