FIG. 4.

AQ9/NP10 epitope focus reveals active CTL selection and insight into population-level genetic dynamics. (A) High-resolution focus on substitutions observed in the Gag epitope AQ9/NP10 from amino acids 119–133 by visit time point. The y-axis is in log percentage, with the blue horizontal dotted line showing the sensitivity cutoff (0.0034%), and silent versus missense mutations shown in green and red, respectively. Interferon (IFN)-γ ELISpot confirmation of patient CTL targeting AQ9/NP10 using consensus subtype B Gag peptide (117–131), with the number of positive spots/10⁶ CD8 at 298.5, 340, 468, and 43 for V1–V3 and V6, respectively. (B) Neighbor-joining tree constructed using AQ9/NP10 containing amplicon 4 using all 20 haplotypes with a maximum occurrence frequency of >0.1% showing two distinct clusters distinguished by the key variants D123E and H126N. The corresponding heat map shows the haplotype frequency at each visit time point at log₁₀ frequency from yellow (low frequency) to blue (high frequency). (C) Pairwise Hamming distances for the haplotypes detected in V1 showing a bimodal distribution indicating two or more ancestral viruses are required prior to V1 to generate the distinct phylogenetic viral clusters observed.