Maximum likelihood tree including all sequences from all 81 homogeneous patients illustrating the pattern of change in one site.
The tree is based on all nucleotide sequences and all positions in Env, and illustrates the mutational patterns in the context of the full tree at amino acid position 83. Position 83 is highly conserved, and is His in most sequences in most subjects (indicated by the red Xs). In the 4 subjects that are featured, it changes from His to Tyr in at least some of the sequences in each subject, indicated by the blue 0 s. Although the trees were generated for each patient separately for the HyPhy analysis, this kind of repeated mutation pattern in a single site is an illustration of the kind of change captured in the dN/dS ratio of the HyPhy analysis (Table 2). This site, 83, was also identified as interesting in the full tree analysis as it tended to change from H to Y in patients at later Fiebig stages (Table 2).