Insights on the mutational landscape of the SARS-CoV-2 Omicron variant receptor-binding domain

Abstract

The Omicron variant features enhanced transmissibility and antibody escape. Here, we describe the Omicron receptor-binding domain (RBD) mutational landscape using amino acid interaction (AAI) networks, which are well suited for interrogating constellations of mutations that function in an epistatic manner. Using AAI, we map Omicron mutations directly and indirectly driving increased escape breadth and depth in class 1-4 antibody epitopes. Further, we present epitope networks for authorized therapeutic antibodies and assess perturbations to each antibody's epitope. Since our initial modeling following the identification of Omicron, these predictions have been realized by experimental findings of Omicron neutralization escape from therapeutic antibodies ADG20, AZD8895, and AZD1061. Importantly, the AAI predicted escape resulting from indirect epitope perturbations was not captured by previous sequence or point mutation analyses. Finally, for several Omicron RBD mutations, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBD_down-RBD_down interface.

Keywords: Omicron; RBD interface stability; SARS-CoV-2; antibody escape; antigenic drift; epistasis; epitope-paratope; mutation; network analysis; variant of concern.

Graphical abstract

Figure 1

RBD epitopes and variant mutational constellations (A) AAI networking between a panel of antibodies and nanobodies across the four anti-RBD antibody classes (x axis) and RBD sites (y axis) is shown, with total networking strength annotated as heatmap intensity (colorbar). Only RBD sites that interact with at least three antibodies in the panel are shown for clarity. RBD sites mutated on the Omicron, Beta, Delta, and PMS20 RBDs are highlighted by red, blue, purple, and green arrows along the y axis, respectively. The Beta and Delta variant mutations primarily reside at sites corresponding to class 1 and 2 antibodies, the PMS20 mutations occur at sites residing within class 1–3 epitopes, and the Omicron mutations cover the epitopes of all four antibody classes. (B) VOC mutations affecting class 1–4 antibody epitopes. Two surface representations of RBD are shown for each variant, with the top view displaying surfaces targeted by class 1 and 2 antibodies and the bottom view displaying surfaces targeted by class 3 and 4 antibodies. The surface view highlights the extent of Omicron’s mutational breadth (across all four antibody classes) as well as depth (extent of accumulated mutations within a given epitope surface).

Figure 2

VOCs versus therapeutic mAbs Cumulative AAI networking between mutated sites on the Beta, Delta, Omicron, and PMS20 variant RBDs and the currently authorized therapeutic antibodies REGN10933, REGN10987, LY-CoV16, LY-CoV555, AZD1061, AZD8895, and S309 is shown and broken down into direct, indirect, and total components. Networking strength is annotated as heatmap intensity (colorbar). Network diagrams describing connectivity between specific sites are provided in the supplement as Figures S1–S3. Direct networking results are consistent with point mutation analyses and do not identify certain antibody epitope perturbations resulting from the Omicron mutations such as occurs for AZD1061. Introducing an indirect networking metric that accounts for indirect interactions successfully identifies the Omicron-AZD1061 perturbation. The combination of both direct and indirect features in total networking is highly consistent with experimental observations

Figure 3

The effects of Omicron mutations on the RBD_down-RBD_down interface (A) The RBD_down-RBD_down interface in the three RBD-down conformation, with the repacked WT structure (PDB: 6ZGI) and our Omicron fixed-backbone model shown in light blue and pink, respectively. Omicron mutations S373P, S375F, and Y505H reduced the energetic complementarity of the RBD_down-RBD_down interface at these sites, but enabled a more energetically favorable conformation for R403. Interface buried surface area and surface complementary were also reduced for Omicron by 40 Å² and from 0.60 to 0.54, respectively. (B) Structural model of the RBD_down-RBD_down interface in the one RBD-up conformation, with the WT (PDB: 6XM3) and Omicron (PDB: 7TB4) structures shown in light blue and pink, respectively. Alignment of the protomer 1 of WT and Omicron RBD_down showed a 7 to 10 Å movement of the Omicron protomer two RBD_down toward the distal RBD_up (not shown), which is annotated as red arrows, resulting in loss of all three interface bonds and 190 Å² of buried surface area per RBD.