Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.

<p>Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.</p

Mean average pairwise Hamming distance (APHD) of HIV-1 Env SGA/S sequences distinguishes between single and multiple founder viruses.

<p><b>(A)</b> A training set of SGA/S Env sequences derived from 127 previously published acute HIV-1 infected subjects illustrating a wide range of <i>env</i> diversity. The APHD is calculated using a sliding window of 120bp with a step size of 21bp. The mean APHD is plotted according to Fiebig stages as defined by HIV-1 clinical laboratory test results. <b>(B)</b> A classifier based on a logistic regression segregated 127 subjects into single or multiple infections and correctly assigned 97% of subjects into the respective groups. Each point corresponds to an individual subject with the number of subjects denoted on the x-axis in parenthesis under each Fiebig stage.</p

Mapping of signature sites on the three-dimensional structure of gp120 shows clustering around the CD4-binding site.

<p>A ribbon representation of the crystal structure from the JRFL gp120 molecule (grey) bound to CD4 molecule (green) (PDBID: 2B4C). The CD4 binding site is highlighted in transparent green while signature sites 283, 343, 362, 389, 429, 465 and 471 are all depicted as <i>red</i> space-filling residues.</p

Selection bias intensified for HSX founder viruses compared to MSM founder viruses.

<p>The transmission index of a sequence was calculated using logistic regression with model weights taken from [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005619#ppat.1005619.ref012" target="_blank">12</a>]. Black lines represent the median transmission index for the two risk groups. The overall transmission index of HSX (red circles) viruses is significantly higher than from MSM (blue circles) founder viruses (<i>P</i> = 0.00003, Mann-Whitney two-tailed test). The number of subjects in each category is denoted under each group.</p

Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.

<p>Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.</p

Previously described signature sites enriched in HSX Founder viruses.

<p>Previously described signature sites enriched in HSX Founder viruses.</p

Signature sites identified between MSM and HSX Founder viruses in Env using a phylogenetic corrected method.

<p>Signature sites identified between MSM and HSX Founder viruses in Env using a phylogenetic corrected method.</p

Comparison of sequence variant quantification by 454 deep sequencing and by PCR cloning/sequencing.

<p>Orthogonal regression of variant frequency estimates obtained by 454 and clonal sequence data across the highly variable 1544 nucleotide region spanning Vif to Tat in subject 9213 (slope = 1.01; 95% CI, 0.73 to 1.40).</p

Rapidly expanding sequence diversity during HIV-1 infection.

<p>Heat maps illustrate sites exhibiting amino acid sequence diversity at days 0, 3, 59, 165, 476 and 1543 post-presentation. Plotted is the percentage of amino acid diversity at each position with respect to the dominant baseline (day 0) amino acid residue. All 3174 amino acids of HIV-1 are represented, with the first amino acid of Gag located in the top left corner of the grid and the last amino acid of Nef located in the bottom right corner. Completely conserved residues are <i>dark blue</i>, low-level variant residues (<10% divergent from baseline) are <i>light blue</i>, moderately variable residues (10–50%) in <i>orange</i>, and highly variant residues (>50%) in <i>red</i>. (<b>A</b>) 0 days p.p., (<b>B</b>) 3 days p.p., (<b>C</b>) 59 days p.p., (<b>D</b>) 165 days p.p., (<b>E</b>) 476 days p.p., (<b>F</b>) 1543 days p.p..</p

Limited evolution in the HIV-1 proteome prior to establishment of viral set point.

<p>Sequence diversity is plotted for all evolving codons in each HIV-1 protein as the percent of sequences with an amino acid residue different from the dominant baseline residue. Colored lines denote individual evolving amino acid residues within each protein. The time of infection prior to the establishment of viral set point (day 165) is highlighted in <i>grey</i>.</p