Figure 1

Homogeneity of early/founder env sequences prior to superinfection in three intrasubtype C superinfected individuals. Single genome amplified full-length env sequences were evaluated through Highlighter plots for visualization of viral evolution of early/founder variants. Nucleotide changes from the early/founder consensus env sequence can be visualized by the colored hatch-marks (red = T, green = A, orange = G, light blue = C) as shown with ZM282M (A), in which superinfection was detected at 10 months post-seroconversion (superinfecting sequences not shown). The time point from which amplicons were isolated is shown as months after seroconversion (0-month). Raw pairwise distance from the early/founder consensus sequence to each longitudinal env amplicon sequence (vertical axis) was plotted for the three superinfected cases (B-D). Asterisks on the x-axis indicate time at which superinfection was detected and superinfecting sequences are included, clustering at 9-15% pairwise distance from initial consensus (B-D).