Distinguishing potential mechanisms of HIV persistence

Richard Jefferys, TAG

For researchers attempting to develop a cure for HIV infection, it’s important to understand the mechanisms by which the virus persists in the body despite suppression of viral load to undetectable levels by ART. Debate has centred around two possibilities that aren’t necessarily exclusive:

  • HIV continues to replicate at low levels in body tissues that ART drugs may not penetrate well (often referred to as sanctuary sites).
  • Cells with HIV integrated into their genetic code – latently infected cells – persist and proliferate even though ART has shut down virus replication.

In recent years, evidence has accumulated indicating that, in most people who are adherent to ART, HIV replication is completely suppressed. A new report in the journal Science Advances adds to this evidence by analysing individuals in receipt of long-term ART. The results support the increasing research focus on the persistence and proliferation of HIV-infected cells as the major obstacle to a cure, a topic addressed by several other recently published papers.

The study by Giorgio Bozzi and colleagues described in Science Advances involved a total of six participants – three had initiated ART soon after HIV infection, while the remaining three had been diagnosed with AIDS prior to beginning treatment (one individual in each group had died and autopsy samples were available). The individuals were all male with an average age of 40 at diagnosis, and median time on ART was 17.8 years (range: 8 to 22.7 years).

As was expected, levels of HIV DNA were higher in the group that initiated ART late, both in blood and tissues. HIV was also significantly more genetically diverse in these participants. Lymphoid tissues harboured the largest amounts of HIV DNA in both groups.

Analyses of HIV evolution (changes in the virus’s genetic makeup that occur if it’s replicating) revealed no evidence of ongoing virus replication in any participant during continuous ART. In two cases, antiretroviral monotherapy and dual therapy had been received prior to starting effective ART, and this allowed the researchers to demonstrate that their techniques could detect HIV evolution during these periods when viral load was not fully suppressed (likewise, short-term HIV evolution was seen in one participant as a result of a brief ART interruption).

Overall, when data from all participants were combined, no genetic changes indicative of HIV replication were observed during 60 person-years of suppressive ART.

The researchers did observe evidence of proliferation of some latently infected cells. Certain patterns of HIV hypermutation that are induced by cellular ABOPEC proteins are unique to individual infected CD4 T cells. If these CD4 T cells proliferate, the number of copies of HIV with the same pattern of hypermutation increases. One example cited by the researchers is a single hypermutated HIV sequence identified in one participant prior to ART. After 16 years of treatment, 42 copies of the identical hypermutated HIV were detected in both ileum- and colon-derived tissues. This represents evidence that the original CD4 T cell containing the hypermutated HIV proliferated, generating multiple new CD4 T cells containing duplicates of the same hypermutated virus.

Several other recent papers address the role of CD4 T cell proliferation in maintaining the HIV reservoir.

In the Journal of Clinical Investigation, William McManus and colleagues from Mary Kearney’s laboratory at the National Cancer Institute present evidence that proliferation of latently infected CD4 T cells in lymph nodes underlies the persistence of HIV in people on ART. The researchers documented the phenomenon by identifying genetically identical copies of HIV that were integrated into the genetic code of the CD4 T cells at the same exact location. [2]

Marie-Angélique De Scheerder and colleagues from the HIV Cure Research Center at Ghent University Hospital have published results from the STAR study, an observational assessment of HIV sequences present before and after an analytical treatment interruption (ATI). The study was not able to pinpoint a consistent source of the HIV viral load that rebounded during ATI – either in terms of particular CD4 T cell types or anatomical location – but did find evidence that genetically identical viral expansions played an important role (consistent with the proliferation of latently infected CD4 T cells). The authors write: “Focusing on mechanisms that drive antigenic and homeostatic proliferation of immune cells will be crucial to achieve progress toward an HIV cure.” [3]

A paper by Sarah Joseph and colleagues in Clinical Infectious Diseases describes three study participants on ART with detectable HIV RNA in cerebrospinal fluid (CSF). In two cases the researchers pinpointed trafficking and proliferation of latently infected cells as the likely source, whereas there was some evidence of persistent replication in the third individual. [4]

Lastly, a study published this week in mBio by Xiaomin Li and colleagues identifies CD4 T cells expressing the cell surface marker CD161 as particularly prone to proliferating while harbouring replication-competent latent HIV. The researchers suggest that developing anti-proliferative strategies that focus on CD161-expressing CD4 T cells may offer a means to reduce the HIV reservoir. [5]


Jefferys R. TAG Basic Science Project. (11 October 2019).


  1. Bozzi G. No evidence of ongoing HIV replication or compartmentalization in tissues during combination antiretroviral therapy: Implications for HIV eradication. Science Advances  25 Sep 2019: Vol. 5, no. 9, eaav2045. DOI: 10.1126/sciadv.aav2045
  2. McManus WR et al. HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy. J Clin Invest. 2019.
  3. De ScheerderM-A et al. HIV rebound is predominantly fueled by genetically identical viral expansions from diverse reservoirs. Cell Host and Microbe. (2019) 26 (3); 347–358.(11 September 2019).
  4. Joseph SB et al. HIV Type 1 RNA detected in the central nervous system (CNS) after years of suppressive antiretroviral therapy can originate from a replicating CNS reservoir or clonally expanded cells. Clinical Infectious Diseases, 69(8); 1345–1352. (15 October 2019).
  5. Li X et al. CD161+ CD4+ T cells harbor clonally expanded replication-competent HIV-1 in antiretroviral therapy-suppressed individuals. mBio Oct 2019, 10 (5) e02121-19; DOI: 10.1128/mBio.02121-19.

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