Integrated systems vaccinology reveals distinct metabolic responses to SARS-CoV-2 infection and DNA-based vaccines in ferrets

Understanding how infection and vaccination reshape systemic metabolism is key to defining protective immunity against SARS-CoV-2. Using a ferret model, we performed untargeted serum metabolomics in two experimental settings: SARS-CoV-2 infection alone, and vaccination followed by viral challenge. Ferrets were immunized with four vaccines: a multigenic DNA-construct encoding receptor-binding domain, membrane, and nucleoprotein (OC2); a nucleoprotein-only DNA vaccine (OC12); a recombinant spike protein with QS-21 adjuvant (S+QS21); or a control hepatitis-B/D DNA vaccine (Hep-B/D). SARS-CoV-2 infection induced distinct systemic changes, including reduced lipid remodeling and enrichment of amino acid, carbohydrate, and energy pathways (notably glutathione and methionine-cysteine metabolism and the tricarboxylic acid cycle). Vaccination induced broader, immunogen-specific metabolic remodeling. Post-vaccination, S+QS21 triggered extensive early alterations, mainly suppressing lipid and amino acid pathways. In contrast, OC2 produced balanced remodeling across amino acid, lipid, nucleotide, and glutathione-related metabolism, with temporally consistent shifts. Following viral challenge, OC2 maintained sustained remodeling with enrichment of redox-associated metabolites, including γ-glutamyl amino acids and acylcarnitines, coinciding with anti-spike and anti-nucleoprotein IgG responses and complete viral clearance. OC12 elicited strong anti-nucleoprotein antibodies but limited remodeling and incomplete protection, while S+QS21 showed moderate post-challenge responses with partial clearance. Hep-B/D induced minimal changes and no protection. These findings show vaccination induces immunogen-specific metabolic programs, with OC2 eliciting the broadest remodeling linked to protective immunity. To our knowledge, this is the first demonstration that DNA-based multigenic SARS-CoV-2 vaccination induces systemic metabolic reprogramming in ferrets, linking remodeling to antibody responses and viral clearance. Metabolomics informs host-vaccine interactions within a systems vaccinology framework.