Immune landscape of COVID-19 recovery: Nucleocapsid as a major target of CD8+ T cell antiviral responses in convalescent HLA-A*02+ individuals from Brazil.

Despite advanced knowledge on the SARS-CoV-2-induced immunity, a deeper understanding of how virus-specific responses are assembled upon infection is necessary. Therefore, the present work investigates the major histocompatibility complex-restricted virus-specific responses of acute and postacute COVID-19 patients. Our results indicate that convalescent individuals displayed and maintained higher counts of effector memory and terminally differentiated effector memory (TEMRA) CD4+ T and CD8+ T cells as compared with severe COVID-19. Mild COVID-19 displayed a higher early activation profile in memory subsets as compared with severe and convalescent individuals. Regarding the virus-specific T cell responses, SARS-CoV-2 nucleocapsid (N) protein arose as a major target of CD8+ T cells in convalescent HLA-A*02+ individuals, adding to the specific cellular response mediated by the spike (S) protein. Unsupervised analysis enabled the unbiased clustering of lymphocytes and the assessment of differential expression of CD69, production of intracellular IFN-γ, and reactivity to HLA-A*02 tetramers bearing N or S peptides. Furthermore, cell clones targeting S and N proteins of SARS-CoV-2 undergo cellular expansion in HLA-A*02+ convalescent individuals following in vitro antigenic recall by stimulation with inactivated SARS-CoV-2 and viral proteins. Convalescent from COVID-19 presents higher connectivity of the overall immune response in comparison with the acute phase, regardless of disease severity. Collectively, our data shed new light on the role of the protein N-mediated immunity against SARS-CoV-2 in patients from one of the most affected areas in Brazil.