Concordance between the 4 methods used to analyze HIV tropism in the 102 patients with UDPS sequences of good quality at D0.

<p>Consensus means that the consensus of UDPS sequences has been used as a surrogate of population sequencing; UDPS means that the full set of pyrosequencing sequences has been used; g2p means that the geno2pheno algorithm has been used for analysis; Pyrotrop means that our in-house software has been used for analysis.</p><p>Concordance between the 4 methods used to analyze HIV tropism in the 102 patients with UDPS sequences of good quality at D0.</p

ROC curves testing the ability of individual amino acid substitutions in the HIV V3 loop to predict the response to maraviroc.

<p>p values were <0.011 for H34Y/S, = 0.13 for S11R/K and = 0.08 for D25R/K.</p

Characteristic of the study population.

<p>IQR, interquartile range; NA: non available</p><p>Characteristic of the study population.</p

Sensitivity, specificity, positive and negative predictive values (PPV and NPV) of the 4 methods used to predict HIV RNA level decrease >1.0 log at M1, M3 and M6 on maraviroc therapy in the patients with available HIV RNA levels at D0 and M1.

<p>*: p<0.05 versus all of the other techniques</p><p>The PPV was defined as the capacity of the test (CCR5 tropism) to correctly predict a significant viral level decrease; the NPV was defined as the capacity of the test (CXCR4 tropism) to predict the lack of significant viral level decrease. Consensus means that the consensus of UDPS sequences has been used as a surrogate of population sequencing; UDPS means that the full set of pyrosequencing sequences has been used; g2p means that the geno2pheno algorithm has been used for analysis; Pyrotrop means that our in-house software has been used for analysis.</p><p>Sensitivity, specificity, positive and negative predictive values (PPV and NPV) of the 4 methods used to predict HIV RNA level decrease >1.0 log at M1, M3 and M6 on maraviroc therapy in the patients with available HIV RNA levels at D0 and M1.</p

Results of the 4 technical/analytical methods in patients with discrepant results, and HIV-1 RNA level change at M1.

<p>^§ indicates that the method correctly predicted maraviroc response</p><p>* that it incorrectly predicted maraviroc response. FPR: false-positive rate.</p><p>Results of the 4 technical/analytical methods in patients with discrepant results, and HIV-1 RNA level change at M1.</p

Frequency of H34Y/S and Q32K substitutions in the Los Alamos database.

<p>Frequency of H34Y/S and Q32K substitutions in the Los Alamos database.</p

Primers used for amplicon generation.

<p>Note that forward and reverse primers are linked to primer A and B (454 Life Sciences; Roche) respectively and contain the TCAG key. To distinguish each sample in the multiplexed UDPS, nine unique sequence tags (MID1 to 9, according Roche's protocol) were inserted between the adaptor A or B and the gene specific primer.</p>1<p>RT1: primers under patent process</p>2<p>Primers from Mitzuya's paper <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086771#pone.0086771-Mitsuya1" target="_blank">[29]</a></p

Demographic, clinical and virological characteristics of the included patients (n = 29).

<p>MSM: men who have sex with men, IDU: intravenous drug user, IQR: interquartile range, VF: virological failure</p

List of drug resistance mutations (DRM) detected at baseline (BL) and virological failure (VF) by Sanger sequencing (SS) and UDS for patients failing a PI-based regimen (n = 15).

<p><i>Italic</i>: mutations only detected by UDS/Normal: mutations detected by both UDS and SS</p><p><b>Bold</b>: Major protease mutations</p><p><u>Underlined</u>: mutations associated to prescribed treatment</p><p>GSS, Genotypic Sensitivity Score; ART, antiretroviral treatment; ZDV, zidovudine; DDI, didanosine; D4T, stavudine; 3TC, lamivudine; FTC: Emtricitabine; ABC, abacavir; TDF, tenofovir; NFV, nelfinavir; LPV/r, boosted lopinavir; ATZ/r, boosted atazanavir, FPV/r, boosted fosamprenavir</p

Estimated median (95% CI) CD4 cell count by HIV-1 subtype and time since cART initiation.

<p>(Non acute infection, without AIDS at cART initiation, boosted PI cART, seroconversion to cART >4 years, previously naïve, ≥5 log₁₀ c/ml initial viral load, men having sex with men, 30 years old at cART initiation).</p