FIG 3.

Nonsynonymous and synonymous diversity at multiple time points spanning early SIV infection. The level of nonsynonymous (A) and synonymous (B) diversity was determined for every codon in Env at 2 to 3 weeks p.i. (green bars), 13 to 15 weeks p.i. (red bars), and 29 weeks p.i. (blue bars). Nonsynonymous diversity was determined as the frequency of codons with a nonsynonymous change relative to the majority codon of the sample time point consensus sequence, and synonymous diversity was determined as the frequency of codons with a synonymous change relative to the majority codon of the sample time point consensus sequence.