Epitope-spanning antigenic variation reprograms immunodominance and broadens immunity in sequential influenza vaccination

Immune imprinting, in which prior antigenic exposures biases recall toward dominant epitopes, constrains the breadth and durability of influenza vaccine protection. Here we show that targeted variation across multiple hemagglutinin (HA) head sites (A, B, and D) between sequential A(H3N2) vaccines reprograms epitope hierarchy—redirecting recall toward conserved, subdominant head and stem epitopes. In a controlled ferret model mimicking imprinting-like recall in humans, antigenically distant priming accelerates neutralizing antibody induction, broadens reactivity, enhances cross-protection, and reduces viral shedding after drifted virus challenge. Epitope mapping and structural analysis confirms redirection toward conserved epitopes; single-cell transcriptomics and ELISpot assays reveal amplified germinal center B cell and Th1 responses. This “epitope hierarchy reshaping” links targeted antigenic variation to enhanced B cell competition, amplified T cell help, and improved viral control. This principle is likely applicable to vaccines against other rapidly evolving viruses where strong imprinting effects similarly limit immune breadth. Immune imprinting narrows the vaccine recall response towards dominant epitopes but protection against rapidly evolving viruses is enhanced if the breadth of responses is preserved. Here authors show in a ferret model that introducing optimized antigenic variation between prime and boost vaccines diversify the targeted epitopes and thus broadens immunity in a ferret model of influenza vaccination.