Estimating the total size of the HIV reservoir

28 November 2017. Related: Cure-related research.

Richard Jefferys, TAG

A paper published earlier this month in Nature Medicine by Jake Estes and colleagues addresses the difficult challenge of attempting to define the distribution and total size of the persistent HIV reservoir. [1]

The researchers employed a variety of tests to measure viral RNA and DNA – including new imaging techniques they have developed named RNAscope and DNAscope [2] - in multiple tissues from untreated or ART-treated macaques (infected with SIVmac251, SIVmac239 or SHIV) as well as lymph node and rectal tissue samples from a cohort of 20 individuals on ART in Kampala, Uganda.

The main findings were that the vast majority (~99.6%) of cells expressing viral RNA – indicating some degree of virus production – were found in lymphoid tissues (lymph nodes, gut, spleen, and lung). ART significantly reduced viral RNA levels, but the researchers estimated a total body burden of as many as seven million cells expressing HIV RNA at any given time in tissues, despite viral load suppression to undetectable levels in the blood.

One suggested explanation for the continued viral RNA expression is ongoing replication due to poorer penetration of ART drugs into tissues (the study reports evidence of suboptimal ART levels in tissues of macaques). But the authors’ note that the tests for viral RNA were unable to distinguish between ongoing active viral replication and the production of viruses by reactivated latently infected cells. ART would not be expected to block the latter process; rather, it would prevent any viruses that are produced by reactivated latently infected cells from being able to go on and infect other cells.

The total size of the replication-competent HIV reservoir that persists during ART was estimated as approximately 400 million latently infected cells, based on analyses of viral DNA levels in tissues. The researchers suggest this is broadly consistent with another recent estimate, which, when extrapolated to the whole body, gives a result of 240 million cells. [3]

The paper’s abstract states a more conservative ~100 million (I’m not clear why there’s a difference from the estimate provided within the paper). These numbers are larger than had originally been thought, and underscore the challenge of eliminating latent HIV infection.

The question of whether HIV replication commonly persists in tissues despite ART remains contentious, with many of the authors of this study having previously reported that it does, based on analyses of three people who had been receiving ART for six months (this prior work is cited in the current paper). [4]

But these results were recently challenged by the research group of Mary Kearney, who found no evidence of HIV replication in children who had been on ART with suppressed viral loads for seven to nine years (Kearney’s work was initially presented at CROI 2017 and has since been published in the Journal of Clinical Investigation). [5, 6]

Kearney argued that there was a potential problem with the original claims because the Bayesian methodology for assessing HIV evolution was not appropriate for the task.

A recent paper by David Asmuth and colleagues also presents a contrary perspective, finding that ART concentrations in gut-associated lymphoid tissue (GALT) were adequate in almost all cases studied, with no evidence of residual HIV replication. [7]

Resolving the question of whether the HIV RNA that is detectable despite ART derives from ongoing active viral replication or reactivated latently infected cells (or both) will be important, because it has implications for therapeutic approaches to reducing the reservoir.

NOTE: The discussion on the reservoir size has been modified since the first draft of this article was published online.

References:

Estes JD et al. Defining total-body AIDS-virus burden with implications for curative strategies. Nature Medicine (2017). doi:10.1038/nm.4411. (02 October 2017).
https://www.nature.com/nm/journal/vaop/ncurrent/full/nm.4411.html
Deleage C et al. Defining HIV and SIV reservoirs in lymphoid tissues. Oathogens and Immunity, (2016);1(1):60-106. doi: 10.20411/pai.v1i1.100. (14 June 2016)
https://paijournal.com/index.php/paijournal/article/view/100/43
Bruner KM et al. Defective proviruses rapidly accumulate during acute HIV-1 infection. Nature Medicine 22, 1043–1049 (2016) doi:10.1038/nm.4156. (08 August 2016).
https://www.nature.com/nm/journal/v22/n9/full/nm.4156.html
Lorenzo-Redondo R et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature. 2016 Feb 4; 530(7588): 51–56. doi: 10.1038/nature16933. (27 January 2016).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865637
Katusiime MGK et al. No evidence of ongoing HIV replication after 7 years on ART. CROI, 13-16 February, 2017, Seattle. Oral abstract 120.
http://www.croiwebcasts.org/console/player/33577 (webcast)
Van Zyl GU et al. No evidence of HIV replication in children on antiretroviral therapy. J Clin Invest. 2017;127(10):3827–3834. doi:10.1172/JCI94582. (11 September 2017).
https://www.jci.org/articles/view/94582
Asmuth DA et al. Tissue pharmacologic and virologic determinants of duodenal and rectal GALT immune reconstitution in HIV-infected patients initiating antiretroviral therapy. Journal of Infectious Diseases, jix418, https://doi.org/10.1093/infdis/jix418. (23 August 2017).
https://academic.oup.com/jid/article-abstract/doi/10.1093/infdis/jix418/4092886
Azimuth D et al. Tissue pharmacologic and virologic determinants of duodenal and rectal gastrointestinal-associated lymphoid tissue immune reconstitution in HIV-infected patients initiating antiretroviral therapy. JID: 216(7); 813–818.
DOI: 10.1093/infdis/jix418. (17 October 2017).
https://academic.oup.com/jid/article-abstract/doi/10.1093/infdis/jix418/4092886