HIV-1 genetic distance measures over time.

<p>(<b>A</b>) Average pairwise nucleotide diversity within timepoints (open circles), divergence from the consensus of the initial timepoint sequences (filled squares) was calculated for <i>env-gp120</i> nucleotide sequences. Mean ± standard error is plotted (error bars are not visible as they were not as large as the data points). The proportion of predicted X4-tropic strains (filled magenta circles) computed by the PSSM scoring algorithm from V3 loop sequences is shown at each timepoint. The two distinct variants (1 and 2) within participant F5 were analyzed separately. HIV viral RNA load (copies per mL; red lines), CD4⁺ and CD8⁺ T cell counts (cells per mm³; blue and green lines, respectively), and visits with prescribed ART (black asterisks (*) at the bottom of each panel) are shown. The arrow at the bottom of each panel indicates the first time at which CD4⁺ T cell counts fell below 200. Dashed vertical lines indicate the time of peak viral diversity, when detected, while the solid vertical line indicates the time at which divergence from the initial consensus sequence stabilized (only detected in F6). Time to peak <i>env-gp120</i> diversity is shown associated with time to predicted X4-tropic genotype detection (<b>B</b>) and time to peak X4-tropic genotype representation (<b>C</b>). PSSM scores of ~ -6 or greater were taken as indicative of X4-tropism [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref056" target="_blank">56</a>]). Associations were analyzed using the Spearman’s correlation test; rho and <i>P</i>-values are shown. Lines were fit using a least squares linear regression model.</p

Correlates of disease progression and patterns of selection in the WIHS cohort.

<p>(<b>A</b>) Average pairwise diversity in <i>env-gp120</i> was estimated for each timepoint and is shown relative to peak diversity in each participant. (<b>B</b>) CD4⁺ T cell counts were placed relative to the time to peak diversity in <i>env-gp120</i>. The dashed horizontal line indicates the 200 CD4⁺ T cell count per mm³ AIDS-defining threshold. (<b>C</b>) The association between the time CD4+ T cells dropped below 200 per mm³ and the time of peak <i>env-gp120</i> diversity. Participants F4 and F7 were not included as virus had no observable peak in average pairwise diversity during the period of follow up. (<b>D</b>) Average pairwise diversity in <i>gag</i> for each timepoint is shown relative to the time of peak diversity in each participant. No peak was observed except for Subject F3. (<b>E</b>, <b>F</b>) The average pairwise ratio of nonsynonymous (<i>d</i>_<i>N</i>) to synonymous (<i>d</i>_<i>S</i>) substitutions per site at each timepoint compared to the inferred founder strain (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a> section) for <i>gag</i> and <i>env-gp120</i>, respectively, for each participant. Associations were assessed using the Spearman’s correlation test.</p

Phylogenetic analysis of <i>env-gp120</i> nucleotide sequences and predicted co-receptor use.

<p>(<b>A-D</b>) Maximum likelihood <i>env-gp120</i> phylogenetic trees from each participant were reconstructed using PhyML v3.0 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>) and rooted to earliest timepoint sequences. Data from 4 participants are shown here and from the remaining four in Fig Sx. Tip symbols indicate years post seroconversion (colored circles). Branch colors represent PSSM-predicted V3 loop co-receptor usage (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>). The scale at the bottom measures genetic distances in nucleotide substitutions per site.</p

No differences in HIV-1 subtype B <i>env-C2V5</i> evolutionary rates between females and males.

<p>Intra-host <i>env-C2V5</i> (<b>A</b>) diversity at the first time point and (<b>B</b>) substitution rates for both WIHS and MACS cohorts. Substitution rates for both WIHS and MACS participants were estimated using a relaxed molecular clock model using Bayesian inference (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>). A Mann-Whitney U test was used to test for sex differences. Horizontal bars show the median and interquartile range. 95% HPD is the highest posterior density interval. HPM mean is the evolutionary rate (and 95% HPD) estimated using a hierarchical phylogenetic model applied across the group. Evolutionary rates were defined as nucleotide substitutions/site/year. A non-parametric Mann-Whitney U test was used to test differences between unmatched groups. (<b>C</b> and <b>D</b>) Evolutionary rates from (B) broken out by individual. ESS values were > 200 for meanRate in the analysis of 8/8 <i>env-C2V5</i> WIHS and 10/11 <i>env-C2V5</i> MACS BEAST simulations.</p

Inter-participant <i>env-gp120</i> phylograms.

<p>(<b>A</b>) A Phylogenetic tree of <i>env-gp120</i> for all 8 WIHS participants was inferred using RAxML [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref051" target="_blank">51</a>] with the GTR substitution model +I +G [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref048" target="_blank">48</a>]. External branches from the first available timepoint after infection are colored black. Branches from participants F1, F2, F3, and F7 are shaded light and dark to indicate taxa from early and late infection, respectively, when sequences from early in infection are found at opposite sides of the root node. The scale at the bottom measures genetic distances in nucleotide substitutions per site. Phylograms from each individual were rooted based on outgroup. Bootstrap values are shown along branches extending to each participant’s clade.</p

Cohort description^a.

<p>Cohort description<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#t001fn001" target="_blank">^a</a>.</p