Fig. 1.

Immune evasion analysis of the Omicron variant and identification of a cross-variant neutralizing antibody targeting conserved RBD amino acids. A The key spike mutations present in the Omicron variant (B.1.1.529) are highlighted. B The anti-RBD antibody titer and neutralizing activity of the plasma from COVID-19 convalescent individuals (n = 21) against Wuhan-Hu-1 (wild-type, WT) and the Omicron variant. RBD-specific IgG antibody (Ab) titers were calculated as the endpoint dilution that remained positively detectable for the wild-type and Omicron RBD. Fifty percent neutralizing antibody titers (NT₅₀) were calculated against wild-type and Omicron pseudoviruses. C Neutralization capability of Omicron pseudovirus by a panel of 45 RBD-specific mAbs. The left panel shows the IC₅₀ values of the tested antibodies against wild-type and Omicron pseudoviruses. The middle panel shows the percentage of antibodies with the indicated neutralization activities. The right panel shows the percentage of different degrees of IC₅₀ fold change for antibodies targeting four antigenic sites. The IC₅₀ fold change is the ratio of the IC₅₀ of antibodies against Omicron compared with wild-type pseudovirus. D The percentage of different degrees of antibody binding EC₅₀ fold change of the Omicron RBD or single-amino acid substitutions present in Omicron. The EC₅₀ fold change was calculated as the EC₅₀ of the mutant RBD /the EC₅₀ of the wild-type RBD. E The key immune escape substitutions found in Omicron are highlighted at four distinct antigenic sites in the RBD region. The color-coding scheme: site 1 (orange), site 2 (green), site 3 (slate blue), site 4 (red); ACE2 (wheat). Left and right are shown from different angles. F Electrostatic potential surface representation of the RBD from wild-type and Omicron. Electrostatic surface potentials are colored red and blue for negative and positive charges, respectively; white represents neutral residues. The wild-type positions are shown in black font and Omicron in red. G The melting temperature (Tm) of the recombinant RBD of wild-type and Omicron measured by nano differential scanning fluorimetry (nanoDSF). H IC₅₀ and IC₉₀ values of four RBD-specific NAbs against different SARS-CoV-2 VOC pseudoviruses. I Binding EC₅₀ values of the tested NAbs or ACE2 with the F456A, N487A and K417A RBD mutants. J Structural interaction between F456 on RBD from wild-type and omicron with ACE2. The binding surface of ACE2 is shown by electrostatic surface representations. K Structural interaction between N487 on the RBD of wild-type and omicron with ACE2. Yellow dashed lines, intramolecular hydrogen bond within the RBD; red dashed lines, polar interactions between the RBD and ACE2. All experimentally obtained data represent one of two independent experiments. Nonneutralizing IC₅₀ values were set to over 10 μg/ml, and nonbinding EC₅₀ values were set to over 5 μg/ml. The structures of RBD-ACE2 complexes were obtained from PDB (6m0j for wild-type [12] and 7 WBP for Omicron [10]). P values shown in the figures were determined using paired two-tailed Student’s t tests (****P < 0.0001)