Structure-guided discovery of neutralizing epitopes enables rational design of a multi-epitope nanoparticle vaccine...

Spring viremia of carp virus (SVCV) imposes a significant economic burden on carp aquaculture, whereas the availability of precisely designed vaccines against this pathogen remains limited. Here, we propose a structure-guided strategy for epitope discovery based on the interaction interface between a neutralizing antibody and the SVCV glycoprotein (G). Three conserved antibody-targeted epitopes on the G protein were identified through protein docking and alanine-scanning energy analysis, and their immunological relevance was further validated by epitope-specific antibody depletion assays and immunization experiments. To enhance epitope immunogenicity and antigen presentation, the selected epitopes were concatenated and displayed on zebrafish ferritin to generate a self-assembling multiepitope nanoparticle vaccine. Immunization experiments showed that, compared with the epitope concatemer group (CP) or the ferritin group (CF), the multi-epitope vaccine (MEV) induced significantly stronger IgM responses and conferred superior protection against SVCV challenge, achieving a relative survival rate of 43.48% and a marked reduction in viral loads in target tissues. Histopathological analyses further confirmed reduced tissue damage in key immune organs. Collectively, this results establish a structure-guided, antibody-informed framework for epitope identification and multiepitope vaccine design, providing a conceptual framework for precision vaccine design against viral diseases in aquatic species.