Summary statistics for the only single-site signature found in Env based on within-subject consensus sequence analysis, His at position 12.

The full tree analysis and summary of common changes in position 12 support this signature, and are also provided. The direction indicates the signature amino acids, and H ->!H is read as H changes to “not His” (i.e. any other amino acid). The Fiebig stage indicates the group included in the comparison that gave the p-value shown. For example, F1-F5 means that Fiebig stages F1–F5 were included in the early group, and the p-values for this set are given, as they have the lowest p- and q-values. Five increasing inclusive levels of Fiebig stages were compared, however; all 5 groupings of Fiebig stages had a trend indicting support of this signature, although not always meeting the q-value threshold. The contingency table on the right of each row indicates the number of times the ML tree indicated a change between the ancestral state immediately preceding the consensus sequence, versus when the amino state did not change. Thus H is enriched among transmitted variants. In the consensus tree, it mutates away from H in only 2/37 times in acute/early, versus and 13/34 times in the chronic cases (5% in acutes versus 38% in chronics). In the full tree including all of the sequences, the distinction was similarly pronounced, changing 8/75 in acute cases and 57/111 in chronics (10% versus 51%). H most frequently mutates to R or P during the course of an infection; changes to P were statistically not supported (ns) in the holdout set.