In Vivo Blood Kinetics and Transcript Integrity of Three mRNA–Lipid Nanoparticle Vaccines in Humans

Abstract mRNA–lipid nanoparticle (LNP) vaccines are detectable in human blood after vaccination, but platform-specific differences in systemic persistence and transcript integrity remain poorly defined. We analyzed serial blood samples from 73 participants receiving Moderna mRNA-1273 (three formulations), Pfizer/BioNTech BNT162b2, or an investigational receptor-binding domain (RBD) mRNA vaccine (three different doses). Using droplet digital polymerase chain reaction (ddPCR) assays, we quantified total and long-range linked (“intact”) vaccine mRNA, and we measured vaccine-specific ionizable lipids by liquid chromatography–mass spectrometry (LC–MS). Across platforms, mRNA decay was fastest for mRNA-1273, intermediate for BNT162b2, and slowest for the RBD vaccine, with ionizable lipid decay following the same rank order. Notably, intact spike mRNA declined 2-fold faster after mRNA-1273 than BNT162b2 vaccination. Kinetics modeling revealed platform-dependent coupling of mRNA and lipid kinetics: intact mRNA tracked closely with SM-102 for mRNA-1273, whereas ALC-0315 persisted longer than intact mRNA for BNT162b2. A ten-fragment linkage ddPCR panel spanning the spike transcript showed lower linkage toward 3′-proximal regions that mirrored the administered mRNA-1273 formulation. Together, these data provide a quantitative framework for benchmarking mRNA–LNP platform kinetics and transcript integrity in humans.