Engineered Influenza Virus Virions Reveal the Contributions of Non-hemagglutinin Structural Proteins to Vaccine-Mediated Protection

The development of improved and universal anti-influenza vaccines would represent a major advance in the protection of human health. In order to facilitate the development of such vaccines, understanding how viral proteins can contribute to protection from disease is critical. Much of the previous work to address these questions relied on reductionist systems (i.e., vaccination with individual proteins or virus- like particles [VLPs] that contain only a few viral proteins); thus, we have an incomplete understanding of how immunity to different subsets of viral proteins contributes to protection. Here, we report the development of a platform in which a single viral protein can be deleted from an authentic viral particle that retains the remaining full complement of structural proteins and viral RNA. As a first study with this system, we chose to delete the major influenza A virus (IAV) antigen, the hemagglutinin (HA) protein, to evaluate how the other components of the viral particle contribute en masse to protection from influenza disease. Our results show that while anti-HA immunity plays a major role in protection from challenge with a vaccine-matched strain, the contributions from other structural proteins were the major drivers of protection against highly antigenically drifted, homosubtypic strains. This work highlights the importance of evaluating the inclusion of non-HA viral proteins in the development of broadly efficacious and long-lasting influenza vaccines.