Fig. 1. HMA of pre-STI (week 0) and post-STI (week 12 of STI) samples from each patient. Molecular weight markers (labeled λ) are shown in the left-hand lanes of first and last gels.

Fig. 2. HMA genetic diversity (left), resistance mutation codons (middle) and viral load/CD4 variation during the STI (right) for patients 01, 03, 04, 05 and 19. Amino acid substitutions are represented as single letter codes. Letters in black indicate wild-type viruses and letters in gray indicate mutant viruses. Along the y axis, viral loads are shown on the left, whereas CD4 counts are shown on the right.

Fig. 3. Amino acid sequence alignments for the five patients analyzed. On the right, the genetic diversity (GD) found in pre-STI samples, 1 week of STI (for patient 19) and 12 weeks of STI (post-STI) is shown. The dN/dS ratios and model used for each estimation are indicated. Pre-STI sequences are at the top of the alignment, and post-STI sequences are at the bottom. Samples are labeled with a number representing the number of the clone generated by end-point PCR. All positive PCR clones were sequenced and included in this analysis. The sequence at the top is the consensus sequence for the quasispecies found in the samples obtained from each patient. Dots indicate similarities, whereas dashes indicate the absence of amino acids. The V3 loop, between the two cysteines, is indicated by the break in the upper line. In the alignment, positions 306 and 320, which predict viral phenotype, are marked in bold. For patient 19, alignments at the top are from RNA sequences, whereas the corresponding alignments at the bottom are from proviral DNA.

Fig. 4. Maximum likelihood tree and coalescent intervals of gp120 V3 env region of patient 03. The STI status of the sequences are identified with circles: sequences isolated from the pre-STI time point are grey circles, whereas sequences obtained from the post-STI time point are black circles. The tree was rooted at its midpoint; the topology clustered the sequences in two distinct groups, labeled as clusters A and M. The cluster A includes most of pre-STI sequences whereas cluster M includes most of Post-STI sequences. Numbers above the branches are length of clusters to the root. To the right side of the tree, the panels describe the Bayesian skyline plot depicting the coalescent intervals of each cluster. The x axis is in units of time (substitutions). The y axis represents the effective population size. Hence, panel A is the coalescent interval of cluster M and panel B is the coalescent interval of the cluster A.

Fig. 5. Maximum likelihood tree and coalescent intervals of gp120 V3 env region of patient 05. The STI status of the sequences are identified with circles: sequences isolated from the pre-STI time point are grey circles, whereas sequences obtained from the post-STI time point are black circles. The tree was rooted at its midpoint; the topology clustered the sequences in two distinct groups, labeled as clusters A and I. The cluster A includes most of pre-STI sequences whereas cluster I includes most of Post-STI sequences. Numbers above the branches are length of clusters to the root. To the right side of the tree, the panels describe the Bayesian skyline plot depicting the coalescent intervals of each cluster. The x axis is in units of time (substitutions). The y axis represents the effective population size. Hence, panel A is the coalescent interval of cluster A and panel B is the coalescent interval of the cluster I.

Fig. 6. Maximum likelihood tree and coalescent intervals of gp120 V3 env region of patient 19. The STI status of the sequences are identified with circles: sequences isolated from the pre-STI time point are grey circles, sequences obtained 1 week after STI are white circles and sequences obtained 12 weeks after STI are black circles. The tree was rooted at its midpoint; the topology clustered the sequences in two distinct groups, labeled as clusters GG (presenting the motif GGGR at the tip of the V3 loop) and GW (GW 1 and GW 2, presenting the GWGR motif at the tip of the V3 loop). The cluster GG includes most of pre-STI sequences whereas cluster GW includes most of post-STI sequences. Numbers above the branches are length of clusters to the root. To the right side of the tree, the panels describe the Bayesian skyline plot depicting the coalescent intervals of each cluster. The x axis is in units of time (substitutions). The y axis represents the effective population size. Hence, panels A and B are the coalescent interval of cluster GW 1 and GW 2, respectively, and panel C is the coalescent interval of the cluster GG.