Mapping the specificity of H3N2 strain-specific and cross-reactive human neutralizing antibodies elicited by the 2025-2026 influenza vaccine

An H3N2 variant, named subclade K, continues to circulate widely during the 2025-2026 influenza season. This virus possesses a hemagglutinin (HA) protein that has eleven substitutions relative to the HA of the Northern Hemisphere 2025-2026 H3N2 vaccine strain. Many of these substitutions are in epitopes in well-characterized HA antigenic sites. Despite this, interim vaccine effectiveness studies indicate that the 2025-2026 influenza vaccine provides moderate protection against H3N2 subclade K infection. We previously reported that many individuals who received the 2025-2026 influenza vaccine produced antibodies that inhibit H3N2 subclade K virus cellular attachment. Here, we show these individuals also produced antibodies that neutralize H3N2 subclade K virus infection, and we observed a strong correlation between hemagglutination-inhibition titers and neutralizing antibody titers. We completed additional specificity studies using samples from individuals who did or did not have antibodies that cross-reacted to H3N2 subclade K viruses. Using high-throughput neutralization assays, we determined that antibodies that bound to the vaccine strain but not H3N2 subclade K viruses typically targeted antigenic site B of HA. Conversely, we found that cross-reactive neutralizing antibodies elicited by vaccination commonly targeted antigenic site A, D, and E of HA that are conserved between the vaccine strain and H3N2 subclade K viruses. Additional electron microscopy-based polyclonal epitope mapping studies confirmed that cross-reactive antibodies elicited by vaccination typically target epitopes on the side of HA. Together, our studies provide an immunological explanation of why the 2025-2026 influenza vaccine was partially effective against antigenically advance H3N2 subclade K viruses. Our data suggest that vaccine strains for subsequent seasons need to be carefully considered, since subclade K viruses have already started to acquire additional substitutions in HA antigenic sites targeted by cross-reactive antibodies.