Figure 5. Highlighter plots of sequences from longitudinal samples. (A–C) Samples were from subjects CH40 (A), CH58 (B), and CH77 (C). The dark line represents the transmitted/founder sequence (T/F) for each subject. Sequences from different sample dates are indicated by the grouped horizontal lines, with tic marks indicating differences from the T/F sequence. The screening sample (S) was in each case obtained from a preseroconversion Fiebig stage II sample near peak viremia. The sampling times in days after screening and corresponding viral loads are indicated (left). Light blue tic marks indicate differences in noncoding regions of the genomes. Gray tic marks indicate deletions. Green tic marks indicate differences that are synonymous in the reading frames indicated at the bottom of the figure. Red tic marks indicate differences that are nonsynonymous in a coding gene. Short horizontal lines (labeled A, B, and C) indicate short (∼1-kb) sequences from a screening sample used to verify the presence or absence of a shared polymorphism (Figs. S3–S6). The horizontal axis indicates nucleotide positions in the alignment beginning at position 582 in the 5′ LTR (U5) and extending to position 9,606 in the 3′ LTR (R) based on HXB2 reference sequence numbering (http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/HXB2.html).