Mutations in emerging variants lower antibody access score on the surface of SARS-CoV-2 spike relative to WT and earlier variants.

Spike renders with color intensity (white to red) indicating AAS, in which the AAS is set to zero in regions within 1 nm of a mutated site with respect to the reference sequence. (A, E): “Naive” antibody access by antibodies produced after (A) first WT vaccination (no previous infection) or (E) first infection by any variant (no previous vaccination). We assume here that all variants confer approximately the same accessibility to antibodies of naive hosts, and renders in (A) and (E) are identical. (B-D) Calculated reduction of AAS for antibodies produced against WT vaccination. (F) Calculated reduction of AAS for antibodies produced against BA.1 infection. Blue circles indicate notable reductions in AAS. Regions are labeled according to epitope candidates in [18]. N: N-terminus. In these renders, the AAS was set to zero for amino acids within 1 nm of any amino acid that was mutated with respect to the reference sequence.