Omicron is always finding new evolutionary tricks to outsmart our immunity

During the pandemic, the virus that causes COVID-19 has evolved rapidly, blinding the world with variant after variant.

But the World Health Organization has not given a Greek name to a SARS-CoV-2 variant for almost a year, a move reserved for new variants that have or could have significant public health implications, such as the disease.

That begs the question: has the virus finally started to tail off, potentially making it more predictable?

The answer is no, according to a dozen evolutionary biologists, virologists, and immunologists interviewed by NPR.

“SARS-CoV-2 is evolving extremely rapidly,” says Trevor Bedford, a computational biologist who studies viral evolution at the Fred Hutchinson Cancer Center in Seattle. “There is no evidence that evolution is slowing down.”

Instead, the most consequential evolutionary changes have been confined to the Omicron family, rather than appearing in entirely new variants.

While Alpha, Beta, Gamma, and the other named variants spawned new branches in the SARS-CoV-2 family tree, those branches have been dwarfed by the Omicron branch, which is now littered with a plethora of subvariant strains.

“The children of omicron – so the many direct children and cousins ​​within the diverse omicron family – have crowded out each other” as the dominant tribes driving the pandemic, says Emma Hodcroft, a molecular epidemiologist at the University of Bern. “But the same family has dominated” by outperforming other varieties.

One variant to rule them all

The ever-growing Omicron spawn has maintained its dominance by what is known “convergent” development — when entities independently develop similar properties due to similar environmental stresses, according to Manon Ragonnet-Cronin, who studies viral genetics at the University of Chicago.

“We seem to be seeing evidence for large-scale convergent evolution for the first time,” says Ragonnet-Cronin. “We have what people call a swarm of omicron viruses that have different ancestors within omicron but share the same mutations.”

Confer these mutations these Omicron offspring with the one power they need most right now: the ability to sneak past the immunity humans have built up through infection, vaccination, or both.

“When you see convergence in evolution, that’s evolution’s way of saying that this mutation gets picked over and over again because it’s really helpful,” says Jesse Bloom, a bioinformatician at Fred Hutchinson Cancer Center in Seattle.

These mutations in the virus’s spike protein have increased its ability to evade protective antibodies and continue to infect large numbers of people.

“This virus gets a lot of lottery tickets, if you will. And it looks like these new mutations are like the jackpot with these new variants,” says Jeremy Kamil, an immunologist at Louisiana State University.

The Centers for Disease Control and Prevention is currently tracking more than a dozen omicron subvariants, including BF.7, BQ.1, and BQ.1.1, some of which are among the most immune-preventable to date.

Fortunately, the immunity that people have built up through vaccination and infection still seems to protect most from serious illness and death.

But the newer ones Highly contagious Omicron subvariants could help fuel another surge. They also give the virus plenty of chances to reproduce, mutate, and evolve even further.

A family tree full of surprises?

While all of this sounds bleak, Omicron’s long history of dominance gives some scientists some hope.

In a relatively optimistic scenario, the virus could go on evolving this way for a long time, drifting in more subtle evolutionary directions like the flu, without sudden behavioral changes that make it more dangerous.

“The fact that we may have stepped out of a phase [in the pandemic] where we get entirely new viruses from different parts of the family tree breaking in and dominating could be a sign that we’re moving towards a more stable future for the virus,” says Hodcroft.

But that would mean that many people would still contract the virus. Many would still become seriously ill, die or be left with long-term COVID. And because the virus is so new, it’s impossible to know how the virus might develop in the future, experts tell NPR.

“We are literally dealing with a completely new type of virus here,” says Kristian Andersen, an immunologist at Scripps Research. “We don’t know how many other pathways this particular virus could have. We just don’t know at this point.”

For example, it can’t be ruled out that a dramatically different variant might reappear, perhaps after cooking in someone with a compromised immune system who can’t expel the virus. This allows the virus to interact extensively with the human immune system and find even more beneficial mutations.

“I guarantee you there are people who are permanently infected with delta and alpha and have some really weird combinations of mutations,” says Michael Worobey, an evolutionary biologist at the University of Arizona. “And I’m fully prepared for a delta-based or alpha-based Omicron-like event where one of these zombie viruses that cooked inside someone shows up.”

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