KS is supported by the AMED Strategic Center of Biomedical Advanced Vaccine Research and Development for Preparedness and Response (SCARDA) Initiative for World-leading Vaccine Research and Development Centers (JP243fa627001h0003); the AMED SCARDA programme on research and development of new generation vaccine, including a new modality application (JP243fa727002); the AMED Research Program on Emerging and Re-emerging Infectious Diseases (JP24fk0108690); the JSPS KAKENHI Grant-in-Aid for Scientific Research A (JP24H00607); and the Cooperative Research Program (Joint Usage/Research Center programme) of the Institute for Life and Medical Sciences at Kyoto University (Kyoto, Japan); receives consulting fees from Moderna Japan and Takeda Pharmaceutical; and receives honoraria for lectures from Moderna Japan and Shionogi. JI is supported by the Japan Science and Technology Agency PRESTO (JPMJPR22R1) and the JSPS KAKENHI Grant-in-Aid for Early-Career Scientists (JP23K14526) and receives consulting fees and honoraria for lectures from Takeda Pharmaceutical. JI and KS are supported by the Mitsubishi United Financial of Japan Financial Group Vaccine Development Grant. MSY is supported by the Japanese Government Ministry of Education, Culture, Sports, Science and Technology Scholarship–Research Category (240042). JET is supported by the Japanese Government Ministry of Education, Culture, Sports, Science and Technology Scholarship–Research Category (220235). The Genotype to Phenotype Japan Consortium and KS are supported, in part, by the Japan Agency for Medical Research and Development (AMED) Adopting Sustainable Partnerships for Innovative Research Ecosystem programme (JP24jf0126002) and the Japan Society for the Promotion of Science (JSPS) KAKENHI Fund for the Promotion of Joint International Research (JP23K20041). All other authors declare no competing interests.