FIG 8.

Evolution of sequence diversity in SIV Env V4 loop. 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) Three sites within V4 are plotted over the first 29 weeks of in vivo viral replication of 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 of SP1 (D) and are representative of sites with the highest codon variation in the V4 loop.