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

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

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

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