SARS-CoV-2 mRNA vaccine elicits a potent adaptive immune response in the absence of IFN-mediated inflammation observed in COVID-19

Both SARS-CoV-2 infection and vaccination elicit potent immune responses, but the durability and scope of immune responses remain to be elucidated. Here, we performed multimodal single-cell profiling of peripheral blood of patients with acute COVID-19 and healthy volunteers before and after receiving the SARS-CoV-2 BNT162b2 mRNA vaccine to compare the immune responses elicited by the virus and by the vaccine. Phenotypic and transcriptional profiling of immune cells, coupled with reconstruction of B and T cell receptor repertoires, enabled us to characterize and compare the host responses to the virus and to defined viral antigens. In COVID-19 patients, immune responses were characterized by a highly augmented interferon response which was largely absent in vaccine recipients. Increased interferon signaling likely contributed to the dramatic upregulation of cytotoxic genes in the peripheral T cells and innate-like lymphocytes observed in COVID-19 patients. Analysis of B and T cell repertoires revealed that while the majority of clonal lymphocytes in COVID-19 patients were effector cells, in vaccine recipients clonal expansion was primarily restricted to circulating memory cells. Taken together, our analysis of immune responses to the mRNA vaccine reveals that despite the lack of dramatic inflammation observed during infection, the vaccine elicits a robust adaptive immune response.