The authors would like to thank Thierry Pedron and Azadeh Saffarian from the Institut Pasteur in Paris for their valuable contributions and advice concerning this study. The authors also would like to thank the Biomics Pole of the CITECH structure at the Institut Pasteur in Paris for the sequencing services and all members of the ASW and L2I groups of the IDMIT infrastructure.
This work was funded by the French Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS). This work was supported by the French government “Programme d’Investissements d’Avenir” (PIA) under Grant ANR-11-INBS-0008 funding the Infectious Disease Models and Innovative Therapies (IDMIT, Fontenay-aux-Roses, France) infrastructure and the Grant ANR-17-E15-0020-03 funding the ACROBAT project. J.R. was supported by the National Institute for Allergy and Infectious Diseases of the National Institutes of Health under award number U19AI084044. N.T. was supported by a fellowship from the ANRS. F.B. was supported by fellowships from the ANRS, Sidaction, and the Institut Carnot “Pasteur Microbes & Santé”.