In a study recently published on Cell, researchers used cryogenic electron microscopy (cryo-EM) analysis to capture the open and closed states of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant’s spike protein.

The open and closed states of the Omicron spike appeared more compact compared to that of the SARS-CoV-2 G614 strain, which is likely due to the enhanced protomer-protomer and S1-S2 subunit interactions induced by the unique substitution mutations in the Omicron variant.

The SARS-CoV-2 Omicron variant has 37 mutations in its S protein which confer significant immune evasion to the variant. Out of the 37 Omicron spike mutations, 15 are in the receptor-binding domain (RBD) which mediates the binding of the virus to the host angiotensin-converting enzyme 2 (ACE2) receptor. The RBD is also a major target for neutralizing antibodies.

Although nine mutations within the receptor-binding motif (RBM) interact directly with the ACE2, Omicron still uses ACE2 as an entry receptor. Compared to the wild-type (WT) spike protein, the Omicron spike also has an increased binding affinity to the host ACE2 receptor. According to recent reports, the Omicron spike also shows reduced furin cleavage and S1 shedding.

Given that Omicron is spreading across the globe at an unprecedented speed causing considerable morbidity, it is essential to achieve a better understanding of the structural basis of the increased transmissibility and enhanced immune escape of Omicron.

The study

In the present study, researchers addressed the structural aspects of Omicron spike protein binding to the ACE2 receptor and how Omicron identifies or evades neutralizing antibodies against the original strain. They obtained two cryo-EM structures of the Omicron S trimer in the open and closed states at 3.21 and 3.08 Å resolution, respectively.

Bio-layer interferometry (BLI) assay was used to determine the binding affinities of S trimers to the ACE2 receptor. An enzyme-linked immunosorbent assay (ELISA) was used to test the binding of recombinant Omicron spike with anti-SARS-CoV-2 monoclonal antibodies (MAbs) previously developed by the researchers. Recombinant S trimer proteins from the SARS-CoV-2 WT, Delta, or Omicron strains were used in the assay and the data were analyzed using non-linear regression using GraphPad Prism 8.

Findings

The results showed that, compared to the S trimer of the Delta, Beta, and Kappa variants, the S-closed and S-open structures of the Omicron variant appeared more twisted or compact. This could be due to the unique Omicron substitution mutations in the SD1 and S2 regions – T547K, N856K, and N764K – that induce more interactions between the protomers and between Omicron S1 and S2 subunits. The Omicron substitutions may hinder its spike transformation towards the open state, which is prone to fusion, and towards S1 shielding.

Interestingly, the cryo-EM analysis revealed a dominantly populated (61%) conformation for the closed state of the Omicron S trimer where all the RBDs were buried. This results in conformational masking, which prevents antibody binding and neutralization at the receptor binding sites. This conformational masking may be the underlying mechanism of immune evasion for the Omicron spike protein. Comparatively, a previous work by the researchers showed that the Delta S trimer had an open-transition ratio of 75.3%-24.7%, which indicates the conformational masking mechanism of the Delta variant may be less effective.

The researchers also captured two states for the Omicron spike-ACE2 complex with the spike binding to one or two ACE2 receptors. This shows that the substitutions on the Omicron RBD lead to new salt bridges and H-bonds and more beneficial electrostatic surface properties. This strengthens the interaction of the spike protein with ACE2, which is in line with the increased ACE2 affinity of the Omicron variant compared to the G614 strain.

The team also analyzed the cryo-EM structures of the complex formed between the Omicron spike and S3H3 Fab, which is an antibody that can cross-neutralize major variants of concern (VOC) including the Omicron. This illustrates the structural basis for S3H3-mediated broad-spectrum antibody neutralization.

Conclusion

The study shows that Omicron escapes the majority of the RBD-directed MAbs due to its relatively higher residue changes in the RBD and conformational masking. However, this variant of concern is still sensitive to the neutralizing MAb S3H3 which targets SD1.

To summarize, the study findings provide structural insights into the immune evasion and high transmissibility of the Omicron variant and could also help the development of broad-spectrum vaccines against emerging SARS-CoV-2 variants.

In a second study published on Science, researchers at the University of British Columbia (UBC) have conducted the world’s first molecular-level structural analysis of the Omicron variant spike protein.  

The analysis—done at near atomic resolution using cryo-electron microscopy—reveals how the heavily mutated Omicron variant attaches to and infects human cells. 

“Understanding the molecular structure of the viral spike protein is important as it will allow us to develop more effective treatments against Omicron and related variants in the future,” said lead author Sriram Subramaniam, professor in UBC’s department of biochemistry and molecular biology. “By analyzing the mechanisms by which the virus infects human cells, we can develop better treatments that disrupt that process and neutralize the virus.”

The spike protein, which is located on the outside of a coronavirus, enables SARS-CoV-2 to enter human cells. The Omicron variant has an unprecedented 37 mutations on its spike protein—3 to 5 times more than previous variants. 

The structural analysis revealed 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. The researchers concluded that these new bonds appear 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 virus, with levels more comparable to what we see with the Delta variant,” said Subramaniam. “It is remarkable that the Omicron variant evolved to retain its ability to bind with human cells despite such extensive mutations.”

The researchers conducted further experiments showing that the Omicron spike protein exhibits increased antibody evasion. In contrast to previous variants, Omicron showed measurable evasion from all six monoclonal antibodies tested, with complete escape from five. The variant also displayed increased evasion of antibodies collected from vaccinated individuals and unvaccinated COVID-19 patients. 

“Notably, Omicron was less evasive of the immunity created by vaccines, compared to immunity from natural infection in unvaccinated patients. This suggests that vaccination remains our best defence,” said Subramaniam. 
 
Based on the observed increase in binding affinity and antibody evasion, the researchers say that the spike protein mutations are likely contributing factors to the increased transmissibility of the Omicron variant.  

Next, Subramaniam says his research team will leverage this knowledge to support the development of more effective treatments. 

“An important focus for our team is to better understand 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,” he said.