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. 2022 Mar 24;376(6591):eabn8897. doi: 10.1126/science.abn8897

Fig. 3. Functional and structural basis of class I antibody neutralization and mechanistic basis of retained potency against B.1.1.529 VOC.

Fig. 3.

(A) Lentiviruses pseudotyped with SARS-CoV-2 spike proteins from D614G or D614G plus the indicated point substitutions found within the B.1.1.529 spike were incubated with serial dilutions of the indicated antibodies, and IC50 and IC80 values were determined on 293T-ACE2 cells. Ranges are indicated with white (>10,000 ng/ml), light blue (>1000 to ≤10,000 ng/ml), yellow (>100 to ≤1000 ng/ml), orange (>50 to ≤100 ng/ml), red (>10 to ≤50 ng/ml), maroon (>1 to ≤10 ng/ml), and purple (≤1 ng/ml). (B) Mapping of B.1.1.529 amino acid substitutions at the epitope of class I antibody CB6. RBD-bound CB6 was docked onto the B.1.1.529 spike structure. B.1.1.529 amino acid substitutions incompatible with CB6 binding were identified and labeled. The K417N substitution caused a clash in the center of the paratope. B.1.1.529 RBD is shown in green cartoon, with amino acid substitutions as red sticks. CB6 is shown in surface representation, with heavy and light chains in yellow and slate, respectively. (C) Docking of RBD-bound VH1-58–derived class I antibody B1-182.1 onto the B.1.1.529 spike structure identified four substitutions with potential steric hindrance. B1-182 is shown in surface representation, with heavy and light chains colored olive and light blue, respectively. B.1.1.529 amino acid substitutions that may affect binding of VH1-58 antibodies were labeled. (D) Structural basis for effective neutralization of the B.1.1.529 VOC by VH1-58–derived antibodies. Even though VH1-58 antibodies—such as the S2E12, COV2-2196, A23-58.1, and B1-182.1—share high-sequence homology (top right), their neutralization potency against B.1.1.529 varies. Structural analysis indicated that CDR H3 residue 100C, located at the interface formed between RBD and antibody heavy and light chains, may determine their potency against B.1.1.529 (left). Size of this residue correlated with neutralization potency with two-tailed P = 0.046 (bottom right).