Similar Frequency and Inducibility of Intact Human Immunodeficiency Virus-1 Proviruses in Blood and Lymph Nodes

Abstract

Background The HIV-1 latent reservoir (LR) in resting CD4 + T cells is a barrier to cure. LR measurements are commonly performed on blood samples and therefore may miss latently infected cells residing in tissues, including lymph nodes. Methods We determined the frequency of intact HIV-1 proviruses and proviral inducibility in matched peripheral blood (PB) and lymph node (LN) samples from ten HIV-1-infected patients on ART using the intact proviral DNA assay and a novel quantitative viral induction assay. Prominent viral sequences from induced viral RNA were characterized using a next-generation sequencing assay. Results The frequencies of CD4 + T cells with intact proviruses were not significantly different in PB vs LN (61vs104/10 6CD4 + cells), and were substantially lower than frequencies of CD4 + T cells with defective proviruses. The frequencies of CD4 + T cells induced to produce high levels of viral RNA were not significantly different in PB vs LN (4.3/10 6 vs 7.9/10 6), but were 14-fold lower than the frequencies of cells with intact proviruses. Sequencing of HIV-1 RNA from induced proviruses revealed comparable sequences in paired PB and LN samples. Conclusions These results further support the use of PB as an appropriate proxy for the HIV-1 LR in secondary lymphoid organs

Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy

“…Subsequently, these cells produce virus and die within days from viral cytopathic effects or host immune surveillance without entering the circulation. Although infected cells carrying identical proviruses can be detected in blood and lymph node ( 56 – 58 ), recently activated, productively infected CD4 + T cells may be retained in the lymph node until adhesion molecules are down-regulated. The rapid death of the tissue CD4 + T cells that produce most of the plasma virus may contribute to CD4 + T cell depletion, but other mechanisms are likely also involved ( 59 ).…”

Single-Cell Profiling of Latently SIV-Infected CD4 + T Cells Directly Ex Vivo to Reveal Host Factors Supporting Reservoir Persistence

“…Such genomes may have persisted in our analysis following a relatively short period of cART. It is also possible that lymph node specimens represent a distinct reservoir relative to that of peripheral blood, though analyses comparing HIV proviruses in matched lymph node and peripheral blood samples have found similar proportions of intact provirus between compartments ( 74 , 75 ), so this seems less likely.…”

Predicting Post-treatment HIV Remission: Does Size of the Viral Reservoir Matter?

“…However, it is difficult to estimate the real HIV reservoir size, as PCRbased methods that measure HIV DNA and RNA overestimate the reservoir because most of proviruses are genetically defective (Bruner et al, 2016). On the other hand, the quantitative viral outgrowth assay (qVOA) will not score defective proviruses, but is thought to underestimate the reservoir as only a small fraction of genetically intact proviruses can be activated ex vivo (Ho et al, 2013;Bruner et al, 2016;Kwon et al, 2020;Martin et al, 2020). The most accurate surrogate marker of the reservoir size is currently considered to be the number of intact proviruses, estimated by either full-length proviral sequencing (Bruner et al, 2016;Hiener et al, 2017;Pinzone et al, 2019) or the recently developed digital droplet PCRbased intact proviral DNA assay (IPDA) (Bruner et al, 2019).…”