Characterizing HIV persistence and dynamics across the human body is important to develop ways to clear reservoirs. This goal has been hampered by technical difficulties and obtaining fresh tissues.
Samples were obtained from 6 Last Gift participants, who provided blood ante-mortem and their whole bodies for rapid autopsy within 6 hours of death. Two voluntarily stopped their antiretroviral therapy (ART) before death and 4 remained on ART. HIV reservoirs were characterized by digital droplet PCR and single genome amplification and sequencing of full-length (FL) envelope HIV. Phylogeographic methods reconstructed HIV spread and generalized linear models (GLM) tested for associations between HIV diversity, divergence, predicted tropism, DNA level, and viral dispersal.
Across participants, HIV DNA levels ranged from ~0 copies/106 cells in the occipital lobe (interquartile range: [IQR] 0-4.6) to 659 cp/106 cells in lymph nodes (IQR 580-753), mean=98 cp/106 cells (IQR:23-132) across all tissues. We recovered 603 intact FL env sequences in antemortem blood cells and across 28 anatomical sites (mean of 7 viruses/site, IQR: 5-10), including the central nervous system (CNS). Among the 2 participants stopping ART, viral diversity was lower (p<0.01) in blood plasma than in most tissue-derived HIV DNA. Most of the rebounding intact HIV RNA populations in blood (65% and 80% of variants) were clonal (>99% identical). There was also evidence of clonal expansion within tissues (Fig.), especially gut and genital tract (e.g. 30 identical proviruses observed across 8 tissues in 1 participant). While the main sources of viral dispersal were blood, gut and lymph nodes, our models also revealed viral exchanges within the CNS (Fig.) and from blood toward the CNS. The GLM models revealed that low HIV genetic divergence between sites and high HIV diversity in the recipient sites but not HIV DNA levels were associated with viral exchange.
This study found: 1) The emergence of large, clonal, intact HIV RNA populations after stopping ART, which repopulated tissues throughout the body; 2) Multiple sites can act as hubs for dissemination of HIV within the host; 3) Viral exchanges occur within the CNS areas and between the CNS and blood; 4) viral dynamics are associated with low HIV divergence between sites and high HIV divesity at the recipient site.