Intra-patient relative abundance of R5 and X4-using variants identified over time.

<p>Longitudinal analysis of the relative abundance (y left axis: percentage) of R5 (blue range) and X4 (red range) variants at different time points (x axis: sampling times in months). At the first sampling time, the most abundant variant is identified by darker color and named as “R5.1” or “X4.1”, accordingly. Colors become clearer according to the decrease in their relative abundance. “R5.ot” and “X4.ot” include those viral variants with very low relative abundance. For subsequent sampling times, the color palette is respected following the first one in order to allow correlating the longitudinal variation of the viral variants first identified. HIV viral load are represented (y right axis; as log copies/ml). The V3 amino acid sequence (and between brackets, their relative false positive rate by geno2pheno) of the most common variants in each patient is shown.</p

Comparative frequency of amino acid residues between R5- and X4-viruses.

<p>By using the two sample logo (TSL) amino acid residues with significant difference in the frequency between the two datasets (R5-tropic n = 41, lower panel; X4-tropic n = 19, upper panel) are shown at the specific sites in the HIV gp-120 V3 sequences. Residues between the two panels denoted those with the equal frequency in two datasets; when such frequency was approximately equal, positions showed no residues.</p

Results of approximately unbiased (AU) and non-scaled bootstrap probability (NP) tests¹.

1<p>Significant differences (<i>p</i><0.01) in bold.</p>2<p>Unconstrained.</p>3<p>Fitness Valley.</p>4<p>Lineage extinction.</p>5<p>Not applicable.</p

Demographic characteristics of the study population¹.

1<p>Mean (±standard deviation).</p>2<p>HIV infection date calculated as mid-point between last negative and first positive samples are indicated as years.</p>3<p>Expressed as log copies/ml.</p>4<p>Expressed as cells/µl.</p>5<p>Median [IQR].</p

Maximum likelihood phylogenetic tree of C2-V3-C3 nucleotide sequences from patients included in the study.

<p>Patient-related clusters are identified in different colors as indicated at the bottom of the figure. The vertical size of the clusters is proportional to the number of reads in the cluster and the horizontal size of the clusters shows their maximum genetic depth. Bootstrap values are given on branches. Branch lengths are proportional to the number of nucleotide substitutions per aligned site (bar = 0.1 substitutions).</p

Bootstrap (<i>B</i>) and Shimodaira-Hasegawa (<i>SH</i>) supports observed inside single-patient datasets¹.

1<p>Mean (<i>MN</i>), median (<i>MD</i>), standard deviation (<i>SD</i>).</p