Additional file 1: Figure S1. of Early antiretroviral treatment (eART) limits viral diversity over time in a long-term HIV viral suppressed perinatally infected child

Neighborg phylogenetic tree constructed on the pol gene sequences of 400 isolates and additional 163 HIV-1 subtype references. The bar at the bottom indicating 0.01 nucleotide substitution per site. Bootstrap support >90% were showed along the branches. Isolates of sutypes C are shown in red. The sequences involved in mother to child transmission chain are in bold red. (PPTX 160 kb)

Lymphoproliferative responses are shown as Stimulation Index (SI) to virion HIV-1 MN (A), recombinant Gag p24 (B) and recombinant RT (C) viral antigens among vaccinated (n = 10; black dots and lines) and controls (n = 10; grey squares and lines).

<p>Black arrows show vaccinations (weeks 0, 4, 12 and 36).</p

Patient data at enrolment.

<p>ART signifies antiretroviral treatment with PI = protease inhibitors, NRTI = nucleoside reverse transcriptase inhibitors, NNRTI = non nucleoside reverse transcriptase inhibitors.</p

Safety Profile of the PEDVAC trial: distribution of adverse events during the 96 weeks follow-up of the study.

<p>The black dashed line shows total number of solicited and unsolicited adverse events in control Group A. The gray dashed line indicates total number of solicited and unsolicited adverse events in vaccine Group B, while the black solid line indicates all local and systemic adverse events which were vaccine related. Black arrows show vaccinations (weeks 0, 4, 12 and 36).</p

Cellular immune responses to HIV-1 antigens.

<p>^AUCarea under the curve.</p>a<p>week 0–96.</p><p>^bweek 0–60.</p

Viral dynamics during the vaccination schedule for the control Group A (n = 10) (A) and vaccine Group B (n = 10) (B).

<p>HIV-RNA with a limit of detection of 50 copies/ml is shown as black dots, HIV-RNA ultrasensitive assay with a limit of detection of 1 copy/ml plasma is shown as circles and cell associated HIV-DNA of PBMC shown as triangles indicating number of total HIV-proviral DNA copies/10⁶ PBMC. Black arrows show vaccinations (weeks 0, 4, 12 and 36).</p

Functional profiles of between groups HIV-specific CD4+ and CD8+ T-cells analyzed by ICS at weeks 0, 16, 20 and 60.

<p>The panels show the percentage of T-cells releasing IFN-γ (A) and IL-2 (B) for CD4+ T-cells, and IFN-γ (C) and perforin (D) for CD8+ T-cells for each patient in control Group A (n = 10, circles), and vaccine Group B (n = 10, black dots). T-cell functions were analyzed after stimulation for 16 h with a pool of proteins representing the vaccine sequences. Lines represent median values. In panel (E) CD8+ cells releasing perforin at baseline week 0 and after 60 weeks in vaccine and control groups are shown. Differences within groups between baseline and week 60 levels in panel (E) are indicated for each individual, and the p-value calculated by Wilcoxon signed rank test.</p

CONSORT 2010 flow diagram.

<p>CONSORT 2010 flow diagram.</p

Changes in CD45RA, CD45RO and CD45A+CD31+ cells.

<p>Changes in absolute numbers of CD45RA cells (a), CD45RO cells (b) and CD4 RA and RO cells as a % of CD4 cells, for children in the trial where of CD4 sub-populations were evaluated (including the children in the substudy) (c). Change in CD45RA+ CD31+ cells from baseline for children in the substudy (d). CT  =  continuous ART (antiretroviral therapy), PTI  =  planned treatment interruption (off ART). Changes from baseline were estimated using normal regression of actual measurements adjusting for baseline using the overall mean at randomisation as the reference category.</p

Change in % Ki67, HLA-DR and LPS from baseline.

<p>Change in % Ki67 (a) and % HLA-DR (b) in CD45RA- CD31- cells and in LPS (c) from baseline for children in the substudy. CT  =  continuous ART (antiretroviral therapy), PTI  =  planned treatment interruption (off ART). Changes from baseline were estimated using normal regression of actual measurements adjusting for baseline using the overall mean at randomisation as the reference category.</p