High-throughput profiling of innate immune cells following SARS-CoV-2 mRNA-based vaccination and SARS-CoV-2 natural infection

The COVID-19 pandemic, caused by SARS-CoV-2, has posed significant global health challenges due to its complex pathogenesis and continuous emergence of new variants. This has made it necessary to develop prophylactic vaccines to achieve herd immunity. Beyond adaptive immunity, vaccines may also activate the innate immune system, contributing to the establishment of "trained immunity". Despite advances in understanding the adaptive immune response to SARS-CoV2, there is a significant gap in studies examining the interplay between innate and adaptive immunity in the context of the severity of clinical manifestations and the variability in individual susceptibility to different viral strains. Additionally, the detailed characterization of both innate and innate-like immune responses following SARS-CoV-2 vaccination, as well as the establishment of trained immunity, remains underexplored. In the present study, we investigated two key aspects. Firstly, high-throughput single-cell technologies, combined with an unsupervised computational model, were used to identify and correlate the blood immunological signatures in response to SARS-CoV-2 infection, with different clinical outcomes and viral variants, in a heterogeneous cohort of infected patients. Secondly, we examined the longitudinal impact of the BNT162b2 vaccine on the homeostasis of circulating innate and innate-like immune cells, in a cohort of healthy vaccinated individuals. The scITD analysis has identified patterns of heme and iron metabolism dysregulation, marked in cMono, that vary according to the SARS-CoV-2 variant. Speci^ically, a clear separation was observed between patients infected with the pre-Alpha variant and those with other variants. The high-throughput pro^iling of immune cells following mRNA vaccination has demonstrated a robust activation state after the boost. Indeed, while the ^irst dose effectively primed the innate immune system, the second dose was necessary to elicit the strongest response in terms of activation. Speci^ically, for MAIT cells, we observed a TNFmediated mechanism by which MAIT cells facilitate B cell immune memory formation. For γδ T cells, we detected the generation of Vδ2 T proliferative clones with higher effector potential and long-lasting central memory features. For DCs, we identi^ied possible innate immune-related long-term memory.