A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike

Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking

“…Antibodies 12-16 and 12-19 effectively neutralized all the Omicron subvariants tested, including BQ.1.1, XBB.1.5, CH.1.1, and DS.1, with similar potencies as the ancestral D614G strain (Figure 1A). To understand 12-19 mutational tolerance, we employed lentivirus-based deep mutational scanning libraries 57 to map the escape mutations in the background of BA.1 for 12-19. The key spike alterations for escape from this mAb mapped to the base of the N4 loop in NTD (residues 172-176) (Figure 6A and S8A).…”

“…The BA.1 full spike deep mutational scanning libraries have been previously described 57 . These libraries have ~7000 mostly functional amino-acid mutations across all of the spike protein.…”

“…These libraries have ~7000 mostly functional amino-acid mutations across all of the spike protein. Antibody escape mapping experiments for 12-19 antibody were performed as described 57 . Different concentrations of 12-19 antibody were incubated with the library virus for 1 h at 37˚C.…”

“…After virusantibody incubation, HEK-293T cells expressing medium amounts of ACE2 as described 87 were infected. 15 h after infection viral genomes were harvested from cells and barcodes were sequenced as described 57 . Two biological library replicates (using independent mutant libraries) were used to map escape mutations.…”

“…Escape for each mutation in the library was calculated relative to a non-neutralized VSV-G pseudotyped standard as described 57 . This analysis uses a biophysical model described previously…”