Integrated longitudinal immunophenotypic, transcriptional and repertoire analyses delineate immune responses in COVID-19 patients.

Notarbartolo, Samuele; Ranzani, Valeria; Bandera, Alessandra; Gruarin, Paola; Bevilacqua, Valeria; Putignano, Anna Rita; Gobbini, Andrea; Galeota, Eugenia; Manara, Cristina; Bombaci, Mauro; Pesce, Elisa; Zagato, Elena; Favalli, Andrea; Sarnicola, Maria Lucia; Curti, Serena; Crosti, Mariacristina; Martinovic, Martina; Fabbris, Tanya; Marini, Federico; Donnici, Lorena; Lorenzo, Mariangela; Mancino, Marilena; Ungaro, Riccardo; Lombardi, Andrea; Mangioni, Davide; Muscatello, Antonio; Aliberti, Stefano; Blasi, Francesco; De Feo, Tullia; Prati, Daniele; Manganaro, Lara; Granucci, Francesca; Lanzavecchia, Antonio; De Francesco, Raffaele; Gori, Andrea; Grifantini, Renata; Abrignani, Sergio

To understand how a protective immune response against SARS-CoV-2 develops over time, we integrated phenotypic, transcriptional and repertoire analyses on PBMCs from mild and severe COVID-19 patients during and after infection, and compared them to healthy donors (HD). A type I IFN-response signature marked all the immune populations from severe patients during the infection. Humoral immunity was dominated by IgG production primarily against the RBD and N proteins, with neutralizing antibody titers increasing post infection and with disease severity. Memory B cells, including an atypical FCRL5+ T-BET+ memory subset, increased during the infection, especially in patients with mild disease. A significant reduction of effector memory, CD8+ T cells frequency characterized patients with severe disease. Despite such impairment, we observed robust clonal expansion of CD8+ T lymphocytes, while CD4+ T cells were less expanded and skewed toward TCM and TH2-like phenotypes. MAIT cells were also expanded, but only in patients with mild disease. Terminally differentiated CD8+ GZMB+ effector cells were clonally expanded both during the infection and post-infection, while CD8+ GZMK+ lymphocytes were more expanded post-infection and represented bona fide memory precursor effector cells. TCR repertoire analysis revealed that only highly proliferating T cell clonotypes, which included SARS-CoV-2-specific cells, were maintained post-infection and shared between the CD8+ GZMB+ and GZMK+ subsets. Overall, this study describes the development of immunity against SARS-CoV-2 and identifies an effector CD8+ T cell population with memory precursor-like features.