Researchers at UBC’s faculty of medicine have conducted the world’s first molecular-level structural analysis of the Omicron variant spike protein. The findings were published in Science.
The analysis—done at near atomic resolution using cryo-electron microscopy—reveals how the heavily mutated Omicron variant attaches to and infects human cells. The Omicron variant has an unprecedented 37 mutations on its spike protein—three to five 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.
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.
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, lead author Sriram 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.”
Photo; Atomic structure of the Omicron variant spike protein (purple) bound with the human ACE2 receptor (blue). Credit: UBC Faculty of Medicine