FIG 9.

nef sequence diversity in acute-phase plasma from four group 2 controllers. Heat maps illustrate the levels of sequence diversity at each codon in the nef open reading frame. The range of amino acids covered by each row is indicated on the right-hand side of the figure and should be used only as a reference because both synonymous and nonsynonymous mutations are considered in these heat maps. The codon corresponding to the first amino acid in Nef is located in the top left corner of each grid. Each row spans 17 amino acids of the Nef protein, except for the bottom row, which covers 9 amino acids and includes the last codon at position 264. The images on the left correspond to plasma samples collected at week 2 postinfection. The images on the right correspond to plasma samples collected at week 3 p.i., or week 4 p.i. in the case of r08046. Data from r08046, r05007, r08062, and r08047 are shown in panels A, B, C, and D, respectively.