Evolutionary relationships of the 108 HIV-1 reverse transcriptase sequences involved into chained transmissions.

<p>Viruses isolated in patients infected for less than 6 months (VEP) (Δ), patients chronically-infected with CD4⁺ T-cell count >500/mm³ (EP) (o) or ≤500/mm³ (●). Subjects with unknown duration of infection (□) are shown.</p

Comparison of the characteristics of chained and non-chained population.

<p>nb: number; CI: confidence interval; MSM: men who have sex with men. VEP: very early presenter; EP: early presenter; LP: late presenter; and ELP: extremely late presenter.</p><p>Comparison of the characteristics of chained and non-chained population.</p

Factors associated with inclusion in chains, pairs and clusters.

<p>HAART: Highly active antiretroviral therapy. VEP: Very Early Presenter.</p><p>*: pairs or clusters.</p><p>Factors associated with inclusion in chains, pairs and clusters.</p

Phylogenetic tree of the entire population.

<p>The evolutionary history was inferred using the Neighbour-Joining method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135367#pone.0135367.ref017" target="_blank">17</a>]. The optimal tree with the sum of branch length = 11.53297849 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. All positions containing alignment gaps and missing data were eliminated only in pairwise sequence comparisons. There were a total of 1308 positions in the final dataset. Branches corresponding to clusters are in red.</p

Distribution of the study population between chained and non-chained groups by time lapse between infection and genotyping.

<p>VEP: Very early presenter, EP: early presenter; LP: late presenter; and ELP: extremely late presenter.</p