Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods

Fabian Otte; Yuepeng Zhang; Julian Spagnuolo; Alexander Thielen; Martin Däumer; Carsten Wiethe; Marcel Stoeckle; Katharina Kusejko; Florian Klein; Karin J Metzner; Thomas Klimkait; Swiss HIV Cohort Study

doi:10.1016/j.crmeth.2023.100485

Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods

Cell Rep Methods. 2023 May 23;3(6):100485. doi: 10.1016/j.crmeth.2023.100485. eCollection 2023 Jun 26.

Collaborators

Swiss HIV Cohort Study:
I Abela, K Aebi-Popp, A Anagnostopoulos, M Battegay, E Bernasconi, D L Braun, H C Bucher, A Calmy, M Cavassini, A Ciuffi, G Dollenmaier, M Egger, L Elzi, J Fehr, J Fellay, H Furrer, C A Fux, H F Günthard, A Hachfeld, D Haerry, B Hasse, H H Hirsch, M Hoffmann, I Hösli, M Huber, D Jackson-Perry, C R Kahlert, L Kaiser, O Keiser, T Klimkait, R D Kouyos, H Kovari, K Kusejko, N Labhardt, K Leuzinger, B Martinez de Tejada, C Marzolini, K J Metzner, N Müller, J Nemeth, D Nicca, J Notter, P Paioni, G Pantaleo, M Perreau, A Rauch, L Salazar-Vizcaya, P Schmid, R Speck, M Stöckle, P Tarr, A Trkola, G Wandeler, M Weisser, S Yerly

Affiliations

¹ Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland.
² Experimental Immunology, Department Biomedicine, University of Basel, 4056 Basel, Switzerland.
³ Seq-IT GmbH & Co.KG, 67655 Kaiserslautern, Germany.
⁴ Biolegend GmbH, 56070 Koblenz, Germany.
⁵ Infectiology, University Hospital Basel, 4031 Basel, Switzerland.
⁶ Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland.
⁷ Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.

Abstract

While combination therapy completely suppresses HIV-1 replication in blood, functional virus persists in CD4⁺ T cell subsets in non-peripheral compartments that are not easily accessible. To fill this gap, we investigated tissue-homing properties of cells that transiently appear in the circulating blood. Through cell separation and in vitro stimulation, the HIV-1 "Gag and Envelope reactivation co-detection assay" (GERDA) enables sensitive detection of Gag+/Env+ protein-expressing cells down to about one cell per million using flow cytometry. By associating GERDA with proviral DNA and polyA-RNA transcripts, we corroborate the presence and functionality of HIV-1 in critical body compartments utilizing t-distributed stochastic neighbor embedding (tSNE) and density-based spatial clustering of applications with noise (DBSCAN) clustering with low viral activity in circulating cells early after diagnosis. We demonstrate transcriptional HIV-1 reactivation at any time, potentially giving rise to intact, infectious particles. With single-cell level resolution, GERDA attributes virus production to lymph-node-homing cells with central memory T cells (T_CMs) as main players, critical for HIV-1 reservoir eradication.

Keywords: DBscan; GERDA; Gag and Envelope co-detection assay; HIV-1 quantification; HIV-1 reservoir; HIV-1 reservoirs; HIV-1 viral outgrowth; HIV-1 virus dynamics; bNAbs; cell homing; tSNE.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CD4-Positive T-Lymphocytes
HIV Infections*
HIV Seropositivity*
HIV-1* / genetics
Humans
T-Lymphocyte Subsets