The scatterplot of baseline HIV-1 DNA levels and change between EOT and baseline.

<p>The scatterplot of baseline HIV-1 DNA levels and change between EOT and baseline.</p

Phylogenetic tree of HIV-1 C2V5 nucleotide clonal sequences of subject #53 during DAA therapy.

<p>The viral sequences at the various time points are indicated by different colours, see table insert. Bootstrap values ≥80% are indicated. Bars indicate p distance scale. In the insert mean diversity (number of nucleotide substitutions/site) of the sequences detected at different time points is reported.</p

Factors associated with increase of HIV-1 DNA (≥0.5 log₁₀ copies/million PBMC) at EOT when compared to baseline at univariable and multivariable analysis.

<p>Factors associated with increase of HIV-1 DNA (≥0.5 log₁₀ copies/million PBMC) at EOT when compared to baseline at univariable and multivariable analysis.</p

Median PBMC-associated total HIV-1 DNA at baseline, EOT and 3 months after DAA in OVC and SVC.

<p>Median PBMC-associated total HIV-1 DNA at baseline, EOT and 3 months after DAA in OVC and SVC.</p

Characteristics of 305 HIV-1 B subtype infected patients starting their first-line HAART.

<p>a. Viremia was not quantifiable above 500,000 copies/mL only for one patient. We arbitrarily included this patient in the viremia level 500,001–1,000,000 copies/mL; b. Geno2pheno false positive rate set at 10%; c. As least 1 mutation associated with resistance to protease inhibitors, nucleos(t)ide reverse transcriptase inhibitors and/or non-nucleoside reverse transcriptase inhibitors, according to surveillance list from Bennett <i>et al.</i> 2009 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105853#pone.0105853-Bennett1" target="_blank">[39]</a>; d. ABC+3TC (n = 11); TDF+3TC (n = 3); DDI+3TC (n = 1); NRTI sparing (n = 15); e. Patients treated with raltegravir were considered as independent category regardless the other drugs included in the same regimen; f. Data about adherence levels were retrieved from physicians' reports. ABC: Abacavir. AZT: Zidovudine. DDI: Didanosine. FTC: Emtricitabine. IQR: Interquartile range. HAART: Highly active antiretroviral therapy. NRTI: Nucleos(t)ide reverse transcriptase inhibitor. NNRTI: Non-NRTI. PI: Protease inhibitor. TDF: Tenofovir. 3TC: Lamivudine.</p

Kaplan-Meier estimates of the probability of immunological reconstitution according to HIV-1 pre-HAART genotypically-inferred tropism.

<p>The estimations of the probability of immunological reconstitution (defined as a CD4 cell count gain of at least 150 cells/mm³) are indicated in panels A-B. Kaplan-Meier estimation was performed considering FPR set both at 10% (panel A) and at several FPR ranges (≤2%; 2–5%; 5–10%; 10–20%; 20–60%; >60%, panel B). In each panel, the number at risk and the probability of reaching the event by 3–12 months are indicated. P values were calculated by log-rank test for trend.</p

Relative hazard to achieve viro-immunological response according to baseline FPR ranks in HIV-1 infected patients starting their first-line HAART (Cox Models).

<p>a. Adjusted for: age, gender, risk factor, pre-HAART CD4 cell count, pre-HAART HIV-RNA, hepatitis C coinfection, year of starting treatment, transmitted drug resistance, third drug used (non-nucleoside reverse transcriptase inhibitor vs. boosted protease inhibitor vs. raltegravir), NRTI backbone used, number of drug administered (≤3 vs. >3 drugs); b. Reference group (dummy); Boldface indicates the geno2pheno false positive rate (FPR) ranks that were significantly associated (p<0.05) with viro-immunological response. C.I.: confidence interval.</p

Proportion of patients infected with ×4- and R5-tropic viruses.

<p>Pie plot represents: i) the proportions of R5-infected (FPR >10%) patients according to the following FPR ranges: 10–20%, 20–60%, >60%; ii) the proportion of ×4-infected (FPR ≤10%) patients (in black). Exploded bars represent the stratification of ×4-infected patients according to the following FPR ranges: ≤2%, 2–5% and 5–10%.</p