Additional file 1: of Harvesting multipotent progenitor cells from a small sample of tonsillar biopsy for clinical applications

Supplementary Table 1. (XLSX 12 kb

Viral measurements do not predict off-ART rebound in d4 and d5 ART RMs.

The stochastic nature of RCVR generation and maintenance is highlighted in RMs B1 and B2 (dark red), which failed to rebound despite viral measurements slightly lower than the comparable d5 RMs (green). Decay kinetics of CA-RNA and CA-RNA within PBMC (circle), LNMC (square), DUO (up triangle) and BM (down triangle) from 3-, 70- or 250-days following ART initiation. (EPS)</p

Barcode assessment post rebound.

Rebound kinetics and barcodes for each rebounding RM are presented based on the post-infection day ART was initiated with the rebound pVL of each RM shown on the left and the relative barcode proportion at peak rebound shown on the right (A-F). Representative (d5 ART group) of barcode comparisons across time post rebound and compared to pre-ART population (G). LOD is determined by viral input levels and is shown as elevated x-axis levels. Groups are color-coded based on days post infection until ART: d3 (blue), d4 (red), d5 (green), d6 (purple), d7 (orange), d9 (black) and d12 (brown).</p

Viral decay dynamics affected by timing of ART initiation.

Delay in first phase viral decay following ART initiation (A). The primary phase 1 decay rate using both a maximal decay rate (B) and a 7-day average rate (C) excluding 6 RMs with low pVL where rates could not be estimated. Decay kinetics of CA-DNA (D-F) and CA-RNA (G-I) within PBMC (circle), LNMC (square), DUO (up triangle) and BM (down triangle) from 3-, 70- or 250-days following ART initiation. Unfilled symbols represent samples with no viral signal detected and are plotted at the calculated limit of detection (LOD) for each sample based on specimen input. Groups are color-coded based on days post infection until ART: d3 (blue), d4 (red), d5 (green), d6 (purple), d7 (orange), d9 (black) and d12 (brown).</p

Barcode comparisons pre-ART versus post-ART rebound.

Rebound kinetics and barcodes for each rebounding RM based on day ART initiated (left panel). Barcode comparisons across time post rebound and compared to the pre-ART population (right panel). Groups are color-coded based on days post infection until ART: d6 (purple), d7 (orange), d9 (black) and d12 (brown). (EPS)</p

Delay in first phase viral decay kinetics when ART is started pre-peak.

The time from ART initiation until onset of exponential decay is shown from 63 animals previously published but also infected with SIVmac239 and initiating ART between 4 and 42 dpi [18]. The number of days between ART and decay are shown by vertical line with the days listed for each RM. Groups are color-coded based on days post infection until ART: 4–5 (red), 6 (purple), 7 (orange), 8–9 (black), 12 (brown), and 42 (pink). (EPS)</p

Consistent barcode distribution across multiple tissues during primary infection.

Plasma viral RNA barcode distribution was compared with barcodes in up to 5 distinct sites including lymph node mononuclear cells (LNMCs), bone marrow (BM), peripheral blood mononuclear cells (PBMCs), duodenum (DUO) and bronchial alveolar lavage (BAL). Groups are color-coded based on days post infection until ART: d5 (green), d6 (purple), d7 (orange), d9 (black) and d12 (brown). (EPS)</p

SIV CA-DNA, SIV CA-RNA, and IPDA levels prior to ART interruption using CA-DNA and RNA values and IPDA.

Viral RNA and DNA copies/million cells from PBMC, mesenteric LN, and spleen just prior to ART release (A). Unfilled symbols represent samples with no viral signal detected and are plotted at the calculated LOD for each sample based on specimen input. IPDA vs CA-DNA measurements in PBMC (B) and mesenteric LNMCs (C). Groups are color-coded based on days post infection until ART: d3 (blue), d4 (red), d5 (green), d6 (purple), d7 (orange), d9 (black) and d12 (brown).</p

Excel spreadsheet containing, in separate sheets, the underlying numerical data and statistical analysis for Figs 1–7 and all supplemental figures.

Excel spreadsheet containing, in separate sheets, the underlying numerical data and statistical analysis for Figs 1–7 and all supplemental figures.</p

Early CA-DNA accumulation prior to and following ART initiation.

CA-DNA was measured for individual RMs within each ART initiation group. ART initiation is shown by dashed line. (EPS)</p