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

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

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

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

Description of patients and <i>vpr</i> alleles analyzed in the study.

<p>A) Immunological and viral profiles of the patients analyzed. These patients were selected from the HIV-1-infected patient cohort of the St-Antoine Hospital (Paris), and the samples were collected with written informed consent <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007514#pone.0007514-Lefrere1" target="_blank">[45]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007514#pone.0007514-Lefrere2" target="_blank">[46]</a>. The graphs show the time-course evolution of the blood CD4+ T cell counts (green curves) and plasmatic virus load (viral RNA, red curves); the PBMC samples analyzed in the present study are indicated by the blue arrows. B) Alignment of the amino acid sequences derived from DNA sequencing of the <i>vpr</i> alleles cloned from PBMC DNA samples. Excepted for LTNP-05 and LTNP-07 sequences that were obtained by direct sequencing of the bulk PCR fragments amplified from these samples, at least 40 independent clones were sequenced from each other samples. The sequences of the primary Vpr proteins are aligned with respect of the prototypic HIV-1<i>Lai</i> sequence (upper sequence). The <i>vpr</i> alleles from the LNTP (patient 5071) that were selected for subsequent functional analysis are in the box; the R77Q substitution identified in some <i>vpr</i> alleles is indicated in blue, while the Q65R substitution identified in the Vpr LTNP-04-2 is indicated in red.</p

Interaction of the Vpr proteins from the LTNP and PR patients with hCG1, UNG2 and DCAF1 in the yeast two-hybrid system.

<p>The L40 reporter yeast strain expressing Vpr<i>Lai</i> or the indicated primary Vpr proteins from the LTNP and PR patients fused to LexA (LexA hybrid), in combination with either hCG1, UNG2 or DCAF1 fused to the Gal4 activation domain (Gal4AD hybrid), was analyzed for histidine auxotrophy. Growth in the absence of histidine indicates interaction between hybrid proteins.</p

Description of pro- and anti-inflammatory markers between viremia groups.

<p>All patients were male, non smokers.</p><p>Medians (25th and 75th %tiles) were adjusted by age, hypertension, and duration of antiretroviral therapy using quantile regression.</p><p>*Significance determined using a two-tailed t-test based on estimated variance.</p><p>**Thresholds for biochemical markers were included in the summary statistic and calculated using the median between the commercial threshold given and 0.</p><p>D – detectable; UD – undetectable; us-CRP – ultra-sensitive C-reactive protein; IL – interleukin; HMW – high molecular weight; ICAM-1 – intercellular adhesion molecule-1; I-TAC – interferon inducible T-cell alpha chemoattractant; IP-10 – inducible protein-10; VCAM-1 – vascular cell adhesion molecule-1; MCP-1 – monocyte chemoattractant protein-1.</p><p>Description of pro- and anti-inflammatory markers between viremia groups.</p

Total and common carotid artery intima media thicknesses between viremia groups.

<p>All patients were male, non smokers.</p><p>*Difference in intima media maximal thickness between groups.</p><p>**Hypertension was defined by prior physician‘s diagnosis or systolic blood pressure ≥140 mmHg or diastolic blood pressure ≥90 mmHg.</p><p>c-IMT – carotid intima media thickness; cca-IMT – common carotid artery intima media thickness; D – detectable; UD – undetectable; SBP – systolic blood pressure; HDL – high-density lipid; LDL – low-density lipid; CVD – cardiovascular disease; HOMA-IR – homeostatic model assessment of insulin resistance; ART – antiretroviral therapy; VL – viral load; PI – protease inhibitors.</p><p>Total and common carotid artery intima media thicknesses between viremia groups.</p

Demographic and HIV characteristics between viremia groups.

<p>All patients were male, non smokers.</p><p>*Significance determined using a Kruskal-Wallis equality-of-populations rank test for continuous variables and Pearson χ² test or Fisher's Exact test for categorical variables;</p><p>**number (%);</p><p>^†median (25-75^th%tile).</p><p>^†^†Medians (25th and 75th %tiles) adjusted by age, hypertension, and duration of ART using quantile regression. Significance determined using a two-tailed t-test based on variance estimations.</p><p>D – detectable; UD – undetectable; HDL – high-density lipid; LDL – low-density lipid; HOMA-IR – homeostatic model assessment of insulin resistance; QUICKI – quantitative insulin sensitivity check index; HIV – human immunodeficiency virus; ART – antiretroviral therapy; cp/mL – copies/mL; VL – viral load; NRTI – nucleos(-t)ide reverse transcriptase inhibitor; NNRTI – non-nucleos(-t)ide reverse transcriptase inhibitor; PI – protease inhibitor; <i>ntp</i> – no test performed.</p><p>Demographic and HIV characteristics between viremia groups.</p