FIG 10.
Evolution of substitutions in Env V2 and V3 loop of SIVmac251. The frequency of codons was determined from deep sequence reads of each sample assembled to the de novo consensus sequence of the same sample using the V-Profiler software program (Broad Research Institute). (A to D) Sites within V2 and V3 site W345 are plotted over the first 29 weeks of in vivo viral replication in TP1 (A) and TP2 (B), over the first 15 weeks of in vivo viral replication in RP1 (C), and over the first 13 weeks of in vivo viral replication in SP1 (D) and are representative of sites with the highest codon variation in V2 and V3 loops.