AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal embecovirus antigen design

The continued threat of zoonotic coronavirus spillovers underscores the need for cross-species applicable vaccine design strategies. The genus Embecovirus includes human coronaviruses OC43 and HKU1 as well as relevant veterinary pathogens. The coronavirus spike (S) fusion glycoprotein, key to viral entry and protective immunity, is inherently metastable, complicating vaccine development. Using the ReCaP AI tool, we stabilized the prefusion conformation of OC43 S through rationally combined amino acid substitutions, resulting in markedly enhanced expression and thermal stability. The substitutions were transferable to equine coronavirus (ECoV) S and HKU1. Cryo-EM structures of stabilized OC43 and ECoV S revealed that stabilization was achieved by arresting the release of the fusion peptide and keeping the S1B receptor binding domain in the 'down' state by improving the complex polar interactions of neighboring S1B domains and the bound free fatty acid at the interprotomer S1B interface. This work provides the first ECoV S structure and a broadly applicable framework for engineering stabilized Embecovirus S antigens.