UBC researchers conduct the first molecular-level analysis of omicron variant spike protein

UBC researchers are the first in the world to conduct a molecular-level structural analysis of the omicron variant spike protein.

The analysis – done at near atomic resolution using a cryo-electron microscope – reveals how the heavily mutated variant infects human cells and is highly evasive of immunity.

The findings shed new light on why omicron is highly transmissible and will help accelerate the development of more effective treatments.

Dr. Sriram Subramaniam (he/him), professor in UBC faculty of medicine’s department of biochemistry and molecular biology, discusses the implications of his team’s research, which is currently under peer review and available as a preprint at bioRxiv.

What did you examine with this study?

The omicron variant is unprecedented for having 37 spike protein mutations – that’s three to five times more mutations than any other variant we’ve seen.

This is important for two reasons. Firstly, because the spike protein is how the virus attaches to and infects human cells. Secondly, because antibodies attach to the spike protein in order to neutralize the virus. Therefore, small mutations on the spike protein have potentially big implications for how the virus is transmitted, how our body fights it off, and the effectiveness of treatments.

Our study used cryo-electron microscopy and other tests to understand how mutations impact the behavior of the omicron variant at a molecular level.

What does your analysis reveal?

We see that several mutations (R493, S496 and R498) create new salt bridges and hydrogen bonds between the spike protein and the human cell receptor known as ACE2. This appears to increase binding affinity – how strongly the virus attaches to human cells—while other mutations (K417N) decrease the strength of this bond.

Overall, the findings show that omicron has greater binding affinity than the original SARS-CoV-2 virus, with levels more comparable to what we see with the delta variant. It is remarkable that the omicron variant evolved to retain its ability to bind with human cells efficiently despite such extensive mutations.

What about the effectiveness of antibodies?

Our experiments confirm what we’re seeing in the real world—that the omicron spike protein is far better than other variants at evading monoclonal antibodies that are commonly used as treatments, as well as at evading the immunity produced by both vaccines and natural infection.

Notably, omicron was less evasive of the immunity created by vaccines, compared to immunity stemming from natural infection in unvaccinated COVID-19 patients. This suggests that vaccination remains our best defense against the omicron variant.

What do these molecular-level changes tell us about the macro behavior of the omicron variant?

Both the characteristics we see as a result of spike protein mutations – strong binding with human cells and increased antibody evasion—are likely contributing factors to the increased transmissibility of the omicron variant.

These are the underlying mechanisms fuelling the variant’s rapid spread and why omicron could become the dominant variant of SARS-CoV-2 very quickly.

How do we treat a variant that is so effective at evading immunity?

The good news is that knowing the molecular structure of the spike protein will allow us to develop more effective treatments against omicron and related variants in the future. Understanding how the virus attaches to and infects human cells means we can develop treatments that disrupt that process and neutralize the virus.

An important focus for our team is to understand better the binding of neutralizing antibodies and treatments that will be effective across the entire range of variants, and how those can be used to develop variant-resistant treatments.

… very important

We used a panel of neutralizing monoclonal antibodies that include RBD-directed antibodies (ab1, ab8, S309, S2M11;(20-23)) and two N-terminal domain (NTD)-directed antibodies (4-8 and 4A8; (24, 25)) to investigate the impact of Omicron RBD and NTD mutations on monoclonal antibody escape. In contrast to the Alpha, Beta, Gamma, Kappa, Epsilon, and Delta variants of SARS-CoV-2, the Omicron variant exhibited measurable evasion from every antibody in this panel with complete escape from five of the six antibodies tested (Figure 4A) (26).

The neutralizing activity of both the NTD-directed antibodies (4-8 and 4A8) is completely knocked out for the Omicron variant, as seen previously in the Alpha variant which contains identical or similar deletions in its NTD (Δ69-70 and Δ144-145). The Omicron variant does not show complete escape from S309, an antibody undergoing evaluation in clinical trials to treat patients with COVID-19 although there is still a 4-fold decrease in its neutralization potency relative to the ancestral strain(27). The unusually high number of mutations in the Omicron variant spike protein thus appear to confer unprecedently broad antibody escape relative to previously emerged variants of SARS-CoV-2 (17).

Figure 4.Monoclonal antibodies and vaccinated and convalescent patient-derived sera exhibit decreased Omicron neutralization potency.

(A) Fold-changes in monoclonal antibody neutralization for Omicron variant pseudoviruses relative to wild-type (D614G). (B) Log-fold EC50 dilutions for vaccinated and convalescent patient sera for either wild-type (D614G) versus Omicron variant pseudoviruses (top) or Delta and Omicron variant pseudoviruses (bottom). (C) As in (B) with a breakdown of the convalescent patients into previous infection with Delta, Alpha, and Gamma variants of concern. A pairwise statistical significance test was performed using the Wilcoxon matched pairs test (*P≤0.05, **P≤0.01, ***P≤0.001, ****P≤0.0001). Each data point is the average of n = 2 replicates. The fold-change in the geometric mean between the two groups is shown in red text at the top of each plot.

Sera from convalescent patients displayed on average a 6.3x decrease in ability to neutralize the Omicron variant relative to the wild-type (Figure 4B upper panel). Sera from the vaccinated cohort also displayed reduced neutralization ability (4.4x decrease) with a wider variation driven by some individuals that showed exceptional loss of neutralization ability to Omicron. The comparison of change in neutralization potential between Delta and Omicron variants is a more relevant comparison given the world-wide dominance of Delta. Sera from convalescent patients shows an even greater drop in neutralization potency relative to the Delta variant (8.2x decrease) while the vaccinated group also shows reduction in potency, although to a lesser extent (3.4x decrease). We note that the majority of the doubly vaccinated cohort consisted of individuals who were vaccinated with a schedule of at least 8 weeks between doses, recently shown to generate a better humoral response than the manufacturer-recommended interval of 3-4 weeks (28). The longer interval between doses could result in less pronounced reduction in neutralization of the Omicron variant.

A finer analysis of the unvaccinated convalescent cohort stratified into those who recovered from infection by either Delta, Alpha, or Gamma variants (figure 4C) reinforces the reduction in neutralization potency against the Omicron variant in all populations, with especially striking drops for patients who recovered from infection from the earlier Alpha and Gamma variants. The findings we report here are consistent with several other recent reports (17, 29-31) that the Omicron variant is more resistant to neutralization than any other variant of concern that has emerged over the course of the pandemic.

The mechanisms underlying the rapid spread of the newly emerged Omicron variant are of fundamental interest given the likelihood that this virus could become the dominant variant of SARS-CoV-2. The large number of mutations on the surface of the spike protein including the immunodominant RBD (Figure 1) would be expected to help the virus evade from antibodies elicited by vaccination or prior infection. However, it is remarkable that the Omicron variant evolved to retain its ability to bind ACE2 efficiently despite these extensive mutations.

The cryo-EM structure of the spike protein-ACE2 complex provides a structural rationale for how this is achieved: interactions involving the new mutations in the Omicron variant at residues 493, 496 and 498 appear to restore ACE2 binding efficiency that would be lost due to other mutations such as K417N. The Omicron variant thus appears to have evolved to selectively balance two critical features, namely the increase in escape from neutralization but without compromising its ability to interact efficiently with ACE2. The increase in antibody evasion and the retention of strong interactions at the ACE2 interface are thus likely to represent key molecular features that contribute to the increase in transmissibility of the Omicron variant.

More information: Dhiraj Mannar et al, SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion (2021). DOI: 10.1101/2021.12.19.473380