Establishment and stability of the latent HIV-1 DNA reservoir
- Karolinska Institute, Sweden
- Max Planck Institute for Developmental Biology, Germany
- Stockholm South General Hospital, Sweden
- Karolinska University Hospital, Sweden
Figures
Figure 1
Sampling times before and after start of suppressive antiretroviral therapy.
For each study participant, the thick grey bar indicates the period of untreated HIV-1 replication. Circles indicate the collection times of the plasma samples used for whole genome deep sequencing …
Figure 2 with 3 supplements
Reconstructed phylogenetic trees of plasma HIV-1 RNA sequences (circles) and PBMC HIV-1 DNA (triangles and squares) from two patients.
The RNA sequences were obtained from plasma samples collected before the start of suppressive antiretroviral therapy (ART). DNA sequences 1, 2, and 3 were obtained from PBMCs collected after many …
Figure 2—figure supplement 1
Phylogenetic trees of plasma HIV-1 RNA and PBMC HIV-1 DNA sequences from all patients included in the study.
https://doi.org/10.7554/eLife.18889.005
Figure 2—figure supplement 2
Distributions of frequencies of haplotypes.
We found a wide variation in haplotype frequencies (measured by fraction of reads), from <0.001 to >0.5. Most of the haplotypes were present at frequencies of approximately 0.01 (note the …
Figure 2—figure supplement 3
Distributions of mutations in reads classified as hypermutanted or as non-hypermutated.
https://doi.org/10.7554/eLife.18889.007
Figure 3 with 3 supplements
Root-to-tip distances.
The plasma HIV-1 RNA sequences evolved steadily before the start of antiretroviral therapy (ART), while no evidence of evolution was found in the PBMC HIV-1 DNA sequences obtained after the start of …
Figure 3—figure supplement 1
Mean root-to-tip distances for plasma HIV-1 RNA sequences obtained before the start of ART and PBMC HIV-1 DNA sequences obtained after the start of ART.
This figure is analogous to Figure 3 in the main text, but presents root-to-tip distance values for DNA sequences classified as hypermutants. The root-to-tip distances of the hypermutant HIV-1 DNA …
Figure 3—figure supplement 2
Mean root-to-tip distances for plasma HIV-1 RNA sequences obtained before the start of antiretroviral therapy (ART) and PBMC HIV-1 DNA sequences obtained after the start of ART.
This figure is analogous to Figure 3 in the main text. Instead of weighing each sequence by its number of reads, each sequence was counted only once. The two approaches yielded similar results. The …
Figure 3—figure supplement 3
Short lived cells can generate a false signal of evolution.
HIV-1 DNA from cell samples taken at the initiation of antiretroviral therapy (ART) will be dominated by virus variants that have very recently infected short-lived cells (blue). The short-lived …
Figure 4 with 2 supplements
Probable origin of sequences in the DNA reservoir.
For each HIV-1 DNA read obtained from the PBMCs, we determined the pre-treatment plasma sample and HIV-1 RNA variant that was the most likely origin of the read. Panel A presents the results for the …
Figure 4—figure supplement 1
The distribution of plausible seeding times of reservoir HIV-1 DNA sequences for all 10 patients.
For each HIV-1 DNA read obtained from the PBMCs, the plasma sample and HIV-1 RNA variant from which the read was most likely derived was determined. The plots present the distributions of these most …
Figure 4—figure supplement 2
Same as Figure 4—figure supplement 1, but counting each sequence once instead of weighted by the number of reads it represents.
https://doi.org/10.7554/eLife.18889.015Tables
Table 1
Summary of patient characteristics.
| Patient | Gender | Transmission | Subtype | Age* | HIV RNA from plasma | HIV DNA from PBMCs | |||
|---|---|---|---|---|---|---|---|---|---|
| # samples | First/last since EDI† | Time on ART† | # templates | ||||||
p1 | F | HET | 01_AE | 37 | 12 | 0.3 | 8.2 | 7.9/9.9/10.4 | 820/148/38 |
p2 | M | MSM | B | 32 | 6 | 0.2 | 5.5 | 6.9 | 75 |
p3 | M | MSM | B | 52 | 10 | 0.4 | 8.4 | 4.6/6.7/7.2 | 243/102/108 |
p5 | M | MSM | B | 38 | 7 | 0.4 | 5.9 | 4.0/6.3 | 180/72 |
p6 | M | HET | C | 31 | 7 | 0.2 | 7.0 | 3.0/5.0/5.5 | 115/15/nd |
p7 | M | MSM | B | 31 | 11 | 6.3‡ | 16.1 | 6.3/8.4/8.8 | 88/279/108 |
p8 | M | MSM | B | 35 | 7 | 0.2 | 6.0 | 8.4/10.6/10.9 | 180/55/175 |
p9 | M | MSM | B | 32 | 8 | 0.3 | 8.1 | 7.7/9.7/10.2 | 60/72/72 |
p10 | M | MSM | B | 34 | 9 | 0.1 | 6.2 | 16.2/18.3/18.6 | 249/116/51 |
p11 | M | MSM | B | 53 | 7 | 0.6 | 5.6 | 6.4/8.4/8.8 | 124/120/123 |
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*at diagnosis;
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†EDI: estimated date of infection; all times are given in years;
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‡sequencing failed in earlier samples due to low plasma HIV-1 RNA levels.
Table 2
Rates of evolution in plasma HIV-1 RNA and PBMC HIV-1 DNA sequences obtained before the start and after the start of suppressive antiretroviral therapy, respectively.
| Patient | RNA rate | DNA rate | ||
|---|---|---|---|---|
| [Year−1] | p-value | [Year−1] | p-value | |
| p1 | 4.4 × 10−3 | <10−6 | −6 × 10−4 | 0.22 |
| p2 | 3.7 × 10−3 | <10−2 | −8 × 10−4 | – |
| p3 | 4.1 × 10−3 | <10−6 | −2 × 10−4 | 0.39 |
| p5 | 4.8 × 10−3 | <10−3 | 4 × 10−4 | 0.45 |
| p6 | 1.4 × 10−3 | <10−3 | −9 × 10−4 | 0.22 |
| p7 | 1.3 × 10−3 | <10−2 | −7 × 10−4 | 0.14 |
| p8 | 2.9 × 10−3 | <10−5 | 8 × 10−5 | 0.22 |
| p9 | 2.6 × 10−3 | <10−4 | 1 × 10−4 | 0.12 |
| p10 | 3.6 × 10−3 | <10−5 | −1 × 10−4 | 0.20 |
| p11 | 1.2 × 10−3 | <10−2 | 2 × 10−4 | 0.16 |
Additional files
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Supplementary file 1
Sequencing and hypermutation statistic for all samples.
'good' refers to proviral sequences that are not obviously defective, 'hyper' refers to those with an excess of G→A mutations. The column '% recaptured' indicates the fraction of sequences >1% frequency that were present in other samples from the same patient.
- https://doi.org/10.7554/eLife.18889.016
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Supplementary file 2
PCR primers used for HIV-1 p17gag amplification.
- https://doi.org/10.7554/eLife.18889.017
