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HIV-Infected Cells Recirculate
Throughout Organs During Suppressive ART
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2022 CROI, February 12-16 and 22-24, 2022
Mark Mascolini
What appears to be the first near-full-length proviral sequencing of HIV from diverse organs collected after death from 2 people found that HIV provirus persists and recirculates in these tissues despite viral suppression in blood with antiretroviral therapy (ART) [1]. Researchers from the University of Montreal and collaborators at other centers proposed that clonal expansion of HIV genomes allows HIV reservoirs to persist during viral control and recirculate through anatomical sites during ART.
Prior work established that HIV DNA takes root in multiple deep organs and stays there through ART that makes HIV RNA disappear from the circulation [2,3]. The new study presented at CROI pushed this research forward another step by performing near-full-length sequencing of HIV genomes collected from multiple organs of 2 ART responders immediately after they died.*
With their agreement, both men had rapid deep tissue sampling after death from multiple organs and tissues: brain, spinal cord, lungs, liver, duodenum, jejunum, ileum, colon, rectum, mediastinal lymph node, axillary lymph node, hilar lymph node, mesenteric lymph node, inguinal lymph node, spleen, and testes.
Volunteer 1 was a 67-year-old man diagnosed with AIDS in May 1987. He had several opportunistic infections and took multiple antiretroviral regimens, starting with monotherapy and eventually taking combination therapy. He took ART continuously for 11 years until 1 day before he died in March 2018. He did not have AIDS-related diseases or other illness at death and was undergoing palliative care.
Volunteer 2 was a 68-year-old man diagnosed with HIV in 2003. He died of non-Hodgkin lymphoma in June 2018. He also had diabetes, hypertension, HCV infection, HIV-associated peripheral neuropathy, and minor neurocognitive disorder. He used only two antiretroviral regimens during his life, which he took continuously for 8 years, and he had an undetectable viral load in plasma at death.
The researchers found the highest HIV DNA levels in lymph nodes of Volunteer 1, from whom they analyzed 300 proviral genomes from 14 deep tissues, scrutinizing between 1 and 67 HIV sequences per tissue. The 300 proviral genomes ranged from 150 to 9064 base pairs (average 5797). Only 2% of these 300 proviral sequences were intact; they were found in spleen (2 sequences), mediastinal lymph node (2 sequences), and mesenteric lymph node (1 sequence). Among the other proviral sequences analyzed in Volunteer 1, 41% had large internal deletions, 38% contained hypermutations, 14% had Psi defects, 4% had stop codons, 1% had inversions, and 0.3% had small internal deletions.
Volunteer 2 had 141 proviral sequences analyzed from 8 deep tissues, with 6 to 33 sequences per tissue. Highest HIV DNA levels were measured in liver. These sequences had from 490 to 9051 base pairs (average 4848). Thirty-six (26%) of these proviral sequences were intact; they came from all tissues analyzed except the inguinal lymph node and duodenum. Of the other sequences, 65% had large internal deletions, 6% stop codons, 1% hypermutation, 1% Psi defects, and 1% small internal deletions.
Summarizing proviral sequence findings from both men, the researchers noted that intact sequences are rare, mainly found in lymphoid organs, and sometimes found in lung, liver, and jejunum.
About half of proviruses in tissue reservoirs were clonal expansions, that is, they were 100% identical with each other. The researchers found clonally expanded HIV genomes in every deep tissue from which they sequenced more than 1 provirus. In Volunteer 1, different tissues shared 24 of 28 clonally expanded sequences; in Volunteer 2, different tissues shared 10 of 11 clonally expanded sequences. These high rates of clonally expanded sequence sharing suggested to the researchers that latently infected cells recirculate after expansion.
The investigators outlined four major findings of their work:
• Latently infected cells that persist during long-term ART could be found in all deep tissues analyzed in both volunteers, at different frequencies from tissue to tissue.
• Most HIV proviral sequences found in deep tissue have defects that prevent them from being replication-competent.
• Intact proviruses reside mainly in lymphoid tissue (lymph nodes and spleen) but can be found in other organs as well.
• Half of the persistent proviral reservoir during long-term ART consists of clonally expanded proviruses frequently found in multiple locations.
The researchers concluded that this study—the first to accomplish near-full-length proviral sequencing of latent HIV in multiple deep tissues of humans—underlines the stubborn HIV persistence in all collected tissues throughout the body. They believe their findings "suggest that clonal expansion is an important mechanism of persistence of the HIV reservoir, and that infected cells recirculate throughout different anatomical sites during ART."
*From abstract: "HIV DNA and cell-associated gag RNA were quantified by qPCR in snap-frozen tissues . . . Near-full length proviral sequences were obtained by a modified FLIPS assay followed by PacBio sequencing" [1].
References
1. Dufour C, Ruiz MJ, Pagliuzza A, et al. Expansion and extensive recirculation of HIV-infected cells in multiple organs. 2022 CROI, February 12-16 and 22-24, 2022. Abstract 67.
2. Lamers SL, Rose R, Maidji E, et al. HIV DNA is frequently present within pathologic tissues evaluated at autopsy from combined antiretroviral therapy-treated patients with undetectable viral loads. J Virol. 2016;90:8968-83. doi: 10.1128/JVI.00674-16. https://journals.asm.org/doi/10.1128/JVI.00674-16
3. Chaillon A, Gianella S, Dellicour S, et al. HIV persists throughout deep tissues with repopulation from multiple anatomical sources. J Clin Invest. 2020;130:1699-1712. doi: 10.1172/JCI134815. https://www.jci.org/articles/view/134815
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