Figure 4.

Reasons for attenuation of S309 in different Omicron sub-lineages and correlation of neutralization between antibodies from different responses

(A) S309 is shown as a semi-transparent surface (heavy chain red, light chain blue) with the glycan attached to residue 343 of the RBD drawn as sticks. BA.2 RBD is shown in dark pink (Table S3A) and BA.1 RBD (PDB:7TLY) in gray. The RBD’s have been superimposed. Contacts <2.0 Å between Phe 371 and the glycan are shown as dotted lines.

(B) The contact between Arg 346 of the RBD and S309 light-chain Asp 93 (PDB:7BEP). The electrostatic surface of S309 is shown.

(C) Cross-correlation matrix between pairs of antibodies. Each pairwise value is the correlation coefficient between the normalized log neutralization titers of the corresponding antibodies against a panel of SARS-CoV-2 (Victoria, Alpha, Beta, Gamma, Delta, BA.1).

(D) Cluster4X principal component analysis of the cross-correlation matrix in C from two orthogonal views.

(E) Principal component analysis on the sub-matrix of C consisting of only the BA.1 antibodies. Omi-6, -24, −30, −31, and −34 are shown in purple.