Article Figures & Data
Figures
- FIG 1
Sequence identity between peripheral blood (PB) and lymph node (LN). (a) Pie charts showing the distribution of intact near-full-length (NFL) and VOA-derived env sequences. Numbers in the center of the circles represent the total numbers of intact/replication-competent sequences obtained. White areas in the pie charts represent sequences obtained once (singles). Colored areas represent sequences obtained more than once (clones). Clones, which are found in both PB and LN within an individual, share the same color between the two PB/LN pie charts. The size of the slices in the pie charts is proportional to the relative size of the clone. There is no significant difference between the frequencies of clones in PB and LN for any participant (two-sided Fisher’s exact test). (b) Pie charts showing the distribution of combined intact and defective env sequences from NFL and VOA-derived env sequences. Small black circles denote defective clones. There is no significant difference between the frequencies of clones in PB and LN for any participant (two-sided Fisher’s exact test).
- FIG 2
Quantitative analysis of the latent reservoir. Frequency of gag+ cells per 106 CD4+ T cells in LN and PB, frequency of full-length viruses (amplicon size determined using 0.8% agarose gel; i.e., at least one combination of either A+C, A+D, B+C, or B+D [9]) per 106 CD4+ T cells in LN and PB, and frequency of intact near-full-length (NFL) sequences per 106 CD4+ T cells in LN and PB are shown. There was no statistical difference between the frequencies of gag+ cells (P value = 0.31), full-length viruses (P value = 0.63), or intact NFL sequences (P value = 0.81) per 106 CD4+ T cells (Wilcoxon matched-pairs signed-rank test).
- FIG 3
TLR9 agonist study design and rebound analysis. (a) Study design. The green area represents the time on ART before enrollment and during the 24 weeks of TLR9 agonist treatment. The blue area represents the time off ART. Weeks (w) elapsed are shown. Lymph node (LN) and peripheral blood (PB) were collected 1 to 2 weeks before initiation of the analytical treatment interruption (ATI). Single-genome analysis (SGA) was performed on plasma from the time of viral rebound. (b) Plasma HIV-1 RNA levels (left y axis) and days elapsed following ATI (x axis). The lower limit of HIV-1 RNA detection was 20 copies/ml. Gray shaded areas depict time on ART. (c) Kaplan-Meier plot summarizing the time to rebound for the four TLR9 agonist trial participants (red line) compared to a cohort of 52 ACTG trial participants (black line) who underwent ATI without intervention. The log rank test P value applies to the comparison of time to rebound for the TLR9 agonist-treated cohort and that for the ACTG cohort.
- FIG 4
Sequence identity between peripheral blood (PB), lymph node (LN), and rebound single-genome assay (SGA) viruses. (a) Venn diagrams depicting env sequences from PB near-full-length (NFL) and PB VOA (blue) sequences, LN NFL (gray) sequences, and SGA sequences from the time of viral rebound (pink). The numbers of sequences obtained are indicated in the circles. The relative size of the overlapping areas is proportional to the number of identical sequences. (b) The y axis on the histograms shows the frequency of env sequences, and the x axis shows the nucleotide distance in number of mutations. The gray bars represent the expected distance between the latent reservoir and rebound viruses based on a simulation of the accumulation of mutations for each participant during the ATI. The blue bars represent the observed Hamming distance found between latent reservoir viruses and rebound viruses, ignoring indels. The yellow bars represent the observed distance between the latent reservoir viruses and rebound viruses when the possibility of recombination is included in the analysis.
- FIG 5
Comparison of env from intact sequences obtained from lymph node (LN), peripheral blood (PB) cells, and rebound viruses from participants 101, 114, 116, and 120. (a) Maximum likelihood phylogenetic trees of env from near-full-length (NFL) LN and PB sequences, viral outgrowth assay (VOA) PB culture sequences, and plasma single-genome analysis (SGA) sequences. Symbols are defined in the graph key. Asterisks indicate nodes with significant bootstrap values (bootstrap support ≥ 90%). Green stars indicate parent sequences, which undergo recombination to produce a child sequence (red star). Each recombination event has a number (indicated next to the colored star). (b) Circos plots showing the connection between the two parent sequences and the child/recombinant sequence, which are also depicted in the trees. Blue blocks represent latent reservoir LN sequences. Green blocks represent latent reservoir PB sequences. Red blocks represent plasma virus sequences. Clonal sequences are depicted once. The thickness of the outer black lines surrounding the circles represents the number of sequences retained within the clone, i.e., thin black lines are single sequences, and thicker lines represent sequences obtained several times. Gray lines inside the Circos plots indicate the recombination event. The parent/child relationship is shown in the trees.
Tables
- TABLE 1
Patient characteristics
Baseline characteristic (n = 5) Value Gender male, no. (%) 5 (100) Race or ethnicity, no. (%) Caucasian 4 (80) Hispanic 1 (20) Age (yrs), median (range) 51 (28–57) Yrs since HIV-1 diagnosis, median (range) 9.3 (2–31) Yrs from HIV diagnosis to ART initiation, median (range) 0.25 (0–18) Yrs on ART, median (range) 7.3 (1.8–13.4) ART regimen, no. (%) Protease inhibitor based 2 (40) NNRTI baseda 3 (60) Nadir CD4+ T cell count (cells/mm3), median (range) 390 (210–690) ↵a NNRTI, nonnucleoside reverse transcriptase inhibitors.
Supplemental material
- Supplemental file 1 -
Fig. S1 (Phylogenetic tree depicting intact sequences from all five participants.)
Fig. S2 (Phylogenetic trees showing all env sequences.)
Fig. S3 (Phylogenetic trees with sequence names.)
PDF, 2.6M
- Supplemental file 1 -
