Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

Nash D Rochman; Guilhem Faure; Yuri I Wolf; Peter L Freddolino; Feng Zhang; Eugene V Koonin

doi:10.1101/2021.08.30.458225

Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

bioRxiv [Preprint]. 2021 Dec 22:2021.08.30.458225. doi: 10.1101/2021.08.30.458225.

Authors

Nash D Rochman¹, Guilhem Faure², Yuri I Wolf¹, Peter L Freddolino^{3

4}, Feng Zhang^{2

5

6

7

8}, Eugene V Koonin¹

Affiliations

¹ National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894.
² Broad Institute of MIT and Harvard, Cambridge, MA 02142.
³ Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
⁴ Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
⁵ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139.
⁶ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139.
⁷ Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139.
⁸ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.

Abstract

At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlap with the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple mutations in the RBD have rose to dominance. Non-additive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape is crucial. Epistasis can substantially increase the risk of vaccine escape and cannot be completely characterized through the study of the wild type (WT) alone. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the WT, Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in the Gamma variant, epistasis more substantially destabilizes NAb interaction. Although a small, systematic trend towards NAb destabilization not observed for Delta or Gamma was detected for Omicron, and despite bearing significantly more RBD mutations, the epistatic landscape of the Omicron variant closely resembles that of Gamma. These results suggest that, although Omicron poses new risks not observed with Delta, structural constraints on the RBD hamper continued evolution towards more complete vaccine escape. The modest ensemble of mutations relative to the WT that are currently known to reduce vaccine efficacy is likely to comprise the majority of all possible escape mutations for future variants, predicting continued efficacy of the existing vaccines.

Keywords: Delta Variant; Epistasis; Escape Mutants; Gamma Variant; Omicron Variant; Protein Structure Modelling; Rosetta; SARS-CoV-2.

Publication types

Preprint