Abstract
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.
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Data availability
The raw and assembled genomic data as well as the scRNAseq data generated from this study have been deposited to GenBank under the BioProject accession number PRJNA1193629. This submission includes 178 genomic datasets, encompassing the challenge virus and the corresponding viruses found in ferret nasal washes (n = 27 samples in group gPAN/99 [ID = IAV x 1 to IAV x 27], n = 27 samples in gWIS/05 [ID = IAV x 28 to IAV x 54], n = 30 samples in gBNE/07 [ID = IAV x 55 to IAV x 84], n = 31 samples in gPER/09 [ID = IAV x 85 to IAV x 115], n = 31 in gSingle [ID = IAV x 116 to IAV x 147], n = 32 in Mock [ID = IAV x 148 to IAV x 179]). In addition, this submission included scRNA-seq data for ferret spleen cells collected from gPAN/99 (n = 3), gPER/09 (n = 3), and negative control (n = 3). Source data are provided in this paper.
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Acknowledgements
We would like to thank Dr. Erin O’Connor, Dr. Scott Korte, Dr. Samantha Gerb, and Dr. Sarah N. Schlink for their veterinary support; Carmen De La Nuez Ramírez and Xin Liu for assistance with sample collection; and Samantha Bosland for graphic support. This study was supported by NIH grants R01AI152521 and R01AI147640. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. Research was conducted under an IACUC-approved animal use protocol in an AAALAC International-accredited facility with a Public Health Services Animal Welfare Assurance and in compliance with the Animal Welfare Act and other federal statutes and regulations relating to laboratory animals.
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X.F.W. contributed to the conceptualization of the study. X.F.W., M.G., P.B., H.C., K.P., J.D., A.O., W.G., D.S., and Y.J.T. contributed to the methodology of the study. X.F.W., M.G., P.B., H.C., K.P., J.D., A.O., W.G., C.F., C.G., and Y.J.T. performed the formal analysis and data curation. M.G., H.C., P.B., K.P., A.A., A.O., W.G., D.D.M.C.M., C.F., T.L., W.T., Q.Y., A.R., M.A., and M.Z. conducted the investigation and data collection. X.F.W., H.J., and Y.J.T. provided resources and supervised the project. X.F.W. was responsible for writing the original draft while M.G., H.C., P.B., K.P., A.A., J.D., A.O., W.G., C.F., C.W., L.L., A.S., J.H., H.X., and Y.J.T. contributed to review, discussion, & editing. X.F.W., M.G., H.C., P.B., K.P., G.W., C.G., and Y.J.T. handled visualization. X.F.W. also managed project administration and funding acquisition.
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Wan, XF., Guan, M., Balamalaliyage, P. et al. Epitope-spanning antigenic variation reprograms immunodominance and broadens immunity in sequential influenza vaccination. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70202-y
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DOI: https://doi.org/10.1038/s41467-026-70202-y
