Early innate immune signatures correlate with Ad26.COV2.S vaccine immunogenicity and protective efficacy

The innate immune system is rapidly activated following antigen exposure and plays a critical role in shaping the ensuing adaptive immune responses. In this study, we performed bulk RNA sequencing and proteomic profiling in a cohort of 25 rhesus macaques following Ad26.COV2.S immunization to characterize early innate correlates of vaccine immunogenicity and protection. Our results show that innate immune activation occurred as early as day 1 post-vaccination and demonstrated a systemic enrichment of antiviral interferon pathways, cytokine signaling, and activation of innate immune cell signatures. These early transcriptomic signatures correlated positively with humoral and cellular immune responses at 6 weeks following vaccination and correlated inversely with viral loads following SARS-CoV-2 challenge. Similar correlates of immunogenicity were observed in a cohort of 25 adult healthy participants vaccinated with Ad26.COV2.S. Taken together, these findings highlight the importance of early activation of the innate immune responses following Ad26.COV2.S vaccination in shaping the protective adaptive immune response.IMPORTANCEEarly innate immune responses may shape vaccine immunogenicity and protection. We evaluated responses to Ad26.COV2.S vaccination in rhesus macaques and humans and found that day 1 innate immune signatures correlated with subsequent adaptive responses. These findings suggest that early post-vaccination immune programming influences immunogenicity and protective efficacy months later.