The HIV-1 latent reservoir is largely sensitive to circulating T cells
- Department of Microbiology and Immunology, University of North Carolina, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, United States
- UNC Center For AIDS Research, University of North Carolina, United States
- British Columbia Centre for Excellence in HIV/AIDS, Canada
- Department of Medicine, University of North Carolina, United States
- UNC HIV Cure Center, University of North Carolina, United States
- Department of Urology, University of California San Francisco, United States
- Gladstone Institute of Virology and Immunology, United States
- Faculty of Health Sciences, Simon Fraser University, Canada
Figures
Figure 1
Schema of empirical testing of T cell escape in the HIV-1 reservoir.
Top left panel. The quantitative viral outgrowth assay (QVOA) provided a minimal estimate of the size of the replication-competent reservoir virus from total resting CD4+ T cells of PLWH on ART (n = …
Figure 2
Neighbor-joining phylogenetic trees of sequenced outgrowth virus.
The phylogenetic trees display 5’ (A) and 3’ (B) half genome sequences generated by PacBio sequencing of outgrowth virus from the quantitative viral outgrowth assay from n = 22 PLWH on ART. Each …
Figure 3 with 2 supplements
Neighbor-joining within-host phylogenetic trees inferred from longitudinal outgrowth virus sequences.
Phylogenetic trees displaying 3’ half genome sequences of longitudinal outgrowth virus sequences from seven participants (A–G). Each color represents a different time point in which outgrowth virus …
Figure 3—figure supplement 1
Longitudinal outgrowth virus sequences on neighbor-joining phylogenetic trees.
Phylogenetic trees displaying 5’ half genome sequences of longitudinal outgrowth virus sequences from seven participants (A–G). Each color represents a different time point in which outgrowth virus …
Figure 3—figure supplement 2
Size of the replication-competent reservoir as measured by infectious units per million (IUPM) against the number of sequences obtained by PacBio sequencing (r = 0.755, p<0.0001, Spearman Rank, n = 24 pairs).
Red dots are participants treated during acute HIV infection.
Figure 4 with 2 supplements
Quantifying T cell escape in the HIV-1 reservoir.
(A) HLA associations in OGVs: The proportion of polymorphisms harboring HLA-adapted (blue bar) and HLA-adapted + possibly HLA-adapted polymorphisms (light purple) in PLWH on ART (Clade B infected …
Figure 4—figure supplement 1
HIV-1-specific T cell responses in PLWH on ART.
(A) The % magnitude of each mapped T cell response (n = 25 participants, n = 166 epitopes) was calculated as a percentage of the total response measured by ELISpot in that individual, and graphed by …
Figure 4—figure supplement 2
Outgrowth virus sequences and DNA sequences on neighbor-joining phylogenetic trees.
Phylogenetic trees displaying longitudinal outgrowth virus sequences (red text) and DNA sequences, intact (blue text, DNA no stop codon (DNA no_sc)) and non-intact (black text, DNA stop codon …
Tables
Table 1
Demographic and clinical data of participants (n = 25).
| Participant | Sex | Race* | Ethnicity† | Status at diagnosis‡ | Age§ | Years suppressed¶ | Hiv-1 RNA** | Nadir CD4 | Mean IUPM [n]†† | HLA type |
|---|---|---|---|---|---|---|---|---|---|---|
| 00231 | M | C | NH | A | 66 | 9.66 | 1.5E+07 | 277 | 0.839 [1] | A*11:01, A*24:02, B*35:TDS‡‡‡, B*35:02, C*04:01, C*04:01 |
| 00250 | M | C | NH | A | 48 | 7.44 | 6.8E+05 | 403 | 0.318 [3] | A*01:01, A*31:01, B*27:03, B*44:02, C*02:02, C*06:02 |
| 00531 | M | C | NH | C | 52 | 14.87 | 3.8E+05 | 81 | 1.372 [5] | A*02:01, A*02:01, B*07:02, B*44:02, C*03:04, C*07:02 |
| 00546 | M | C | NH | C | 56 | 20.09§§ | N/A | 195 | 0.453 [2] | A*02:01, A*32:01, B*15:01, B*40:01, C*02:02, C*03:04 |
| 00673 | M | C | NH | C | 49 | 8.05 | 3.2E+05 | 168 | 0.790 [4] | A*24:02, A*30:02, B*15:17, B*18:01, C*05:01, C*07:01 |
| 00674 | M | C | NH | C | 57 | 6.25 | 6.8E+04 | 338 | 2.064 [5] | A*02:01, A*03:01, B*07:TDVB§§§, B*40:01, C*03:04, C*07:02 |
| 00720 | M | C | NH | C | 25 | 2.96 | 4.0E+05 | 168 | 0.499 [4] | A*01:01, A*02:01, B*07:02, B*18:01, C*07:02, C*12:03 |
| 00728 | M | C | NH | C | 30 | 6.00 | 1.8E+04 | 354¶¶ | 0.676 [6] | A*02:01, A*03:01, B*07:02, B*40:02, C*02:02, C*07:02 |
| 00749 | M | AA | NH | C | 25 | 4.10 | N/A | 402 | 0.365 [2] | A*03:01, A*30:02, B*15:03, B*40:01, C*02:10, C*03:04 |
| 00773 | M | C | NH | A | 46 | 2.01 | 2.4E+04 | 234 | 0.233 [1] | A*02:01, A*11:01, B*18:01, B*51:01, C*01:02, C*02:02 |
| 00833 | M | AA | NH | C | 36 | 8.16 | 7.9E+03 | 358*** | 0.048 [1] | A*02:02, A*74:01, B*15:16, B*82:01, C*03:02, C*14:02 |
| 00834 | M | AA | NH | C | 25 | 2.15 | 2.1E+04 | 365 | 0.479 [1] | A*02:05, A*30:02, B*51:01, B*58:01, C*04:01, C*16:01 |
| 00848 | F | C | NH | C | 44 | 4.78 | 1.4E+04 | 800 | 0.022 [1] | A*01:01, A*30:02, B*08:01, B*18:01, C*05:01, C*07:01 |
| 00870 | M | C | NH | C | 54 | 5.28 | 5.3E+04 | 154††† | 1.400 [1] | A*11:01, A*24:02, B*35:01, B*55:01, C*03:03, C*04:01 |
| 00879 | F | AA | NH | C | 54 | 1.60 | 4.5E+02 | 612 | 0.093 [1] | A*03:01, A*33:01, B*14:02, B*58:02, C*06:02, C*08:02 |
| 00926 | F | AA | NH | C | 38 | 3.83 | 1.3E+05 | 508 | 0.262 [1] | A*02:02, A*02:05, B*:39:10, B*45:01, C*12:03, C*16:01 |
| 00929 | F | AA | NH | C | 61 | 1.77 | 1.9E+04 | 528 | 0.268 [1] | A*01:01, A*74:AB****, B*15:MJMN¶¶¶, B*81:AB****, C*02:10, C*18:01 |
| 00930 | M | C | NH | C | 53 | 2.70 | 6.4E+05 | 174 | 2.084 [1] | A*01:01, A*11:01, B*08:01, B*40:01, C*03:04, C*07:01 |
| 00937 | F | AA | NH | C | 45 | 5.84 | 8.8E+04 | 260 | 1.276 [2] | A*03:01, A*30:01, B*35:01, B*52:01, C*04:01, C*16:01 |
| 00941 | F | C | NH | C | 47 | 14.58 | 6.6E+03 | 12 | 1.50E-08‡‡[1] | N/A |
| 01014 | F | C | H | C | 52 | 19.85 | 1.2E+06 | 16 | 0.338 [1] | A*23:01, A*74:01, B*07:02, B*41:02, C*15:05, C*17:03 |
| 01086 | F | AA | NH | C | 30 | 5.81 | N/A | 320 | 0.0529 [1] | A*02:05, A*03:01, B*07:06, B*53:01, C*04:01, C*07:02 |
| 01095 | F | C | NH | C | 54 | 6.56 | 1.1E+05 | 88 | 2.528 [1] | A*03:01, A*31:01, B*40:01, B*44:02, C*03:04, C*05:01 |
| 10430 | M | C | NH | C | 59 | 9.47 | 8.1E+04 | 78 | 1.367 [5] | A*02:01, A*30:01, B*13:02, B*51:01, C*06:02, C*14:02 |
| 20296 | M | C | NH | A | 35 | 6.90 | 2.5E+04 | 427 | 1.50E-08‡‡ [1] | A*29:02, A*31:01, B*08:01, B*44:03, C*07:01, C*16:01 |
| Mean: | 46 | 7.22 | 8.6E+05 | 293 | 0.775 | |||||
| Range: | 25–66 | 1.6–20.10 | 4.5E+02- 1.5E+07 | 12–800 | 1.50E-08–2.528 |
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* C: White/Caucasian, AA: Black/African American.
† NH: Non-Hispanic; H: Hispanic.
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‡A: Initiation of ART during acute HIV-1 infection, prior to establishment of setpoint viremia; C: Initiating of ART during chronic HIV-1 infection.
¶ Durable suppression defined as time from ≤ 40 copies/ml to date of T cell measurement.
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** HIV-1 RNA at start of combination ART.
†† IUPM (infectious units per million). Mean of IUPM measurements over 2 years from date of T cell mapping.
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‡‡ Below the limit of detection.
§§00546 on monotherapy from 1985 to 1996, initiated combination ART in 1996. Years suppressed calculated from data of initiation of cART.
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¶¶ CD4 count 261 on 8/17/17 (after cell collection date).
***Lowest CD4 value, CD4 nadir before ART initiation is 567.
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†††Lowest CD4 value, CD4 nadir before ART initiation is 157.
‡‡‡B*35:01/B*35:42.
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§§§ B*07:02/B*07:61/B*07:16.
¶¶¶ B*15:03/B*15:103/B*15:220.
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**** B*81:01/B*81:02.
Table 2
HIV-1-Specific T cell reponses (n = 25 participants).
| Participant | Summed magnitude (106/PMBC) | Immunodominant T cell response | Total T cell breadth | # of epitopes with escape variant(s) in outgrowth virus | Escape in immunodominant epitope (Y/N) |
|---|---|---|---|---|---|
| 00231 | 2856 | Vif153→170 | 13 | 3 | Y |
| 00250 | 1531 | Env765→782 | 10 | 4 | Y |
| 00531 | 390 | Gag357→374 | 1 | 1 | Y |
| 00546 | 895 | Gag260→277 | 4 | 1 | N |
| 00673 | 2313 | Nef73→90 | 5 | 3 | N |
| 00674 | 1394 | Env838→855 | 7 | 3 | Y |
| 00720 | 1947 | Pol521→538 | 18 | 8 | Y |
| 00728 | 439 | Gag204→221 | 7 | 0 | N |
| 00749 | 418 | Pol481→498 | 6 | 3 | N |
| 00773 | 1174 | Pol273→290 | 3 | 0 | N |
| 00833 | 333 | Gag164→181 | 4 | 0 | N |
| 00834 | 725 | Pol273→290 | 4 | 2 | N |
| 00848 | 276 | Nef89→106 | 3 | 0 | N |
| 00870 | 363 | Nef65→82 | 6 | 0 | N |
| 00879 | 500 | Gag292→309 | 5 | 1 | N |
| 00926 | 234 | Gag180→197 | 7 | 0 | N |
| 00929 | 798 | Gag180→197 | 7 | 2 | N |
| 00930 | 2182 | Nef81→98 | 19 | 7 | Y |
| 00937 | 297 | Pol257→274 | 5 | 3 | N |
| 00941 | 2216 | Nef81→98 | 11 | N/A* | N/A* |
| 01014 | 1463 | Nef65→82 | 9 | 4 | N |
| 01086 | 258 | Gag17→34 | 3 | 1 | Y |
| 01095 | 2337 | Pol313→330 | 4 | 2 | N |
| 10430 | 157 | Nef97→114 | 1 | 1 | Y |
| 20296 | 331 | Gag204→221 | 4 | N/A* | N/A* |
| Total | 166 | 49 (32% - 49/151) | |||
| Mean: | 1033 | 7 | 2 | ||
| Range: | 157–2856 | 1–19 | 0–8 |
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*No outgrowth virus sequence data available to test for the presence of an escape variant in the sequenced outgrowth virus.
Additional files
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Supplementary file 1
Size of the replication-competent reservoir in PLWH on ART (n = 25 participants) as measured by infectious units per million (IUPM) up to 2 years prior to T cell mapping date.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp1-v2.xlsx
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Supplementary file 2
The number of near full-length sequences obtained from p24 antigen positive wells generated in quantitative viral outgrowth assays for each participant, and the pairwise diversity of sequences obtained (5’ and 3’ halves).
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp2-v2.xlsx
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Supplementary file 3
Percentage of clonal sequences obtained from p24 antigen positive wells generated in quantitative viral outgrowth assays for each participant (5’ and 3’ halves).
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp3-v2.xlsx
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Supplementary file 4
Summary of HLA-associated polymorphism by HIV-1 protein.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp4-v2.xlsx
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Supplementary file 5
Summary of reactive T cell epitopes in study participants.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp5-v2.xlsx
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Supplementary file 6
Raw data from studies evaluating viral T cell escape variants in the replication-competent reservoir.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp6-v2.xlsx
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Supplementary file 7
HIV-1-specific T cell measurements and HIV reservoir size.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp7-v2.docx
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Supplementary file 8
HIV-1-specific T cell responses do not correlated with the size of the HIV reservoir.
Correlation between T cell breadth and summed magnitude of T cell response to HIV-1 protein in PLWH on ART (n = 25 participants, n = 166 epitopes), and adjusted for escape variants (n = 23 participants, n = 102 epitopes excluding 49 epitopes at which escape was observed), measured by IFN-γ ELISpot and the size of the replication-competent reservoir as measured by infectious units per million (IUPM) using Spearman Rank.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp8-v2.docx
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Supplementary file 9
Reactive T cell epitopes in PLWH on ART (n = 23 participants, 151 total mapped epitopes including 49 escape epitopes) are targeted by conserved immunogen vaccines.
Escape in the HIV-1 reservoir is consistently lower in T cell epitopes that fall within conserved immunogen vaccines than mapped epitopes that fall outside of the immunogens.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp9-v2.docx
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Supplementary file 10
Comparison of approaches to assess pre-ART escape in the latent HIV-1 reservoir.
- https://cdn.elifesciences.org/articles/57246/elife-57246-supp10-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/57246/elife-57246-transrepform-v2.docx
