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

Demographic characteristics of the study population.

<p>IQR, interquartile range; HE, heterosexual; MSM, men-who-have-sex-with-men; IDU, injection drug user; ND, not determined; IU, international units.</p

The graphs report the proportion of R5 (A) and X4 (B) variants per patient according to the values of FPR at population V3 sequencing.

<p>Distribution of R5 and X4 variants in relationship to the False Positive Rate (FPR) detected by population V3 sequencing. The graphs report the proportion of R5 (A) and X4 (B) variants per patient according to the values of FPR at population V3 sequencing. P-values were calculated by Spearman test. A FPR of 5.75 has been used as cut-off to infer HIV-1 co-receptor usage.</p

Drug resistance mutation detection in limiting dilution series.

<p>Two HIV-1 subtype B samples were used for the dilution series (A, samples 40–44; B, samples 45–49). The four groups shown in the histogram are based on the median frequency of each drug resistance mutation in its respective <i>undiluted</i> sample: >20% (white bars), 10–20% (bright grey bars), 2–10% (dark grey bars), and 1–2% (black bars). The means and standard deviations are given of the percentage of sites reporting drug-resistance mutations in these categories. The number of mutations in each category is represented by n.</p

UDPS species prevalence according to G2P FPR at population V3 genotyping.

a<p>The column reports the range of prevalence for CXCR4-using or CCR5-using strains determined by UDPS in patients stratified according to the FPR values obtained by V3 population sequencing.</p>b<p>The ranges are referred to the intra-patient prevalence of X4- and R5-species by UDPS.</p>c<p>The intra-patient prevalence of X4-variants is 99.1% and 100%, respectively.</p><p>Abbreviations: UDPS, ultra-deep sequencing; G2P, Geno2Pheno; FPR, false positive rate.</p

Triplicate sample analysis.

<p>A set of three samples was measured in triplicate at each of the 11 sites. Variant percentages measured in the triplicate samples are shown for each mutation.</p

The graph reports the distribution of FPR values of all the V3 variants detected by UDPS in each patient according to FPR ranges at population V3 sequencing.

<p>The relative dimension of green and red dots represents the prevalence of R5 and X4 species detected by UDPS. Yellow dots represent the FPR determined by population sequencing and letters within dots indicate the phenotypic tropism determined by ESTA (R =  pure CCR5 tropism, X = pure CXCR4 tropism, D = dual/mixed tropism. For blank yellow dots, ESTA result was not available. A FPR of 5.75 has been used as cut-off to infer HIV-1 co-receptor usage of V3 sequences obtained by both V3 population and ultra-deep sequencing.</p