Correlation between nucleotide diversity of NS1 and viral load.

<p>On x-axis, NS1 nucleotide diversity, expressed as Nucleotide Substitution/Site X 10⁻⁴; on y-axis, viral load expressed as log₁₀ copies/mL.</p

Demographic, Clinical and Virological Features of the Study Patients.

<p>Demographic, Clinical and Virological Features of the Study Patients.</p

<i>In-Depth</i> Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients - Fig 2

<p>Frequency of minority variants of HA (panel A) and NS1 (panel B) proteins in influenza A(H1N1)pdm09 virus present in the nasopharyngeal swabs of 12 out of 13 patients of the study. Each patient is identified by a color code. The amino acid positions are referred to A/California/07/2009(H1N1), adopted as reference for this analysis (H1 numbering excluding the signal peptide).</p

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

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