Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

Abstract

The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these biomedical interventions. With the emergence of new strains of SARS-CoV-2 with altered transmissibility and immune evasion potential, a critical question is this: how easily can the virus escape neutralizing antibodies (nAbs) targeting the spike RBD? To answer this question, we combined an analysis of the RBD structure-function with an evolutionary modeling framework. Our structure-function analysis revealed that epitopes for RBD-targeting nAbs overlap one another substantially and can be evaded by escape mutants with ACE2 affinities comparable to the wild type, that are observed in sequence surveillance data and infect cells in vitro. This suggests that the fitness cost of nAb-evading mutations is low. We then used evolutionary modeling to predict the frequency of immune escape before and after the widespread presence of nAbs due to vaccines, passive immunization or natural immunity. Our modeling suggests that SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist in high numbers due to neutral genetic variation, and consequently resistance to vaccines or other prophylactics that rely on one or two antibodies for protection can develop quickly -and repeatedly- under positive selection. Predicted resistance timelines are comparable to those of the decay kinetics of nAbs raised against vaccinal or natural antigens, raising a second potential mechanism for loss of immunity in the population. Strategies for viral elimination should therefore be diversified across molecular targets and therapeutic modalities.

Fig 1. Epitopes for antibodies targeting the spike protein RBD overlap substantially.

A. Contact residues for spike protein RBD antibody epitopes. Colors and symbols denote antibody clusters: Grey squares: Cluster 1, yellow diamonds: Cluster 2, green circles: Cluster 3. B. RBD structure with each residue colored by the number of antibody epitopes including it, compiled from PDB data. C. RBD structure, colored by the number of antibody epitopes that each residue is part of, by epitope cluster.

Fig 2. The spike protein RBD tolerates mutations that confer resistance to one or more nAbs.

A. Spike protein RBD structure, with each residue colored by the number of distinct amino acid changes present in the GISAID sequencing database. B. RBD structure with residues at which mutations have been shown to confer escape from antibody neutralization marked in blue. C. Experimentally-measured effects of immune escape mutations on ACE2 binding, as taken from [17]. D. ROC curve showing the low predictive value of ACE2 binding measurements (grey) and expression (red) for in vitro infectivity of SARS-CoV-2 mutants. Area under the curve (AUC) is 0.67 for ACE2 binding as a predictor of infectivity and 0.72 for RBD expression as a predictor of infectivity.

Fig 3. SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist at high numbers.

A-D. The expected number of individuals infected with a specific single (A), double (B), triple (C), or quadruple (D) SARS-CoV-2 mutant viruses at different values of the fitness cost. For all panels, the colors denote the total number of individuals with active SARS-CoV-2 infection globally. The horizontal dashed line is the drift boundary calculated at a fitness benefit of 0.1 for the mutation combination.

Fig 4. Resistance to single or double antibody combinations will develop quickly under positive selection pressure.

A-D. Expected time to establishment of a successful single (A), double (B), triple (C), or quadruple (D) immune escape mutant assuming a per-site per-transmission mutation rate of 1x10^-4. The advantageous antibody resistant phenotype is acquired only after a specific combination of 1–4 mutations is present in the same virus. For all panels, the colors denote the total number of individuals with active SARS-CoV-2 infection. The fitness cost for each intermediate mutant is 0.05.

Fig 5. Resistance to single or double antibody combinations will develop quickly across a range of SARS-CoV-2 mutation rates.

A-D. The expected number of individuals infected with a specific single (A), double (B), triple (C), or quadruple (D) SARS-CoV-2 mutant viruses at different values of the per transmission mutation rate. E-H. Expected time to establishment of a successful single (E), double (F), triple (G), or quadruple (H) immune escape. The fitness benefit of resistance is 0.1. For all panels, the colors denote the total number of individuals with active SARS-CoV-2 infection. The fitness cost for each intermediate mutant is 0.05.