Figure 5: Phylogenetic analysis and gag fitness in virus from ES38 and CP2.

(a) Phylogentic tree of clonal nef sequences isolated from resting CD4⁺ T cells (circles) and replication-competent virus isolates for reference. Phylogenies were estimated by using a 'classical' approach, functioning under maximum-likelihood optimality criterion. Other representative B-clade isolates, consensus B-clade nef and the clade C outgroup are denoted. Fitness of patient-specific viral gag. (b) Representative fluorescence-activated cell sorting plots showing GFP expression indicates infection with single cycle, pseudotyped virus. (c) Percent infection with various volumes of pseudotyped virus containing gag from ES38 (red), CP2 (brown) and wild-type NL4-3 (blue) was determined and repeated for three donors, producing similar results. Approximate levels of p24 in each infectious volume are shown, estimated and normalized based on NL4-3. Infection of healthy donor CD4⁺ T cells was normalized by transfection efficiency. Error bars represent standard error of the means from three independent experiments.