Good news... Discovering how "Omicron" infects human cells and "evades immunity"

A team of scientists at the University of British Columbia has revealed the world's first structural analysis at the molecular level of the spike protein in an omicron mutant.

The analysis, carried out at sub-atomic resolution using cryo-electron microscopy, shows how the "strongly mutated" omicron infects human cells and "evades immunity".

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

Dr. Sriram Subramaniam, Professor in the Department of Biochemistry and Molecular Biology at UBC Medical School, discusses the implications of his team's research, which is currently under peer review and is available in the journal bioRxiv.

The analysis indicates that the Omicron variant is unprecedented for having 37 protein mutations in Spike, three to five times more than any other variant we've seen.

This is important for two reasons: First, the spike protein relates to how the virus attaches to and infects human cells.

Second, because the antibodies stick to the spike protein to neutralize the virus.

So, small mutations in the spike protein have potentially big implications for how the virus is transmitted, how it fights our body, and the effectiveness of treatments.

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

The team revealed: "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 decrease (K417N) from the strength of this bond."

Overall, the results show that Omicron has greater affinity for the original SARS-CoV-2 virus, with levels more comparable to what we see with the delta variant.

Remarkably, the omicron variant has evolved to retain its ability to efficiently bind to human cells despite these widespread mutations.

And the experiments confirm, according to Subramaniam, "What we see in the real world, that the spike protein in Omicron is much better than other variants at avoiding monoclonal antibodies that are commonly used as therapeutics, as well as at evading immunity resulting from both vaccines and natural infections."

It is worth noting that "Omicron" was less evasive of vaccine-induced immunity, compared to the immunity resulting from natural infection in unvaccinated "Covid-19" patients.

This indicates that vaccination remains our best defense against the omicron variant.

It is possible that the properties we see as a result of spike mutations, strong binding to human cells and increased antibody avoidance, are contributing factors to the increased transmissibility of the omicron variant.

These are the fundamental mechanisms that fuel the rapid spread of the variant and why 'Omicron' could become the dominant variant of SARS-CoV-2 so quickly.

The good news is that knowledge of 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 this process and neutralize the virus.

An important focus of the research team is now to better understand the association of neutralizing antibodies and which treatments will be effective across a full range of variables, and how they can be used to develop antiviral therapies.

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