Computationally designed proteins mimic antibody immune evasion in viral evolution
Noor Youssef, Sarah F. Gurev, Fadi Ghantous, Kelly P. Brock, Javier A. Jaimes, Nicole N. Thadani, Ann Dauphin, Amy C Sherman, Leonid Yurkovetskiy, Daria Soto, Ralph Estanboulieh, Ben Kotzen, Pascal Notin, Aaron W. Kollasch, Alexander A. Cohen, Sandra Dross, Jesse H. Erasmus, Deborah H. Fuller, Pamela J. Björkman, Jacob E. Lemieux, Jeremy Luban, Michael S. Seaman, Debora S. Marks
Abstract
Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circulating variants, which likely differ in their immune escape potential compared with future variants. To address this, we developed EVE-Vax, a computational method for designing antigens that foreshadow immune escape observed in future viral variants. We designed 83 SARS-CoV-2 spike proteins that transduced ACE2-positive cells and displayed neutralization resistance comparable to variants that emerged up to 12 months later in the COVID-19 pandemic. Designed spikes foretold antibody escape from B.1-BA.4/5 bivalent booster sera seen in later variants. The designed constructs also highlighted the increased neutralization breadth elicited by nanoparticle-based, compared with mRNA-based, boosters in non-human primates. Our approach offers targeted panels of synthetic proteins that map the immune landscape for early vaccine and therapeutic evaluation against future viral strains.