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

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

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

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

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

Comparison of the characteristics of patients included into clustered transmission versus non-clustered: the ANRS PRIMO cohort 1999–2010.

<p>Note: the total of patients for each variable does not always equal the total sample due to some missing values. PHI = primary HIV infection; MSM = men having sex with men; TPHA = <i>Treponema palladium</i> haemagglutination assay; VDRL = Venereal Diseases Research Laboratory test.</p>(1)<p>Urethritis, rectitis, genital herpes infection, vulvo-vaginal candidosis, condyloma and/or syphilis.</p>(2)<p>In the last 6 months preceding PHI diagnosis.</p

Characteritics of the 8 donors.

¶<p>Results based on the declaration of the recipient.</p><p>EIA-RI test = enzyme-linked immunosorbent assay for recent infection <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Barin1" target="_blank">[29]</a>, PBMC = peripheral blood mononuclear cells; Het = heterosexual; MSM = man having sex with men; HBV = hepatits B virus; HBsAg = HBV surface antigen; HBsAb = HBV surface antibodies; HBcAb = HBV core antibodies; HCV = hepatitis C virus; n.d. = not done; n.a. = data not available; und = undetectable.</p

Comparative <i>Highlighter</i> analyses of <i>env</i> diversity in a donor-recipient HIV-1 transmission pair.

<p>(A) Recipient#1 shows evidence of infection with a single virus. (B) Donor#1 was the chronically infected partner of recipient#1. The same reference amplicon, a V3 RNA sequence from recipient plasma, was used to depict the viral diversity in both individuals.</p

Evolutionary relationships between the HIV-1 <i>env</i> genes in the eight donor/recipient pairs.

<p>The evolutionary history was inferred using the Neighbor-Joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Boeras1" target="_blank">[38]</a>. The optimal tree with the sum of branch length = 2.01912678 is shown. The tree is drawn to scale, with branch length 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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Whitney1" target="_blank">[39]</a> and the unit is the number of base substitutions per site. Codon positions included were 1^st+2^nd+3^rd+noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 230 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Redd1" target="_blank">[40]</a>. For each recipient, viruses isolated from PBMC-derived DNA (•) and plasma RNA (○) are represented, with a different color for each donor/recipient pair. Asterisks indicate branches with bootstrap values greater than 98%.</p