We greatly acknowledge Myriam Ben Neji, Flavie Moreau, and Céline Berrone, IPBS and Genotoul Anexplo-IPBS, for accessing the BSL3 facilities; and the Genotoul TRI-IPBS facilities for imaging and flow cytometry, in particular Emmanuelle Näser, Serge Mazères, and Antonio Peixoto, and Raphaëlle Romieu-Mourez (Human immune-monitoring core, Infinity, Toulouse) for her help. We also thank Etienne Cavaignac for providing synovium samples and Aurélien Brindel for the BAL swabs. We greatly thank Loïc Rolas, Loïc Dupré, and Raphael Gaudin for fruitful discussions and Claire Lastrucci for illustration of Fig. 6.

This work was supported by the Centre National de la Recherche Scientifique, Université Paul Sabatier, the Institut National de la Santé et de la Recherche Médicale, the Agence Nationale de la Recherche (ANR16-CE13-0005-01, ANR DFG 2020 JA-3038/2-1), the Agence Nationale de Recherche sur le Sida et les hépatites virales (ANRS) grant nos. ANRS2018-02, ECTZ 118551/118554, ECTZ 205320/305352, ANRS ECTZ103104, and ECTZ101971, Sidaction (13457), the Fondation pour la Recherche Médicale (DEQ2016 0334894, DEQ2016 0334902, ENV202003011510), the Fondation Toulouse Cancer Santé and l’INSERM Plan Cancer. We also thank the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID. R. Mascarau and V. Cantaloube-Ferrieu are PhD candidates at Université Toulouse III Paul Sabatier. M. Woottum is a PhD candidate at Université Paris Cité. R. Mascarau was supported by doctoral scholarships from Toulouse Cancer Santé, ANRS, and the Fondation des Treilles. M. Woottum and V. Cantaloube-Ferrieu were supported by doctoral scholarships from ANRS.

Author contributions: Conceptualization: R. Mascarau, B. Raynaud-Messina, and C. Vérollet; Methodology: R. Mascarau, Z. Valhas, R. Gence, N. Jabrane-Ferrat, J.-L. Davignon, B. Lagane, R. Poincloux, S. Bénichou, B. Raynaud-Messina, and C. Vérollet; Formal Analysis: R. Mascarau; Investigation: R. Mascarau, M. Woottum, L. Fromont, Z. Valhas, F. Bertrand, T. Beunon, A. Métais, V. Cantaloube-Ferrieu, B. Raynaud-Messina, and C. Vérollet; Resources: H.El Costa, N. Jabrane-Ferrat, Y. Gallois, N. Guibert, J-L. Davignon, G. Favre, B. Lagane, and S. Bénichou; Writing—Original Draft: R. Mascarau, B. Raynaud-Messina, and C. Vérollet; Writing—Review & Editing: R. Mascarau, R. Gence, A. Métais, N. Jabrane-Ferrat, N. Guibert, B. Lagane, I. Maridonneau-Parini, R. Poincloux, S. Bénichou, B. Raynaud-Messina, and C. Vérollet; Visualization: R. Mascarau, A. Métais, and R. Poincloux; Supervision: N. Jabrane-Ferrat, G. Favre, B. Lagane, S. Bénichou, B. Raynaud-Messina, and C. Vérollet; Project Administration: B. Raynaud-Messina and C. Vérollet; Funding Acquisition: I. Maridonneau-Parini, R. Poincloux, B. Lagane, S. Bénichou, and C. Vérollet.