A shark-derived broadly neutralizing nanobody targeting a highly conserved epitope on the S2 domain of sarbecoviruses

The continuously evolving Omicron subvariants has diminished the effectiveness of almost all RBD-targeted antibodies in neutralizing these subvariants. The development of broad-spectrum neutralizing antibodies is desired for addressing both current and future variants. Here, we identified a shark-derived nanobody, 79C11, that can neutralize all Omicron subvariants tested so far, including BA.1 to JN.1 and KP.2, and exhibits comparable neutralizing potency against SARS-CoV-1 and pangolin coronavirus. Intranasal instillation of 79C11 can effectively prevent the infection of Omicron subvariant XBB in vivo. The designs of multivalent forms of 79C11 further enhance binding and neutralizing activity. Epitope mapping and structure simulation reveal that this nanobody binds to a highly conserved HR1 region in S2 domain of the spikes from all sarbecoviruses, suggesting that a universal vaccine may be designed to target this region for eliciting broadly neutralizing antibody response. This nanobody can also be developed as an intranasally administered prophylactic agent for preventing the infection of current and likely future SARS-CoV-2 variants, as well as other animal derived sarbecoviruses that may infect humans.