Mutation distribution graphs for the polymerase region.

<p>Sequence alignments were submitted to Mutation Reporter Tool (<a href="http://hvdr.bioinf.wits.ac.za/mrt/" target="_blank">http://hvdr.bioinf.wits.ac.za/mrt/</a>) to produce graphs for genotype A. None mutation found in nine sequences from genotype E. Letters preceding each locus on the X-axis show the reference motifs. To facilitate comparison, conserved loci were not suppressed.</p

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

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

Prevalence rates of patients with detectable HBV DNA results, patients with overt (presence of circulating HBsAg) HBV infection (acute or chronic), and patients with OBI.

<p>Prevalence rates of patients with detectable HBV DNA results, patients with overt (presence of circulating HBsAg) HBV infection (acute or chronic), and patients with OBI.</p

Baseline characteristics of the 987 patients from the ANRS PRIMO cohort 1999–2010.

<p>TPHA = <i>Treponema palladium</i> haemagglutination assay; VDRL = Venereal Diseases Research Laboratory test; HBV = hepatits B virus; HCV = hepatitis C virus.</p

Suggested diagnostic strategy for HBV screening in resource-limited settings.

<p>Suggested diagnostic strategy for HBV screening in resource-limited settings.</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 analysis of a 765 bp HBV-S gene region from different HBV isolates, with Woolly Monkey strain (AY226578) as the root.

<p>The phylogenetic tree was inferred by the Bayesian method in the GTR model, with gamma-distributed rates at sites, 8 million generations and effective sample sizes greater than 1200. BPP (Branching Posterior Probability) are shown along the main nodes. HBV sequences obtained during this study are represented in red.</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

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