Fig 3. Higher diversity in infections with multiple founders in early infection.

Comparisons of sequence diversity as a function of neutralization breadth and founder multiplicity in RV217 participants. Non-broad neutralizers (indicated in blue) are defined as individuals who neutralized <35% of a 34-virus panel three to four years post-diagnosis and broad neutralizers (indicated in red) as individuals who neutralized >70% of the panel. Individuals sampled less than two years post-infection (intermediate neutralizers) are also shown (indicated in lavender). Individuals with single founder infections are shown in grey and with multiple founder infections in pink. Median pairwise distance at one month, six months, and three years post-diagnosis in (A) non-broad, intermediate, and broad neutralizers and in (B) participants with single or multiple founder infections. The number of individuals in each group is shown in parenthesis and p-values for pairwise comparisons are shown above each pair. (C,D) Maximum sequence divergence over time from each participant’s consensus at the earliest sampling day for (C) non-broad neutralizers and (D) broad neutralizers. Circles indicate participants with single (grey) or multiple (pink) founder infections and lines indicate whether the individual achieved broad neutralization (red) or not (blue). A low-transparency representation of (D) is shown in (C) and vice versa. (A,B) P-values calculated after removing individuals identified as superinfected are shown in parentheses.