Research presented in this article answers the question, Are antibodies from natural infection and vaccines effective against the omicron variant?
The omicron variant (B1.1.529) has 60 mutations, and fifteen of them are in the receptor-binding domain (RBD). The mutations can change the shape of the RBD and make it unrecognizable to existing antibodies from previous COVID infections or vaccinations.
The RBD is the part of the spike protein that binds to the ACE2 receptors of cells. Neutralizing antibodies that prevent the attachment of the RBD to the ACE2 receptors avert infections. That is why the goal of vaccination is to make neutralizing antibodies.
Scientists from the Department of Bioinformatics and Genomics and the School of Data Science at the University of North Carolina at Charlotte, North Carolina, did the research.
First, they obtained the sequence of the omicron variant from GISAID.
Then they entered the RBD protein sequence of the omicron variant into software called AlphaFold2. AlphaFold can predict protein structures based on protein sequences. The resulting complex is below.
The next step is to use protein sequences of four neutralizing antibodies (C105, CC12.1, CC12.3, and CV30). These antibodies are from people who recovered from COVID-19. They used AlphaFold 2 again to make the structure of the four neutralizing antibodies.
Then the antibody and RBD structure of the omicron variant were input into another software called HADDOCK 4.
HADDOCK 4 is biomolecular modeling software that provides docking predictions for provided structures. It helps predict the binding affinity between the RBD and neutralizing antibody structures.
The computer model shows that the four antibodies could bind to the omicron RBD. What it means in the real world is that current antibodies from previous COVID infections will be able to prevent omicron infection.
Below is a computer image of an antibody attaching and neutralizing the RBD of the omicron.
The authors conclude that,
Though there are a multitude of mutations in the RBD of
Omicron, these mutations do not appear to be causing any
large conformational change that would totally evade antibody interaction.
In his post in Medium, Colby T. Ford, one of the authors, states that
These analyses solely look at the RBD of the Spike protein (for potential vaccine impacts), only taking into account 15 of the 60 new mutations in B.1.1.529. There could be other mutations that affect pathogenicity, virulence, or other epidemiological factors not investigated here.
Key takeaways:
Current antibodies from natural infections and vaccination can protect omicron based on computer modeling. That’s reassuring since a report showed that Regeneron might not be effective against omicron.
Don’t Get Sick!
Knowledge about Covid-19 is rapidly evolving. Stay current by subscribing. Feel free to share and like.
If you find value in the articles, please consider donating to show your support.
Reference: