Vaccines may not quell omicron mutations

But variant unlikely to be any more severe than other coronavirus strains

As fears of another global surge of COVID-19 cases send jitters through global markets, spur a new round of travel bans and cause Americans to rethink their holiday plans, scientists studying the omicron variant are getting the first hints of what’s in store for the months to come.

The new variant’s mutations suggest that it is likely to evade the protections of vaccines to at least some extent, but that it is unlikely to cause more severe illness than previous versions of the coronavirus.

These early hypotheses appear in line with real-world observations from places like South Africa, where infections have included the vaccinated and previously ill but appear so far largely mild. That data, however, is thus far extremely limited, so much current evidence has come from computer modeling and comparing omicron’s physical structure to past variants.

A lot remains a mystery about omicron, which has more than twice the number of mutations as the delta variant, with the bulk found in the spike, the crown-like protein on the surface of the virus that vaccines train our bodies to attack. The appearance of such a highly mutated virus nearly two years into the pandemic caught the scientific community by surprise, as many had hypothesized that the ultra-contagious delta variant might mark the last major wave, peaking and then eventually burning out, much like the 1918 influenza pandemic.

It will take scientists weeks of careful laboratory testing and study to untangle exactly what omicron’s mutations mean, and definitively nail down details about how much more contagious it is and what the implications are for those who get infected. But early observations have already allowed scientists to make some informed guesses about what’s to come.

The location of omicron’s mutations suggest two things. The first is that the virus is likely to evade vaccines to some extent. Some of the spike mutations are in the same locations seen in other variants that spread quickly. In past variants those mutations have led to what’s known as antibody escape, in which the virus is able to evade the attack of antibodies generated by vaccines or a previous COVID-19 infection.

The second insight is that it appears likely omicron won’t be impervious to the body’s second line of defense, T-cells. They work hand-in-hand with antibodies to ward off infection and the development of disease. If a virus manages to escape the attacks of antibodies, T-cells then get to work killing infected cells.

“Many of the mutations occur in the hot spots on the spike protein, which we know are important for antibodies to bind,” said Wendy Burgers, an immunologist at the University of Cape Town. “What we predict is that a lot of the T-cell response will still be active against omicron.”

Her lab is awaiting samples from omicron-infected patients and spike-protein based on omicron to begin experiments to help confirm this suspicion. But early computer analysis has backed up the theory.

Antibodies have narrow targets of attack on the spike protein, aiming for just two specific regions known as the receptor binding domain and the N-terminal domain. That means that a handful of mutations in those regions can significantly impact the ability of antibodies to attack.

T-cells, on the other hand, target the entire spike.