Early fusion intermediate of ACE2-using coronavirus spike acting as antiviral target

Coronavirus fusion with and entry into the host cell depends on viral spike, which acts as a crucial component of viral infection. However, the lack of receptor-activated spike intermediate conformation has hindered a comprehensive understanding of spike-induced membrane fusion. Here, we captured an ACE2-induced early fusion intermediate conformation (E-FIC) of SARS-CoV-2 spike in which HR1 in S2 has ejected while S1 remains attached. This E-FIC can transition to the late fusion intermediate conformation after S2' cleavage. Leveraging this discovery, we designed an E-FIC-targeted dual-functional antiviral protein AL5E. AL5E effectively inactivated ACE2-using coronaviruses and inhibited their infection, outperforming a mono-functional antiviral in protecting animals against these coronaviruses. This study has identified the E-FIC and used it as target for the development of a dual-functional antiviral for the prevention and treatment of ACE2-using coronavirus infection.