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. 2020 Apr 1;130(4):1699-1712.
doi: 10.1172/JCI134815.

HIV persists throughout deep tissues with repopulation from multiple anatomical sources

Antoine Chaillon  1 , Sara Gianella  1 , Simon Dellicour  2   3 , Stephen A Rawlings  1 , Timothy E Schlub  4 , Michelli Faria De Oliveira  1 , Caroline Ignacio  1 , Magali Porrachia  1 , Bram Vrancken  3 , Davey M Smith  1
Affiliations

HIV persists throughout deep tissues with repopulation from multiple anatomical sources

Antoine Chaillon et al. J Clin Invest. .

Abstract

BACKGROUNDUnderstanding HIV dynamics across the human body is important for cure efforts. This goal has been hampered by technical difficulties and the challenge of obtaining fresh tissues.METHODSThis observational study evaluated 6 individuals with HIV (n = 4 with viral suppression using antiretroviral [ART] therapy; n = 2 with rebound viremia after stopping ART), who provided serial blood samples before death and their bodies for rapid autopsy. HIV reservoirs were characterized by digital droplet PCR, single-genome amplification, and sequencing of full-length (FL) envelope HIV. Phylogeographic methods were used to reconstruct HIV spread, and generalized linear models were tested for viral factors associated with dispersal.RESULTSAcross participants, HIV DNA levels varied from approximately 0 to 659 copies/106 cells (IQR: 22.9-126.5). A total of 605 intact FL env sequences were recovered in antemortem blood cells and across 28 tissues (IQR: 5-9). Sequence analysis showed (a) the emergence of large, identical, intact HIV RNA populations in blood after cessation of therapy, which repopulated tissues throughout the body; (b) that multiple sites acted as hubs for HIV dissemination but that blood and lymphoid tissues were the main source; (c) that viral exchanges occurred within brain areas and across the blood-brain barrier; and (d) that migration was associated with low HIV divergence between sites and greater diversity at the recipient site.CONCLUSIONHIV reservoirs persisted in all deep tissues, and blood was the main source of dispersal. This may explain why eliminating HIV susceptibility in circulating T cells via bone marrow transplants allowed some individuals with HIV to experience therapy-free remission, even though deeper tissue reservoirs were not targeted.TRIAL REGISTRATIONNot applicable.FUNDINGNIH grants P01 AI31385, P30 AI036214, AI131971-01, AI120009AI036214, HD094646, AI027763, AI134295, and AI68636.

Keywords: AIDS/HIV; Infectious disease; Molecular biology.

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Conflict of interest statement

Conflict of interest: The authors have declared that no conflict of interest exists.

Figures

Figure 1
Figure 1. Flow diagram.
Six participants enrolled in the Last Gift cohort (n = 2 participants who stopped ART; n = 4 participants who remained virally suppressed on ART until death) were included in this study. (1) Premortem blood plasma (n = 2 participants) and PBMC samples (n = 6 participants) were collected before death, and tissues were collected during the rapid autopsy procedure. (2) HIV RNA and DNA were extracted from blood plasma and PBMCs and tissues for quantification of HIV DNA/RNA (ddPCR). ( and 4) HIV FL envelopes were sequenced via single-genome amplification and sequencing. Intact FL env sequences from all samples were used to (5) characterize the HIV populations within each compartment and in blood, (6) assess viral dispersal across tissues using Bayesian phylodynamic models, and (7) evaluate factors associated with viral dispersal.
Figure 2
Figure 2. Characteristics of the HIV populations within each compartment.
Scatter dot plots sorted by sampled compartment and colored by participants with the y axis showing (A) the total number of sequences; (B) the proportion of intact sequences; (C) the proportion of nearly identical sequences (any sequences with ≥99% nucleotide identity with at least 1 other sequence from the same participant); (D) the proportion of identical sequences (100%); (E) the pairwise genetic distance between sequences; and (F) the levels of HIV DNA. The pairwise genetic distance between sequences from a compartment was measured using the TN93 algorithm (46). HIV DNA levels were quantified by ddPCR. Copy numbers were calculated as the mean of 3 replicate PCR measurements and normalized to 1 million cells, as determined by RPP30 assay (total cell count) (94, 95). See Methods for details. PIDs, participant identifiers.
Figure 3
Figure 3. HIV DNA levels in compartments for each participant.
HIV DNA levels were quantified by ddPCR. Copy numbers were calculated as the mean of 3 replicate PCR measurements and normalized to 1 million cells, as determined by RPP30 assay (total cell count) (94, 95). See Methods for details. The dots and horizontal bars represent the mean and range (minimum and maximum) of the HIV DNA levels.
Figure 4
Figure 4. ML phylogenies and clonal populations (FL envelope) for 2 participants who either stopped ART or remained virally suppressed on ART.
IQ-TREE (97) was used to estimate phylogenies for the FL HIV env sequences obtained from premortem blood plasma and tissues and from PBMCs collected during rapid autopsy. (A) ML phylogeny for participant LG01, who stopped therapy. (B) ML phylogeny for participant LG03, who remained virally suppressed. Tips are colored by compartment as in the legend. The size and distribution of nearly identical FL env populations (99% identical, populations of at least 3 identical proviruses) for each participant are presented in the middle of each tree. Colors represent the tissues described in the key. For LG01, nearly identical FL env populations including HIV RNA viruses sampled in blood plasma during viral rebound are marked with an asterisk. See also Supplemental Figure 4 for data on the 4 remaining participants.
Figure 5
Figure 5. Lineage dispersal events between compartments.
The circle size is proportional to HIV DNA levels (or RNA for plasma) in each compartment. The thickness of the arrows corresponds to the average number of inferred migration events between compartments. Only transition events between locations for which the adjusted BF was 3 or higher (at least positive evidence) are shown.
Figure 6
Figure 6. Proportion of supported transition events between compartments for 2 participants who either stopped ART or remained virally suppressed on ART.
(A) Data for the participant who stopped ART. (B) Data for the participant who remained virally suppressed on ART. Sankey plot shows the proportion of transition events between locations for which the adjusted BF was 3 or higher (at least positive evidence). The adjusted BF support for each transition type is given next to the corresponding color. The source locations are depicted on the left side of the plots and the destination locations on the right side. See also Supplemental Figure 6.
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