Extended Data Fig. 2: Genetic analyses of rebounding plasma HIV in Participant 04.

a. Phylogenetic tree analysis of the 3’-half of HIV sequences. The phylogenetic tree without subtype B reference sequences was constructed using the neighbor-joining method and was rooted with the predominant sequences from day 56. The tree reliability was estimated by 1000 bootstrap replicates. The nodes that were supported by more than 80% of bootstrap replicates are indicated by asterisks. The sequences derived at multiple time points are shown in different symbols/colors. b. Genetic divergence of the 3’-half of HIV sequences of rebounding plasma HIV from each time point compared to that from day 56. c. Mutations identified in previously known HLA-restricted CD8⁺ T cell epitopes. Amino acid substitutions in all seven viral proteins (Vif, Vpr, Vpu, Tat, Rev, Env, and Nef) in the 3’-half of HIV sequences obtained at the time of plasma viral rebound (days 56, 581, 862, and 875) were examined to identify potential escape mutations at previously known HLA (A*03 and B*40)-restricted CD8⁺ T cell epitopes over time.