Prime editor-mediated functional reshaping of ACE2 prevents the entry of SARS-CoV-2 variants-included Human coronaviruses

The spike protein of SARS-CoV-2 hijacks the host ACE2 to meditate its entry and is the primary target for vaccine development. Nevertheless, SARS-CoV-2 keeps evolving and the latest Omicron subvariants BQ.1 and XBB have gained exceptional immune evasion potential though mutations in their spike proteins, leading to sharply reduced efficacy of current spike-focusing vaccines and therapeutics. Compared with the fast-evolving spike protein, targeting host ACE2 offers an alternative antiviral strategy that are more resistant to viral evolution and can even provide broad prevention against SARS-CoV and HCoV-NL63. Here we use prime editor (PE) to precisely edit ACE2 at structurally selected sites. We demonstrated that residues changes at Q24/D30/K31 and/or K353 of ACE2 could completely ablate the binding of tested viruses, while maintaining its physiological role in host angiotensin II conversion. PE-mediated ACE2 editing at these sites suppressed the entry of pseudotyped SARS-CoV-2 major VOCs and even SARS-CoV or HCoV-NL63. Moreover, it significantly inhibited the replication of the Delta variant live virus. Our work investigated the unexplored application potential of prime editing in high-risk infectious diseases control, and demonstrated that such gene editing-based host factor reshaping strategy can provide broad-spectrum antiviral activity and a high barrier to viral escape or resistance.