Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3

Abstract

SARS-CoV-2 Omicron variant has presented significant challenges to current antibodies and vaccines. Herein, we systematically compared the efficacy of 50 human monoclonal antibodies (mAbs), covering the seven identified epitope classes of the SARS-CoV-2 RBD, against Omicron sub-variants BA.1, BA.1.1, BA.2, and BA.3. Binding and pseudovirus-based neutralizing assays revealed that 37 of the 50 mAbs lost neutralizing activities, whereas the others displayed variably decreased activities against the four Omicron sub-variants. BA.2 was found to be more sensitive to RBD-5 antibodies than the other sub-variants. Furthermore, a quaternary complex structure of BA.1 RBD with three mAbs showing different neutralizing potencies against Omicron provided a basis for understanding the immune evasion of Omicron sub-variants and revealed the lack of G446S mutation accounting for the sensitivity of BA.2 to RBD-5 mAbs. Our results may guide the application of the available mAbs and facilitate the development of universal therapeutic antibodies and vaccines against COVID-19.

Keywords: G446S mutation; Omicron BA.1; Omicron BA.1.1; Omicron BA.2; Omicron BA.3; SARS-CoV-2; epitope; human neutralizing antibodies; immune escape.

Graphical abstract

Figure 1

Amino acid mutation mapping of RBDs from SARS-CoV-2 Prototype and VOCs Three major epitopes on SARS-CoV-2 RBD targeted by seven classes of mAbs (RBD-1–RBD-7), and residue mutation mapping of RBDs from SARS-CoV-2 VOCs. See also Table S1.

Figure 2

Binding and neutralizing abilities of current antibodies to Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-variants 50 mAbs were divided into seven groups (RBD-1–RBD-7) shown in different colors. The indicated antibodies in the supernatant were captured by a Protein A chip. Then, serially diluted Omicron RBD, Delta RBD, and Prototype RBD were flowed over the chip surface to assess binding to the indicated antibodies, respectively. The binding affinity (K_D) of each pair of interaction are shown as mean ± SD of three independent experiments. SARS-CoV-2 Omicron, Delta, and Prototype pseudoviruses were incubated with 4-fold serial dilutions of antibodies, respectively. Then, the mixtures were added to Vero cells. After 15 h, the infected cells were counted with a CQ1 confocal quantitative image cytometer. The experiments were performed at least twice with two replicates (n = 2), and the IC₅₀ values are one representative data of two independent experiments. PT indicates Prototype SARS-CoV-2. See also Figures 1, 2, and 3.

Figure 3

Overall structure and epitope comparison of BD-604, S309, and S304 binding to Omicron BA.1 RBD (A) Overall structure of BD-604, S309, and S304 binding to Omicron BA.1 RBD. All structures are shown in cartoon with different colors. (B) The footprints of BD-604, S309, and S304 in Omicron BA.1 RBD shown in magenta, green, and yellow, respectively. Fifteen mutations in BA.1 RBD are shown in purple color. The RBM region is circled in a blue-dotted line. (C–E) The side (C and D) and top (E) views of BD-604, S309, and S304 binding to BA.1 S trimer in one-RBD-up conformation. The BA.1 RBD/BD-604/S309/S304 complex was superimposed onto the BA.1 S trimer (PDB:7QO7). S trimer is shown in gray color. (F) The sequence alignment of RBDs of Omicron BA.1, BA.2, and BA.3, generated by ESPript 3.0. The binding sites of BD-604, S309, and S304 in BA.1 RBD and Prototype RBD are indicated in triangles with different colors. See also Figure S4 and Tables S2–S5.

Figure 4

Structural details of immune evasion of BD-604 and related antibodies by Omicron sub-variants (A) Electrostatic surface view of BD-604. (B) Electrostatic surface view of Prototype RBD. (C) Electrostatic surface view of Omicron BA.1 RBD. (D) The overall comparison of two complex structures of BD-604/Prototype RBD and BD-604/BA.1 RBD by aligning the two RBDs. BD-604/Prototype RBD complex is shown as gray ribbon, and BD-604/BA.1 RBD is shown in the same color as in Figure 3A. Mutant residues in BA.1 RBD, that contributed to interaction with BD-604, are shown as spheres. (E and F) The detailed interaction between H chain of BD-604 and the BA.1 RBD (E) or Prototype RBD (F). The residues involved in the interaction are labeled, and H-bonds are shown as dotted lines with a cutoff of 3.5 Å. (G and H) The detailed interaction between L chain of BD-604 and the BA.1 RBD (G) or Prototype RBD (H). The residues involved in the interaction are labeled, and H-bonds are shown as dotted lines with a cutoff of 3.5 Å. (I–K) Binding face between RBD and representative mAbs, including CB6 (I), CC12.1 (J), and CC12.3 (K). All structures are shown in cartoon with the key residues in stick. H-bonds are shown as dotted lines with a cutoff of 3.5 Å. See also Tables S3 and S6.

Figure 5

Structural details of immune evasion of S309, S304, and related antibodies by Omicron sub-variants (A) The overall comparison of two complex structures of S309/Prototype RBD and S309/BA.1 RBD by aligning the two RBDs. S309/Prototype RBD complex is shown as gray ribbon, and S309/BA.1 RBD is shown in the same color as in Figure 3A. Mutant residues in BA.1 RBD, which contributed interaction with S309, are shown as spheres. (B and C) The detailed interaction between H chain (B) or L chain (C) of S309 and the BA.1 RBD (left panel) or Prototype RBD (right panel). The residues involved in the interaction are labeled, and H-bonds are shown as dotted lines with a cutoff of 3.5 Å. (D) The overall comparison of two complex structures of S304/Prototype RBD and S304/BA.1 RBD by aligning the two RBDs. S304/Prototype RBD complex is shown as gray ribbon, and S304/BA.1 RBD is shown in the same color as in Figure 3A. Mutant residues in BA.1 RBD, which contributed interaction with S304, are shown as spheres. (E and F) The detailed interaction between H chain (E) or L chain (F) of S304 and the BA.1 RBD (left panel) or Prototype RBD (right panel). The residues involved in the interaction are labeled, and H-bonds are shown as dotted lines with a cutoff of 3.5 Å. (G–I) Binding face between RBD and representative mAbs, including REGN10987 (G), S2A4 (H), and EY6A (I). All structures are shown in cartoon with the key residues in stick. H-bonds are shown as dotted lines with a cutoff of 3.5 Å. See also Tables S4–S6.

Figure 6

Binding characteristics of RBD-5 antibodies to Omicron BA.2 RBD with G446S mutation The indicated antibodies were captured by a Protein A chip. Then, serially diluted BA.2 RBD with G446S mutation were flowed over the chip surface to assess the binding, with BA.2 RBD for comparison. The raw and fitted curves are shown as dotted and solid lines, respectively. The K_D of each pair of interaction are shown as mean ± SD of three independent experiments. See also Figures S2 and S3.