Figure 1

Sequence and Highlighter Analysis of Longitudinal Samples Provides Evidence for Superinfection. Comparison of maximum sequence divergence in gp41 versus the maximum number of degenerate bases at any time point within acutely infected individuals (A) and chronically infected individuals (B). The maximum percentage of degenerate bases is plotted on the y-axis; the maximum percentage of genetic distance is plotted along the x-axis. Black arrows indicate superinfected subjects; arrowhead indicates a subject co-infected with two variants from a single donor. Highlighter plots for gp41 sequences of ZM289M (C), ZM282M (D), ZM247F (E), and ZM211 F (F) sampled at 0 to 36 months post-seroconversion (shown on right of plot). The sequence at each time point is compared to the initial infecting HIV-1 gp41 sequence. Tick marks denote nucleotide changes from the seroconversion sequence (T = red, A = green, C = blue, G = yellow), with dark blue indicating degenerate bases (See Methods).