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Why scientists — and much of the world — reacted so quickly to the omicron variant

Mutations on the spike proteins of the variant caught the attention of researchers who have been on the lookout for changes that could worsen the pandemic.
Image: A man walks through a deserted part of O.R. Tambo airport in Johannesburg, South Africa, on Nov. 29, 2021. The World Health Organization urged countries around the world not to impose flight bans on southern African nations due to concern over the new omicron variant.
A man walks through a deserted part of O.R. Tambo International Airport in Johannesburg, South Africa, on Monday. The World Health Organization urged countries not to ban flights from southern African countries because of concern over the new omicron variant of the coronavirus.Jerome Delay / AP

When Jeremy Kamil got his first look at B.1.1.529, the coronavirus variant that would soon be named omicron, it didn’t take long to see the differences.

More than 30 mutations made the variant's spike proteins, which cover the outside of the virus and are the main targets of vaccines and the body’s immune responses, different from those of the virus that first emerged in late 2019.

“The number of changes blew people’s minds,” said Kamil, an associate professor of microbiology and immunology at Louisiana State University Health Shreveport.

The World Health Organization has identified and tracked more than 20 variants. Yet unlike with others that popped up around the world before they mostly fizzled out (including the lambda variant, which was first documented in December in Peru, or the mu variant, which was detected a month later in Colombia), there were early signs that the omicron variant’s cocktail of mutations made it different and worthy of swift action — even overreaction — experts say.

While it’s too soon to know what the mutations mean for the effectiveness of vaccines or how sick people could become from the variant, the emergence of the omicron strain also highlights the frustrating reality of the Covid pandemic: Variants will continue to pose serious threats until countries around the world have more equal and ready access to vaccines, experts say.

“It’s definitely sobering,” Kamil said. “It’s an exaggeration to say we’re back at square one, but this is not a good development.”

Within hours of the WHO’s designating omicron a “variant of concern” Friday, dozens of countries imposed new travel bans, places that had loosened restrictions reintroduced mask mandates, and anxieties ran high.

It was the kind of quick and intense development reminiscent of early stages of the pandemic, prompting some concern that governments were overreacting before enough about the omicron variant was known.

“It’s partly why people started facetiously calling these things ‘scariants,’” said Dr. Amesh Adalja, an infectious disease doctor and a senior scholar at the Johns Hopkins Center for Health Security.

But even before it was given the “omicron” designation, the variant quickly gained attention among Covid researchers.

South Africa was the first to report clusters of cases involving the omicron variant last week. Days before, data about the newly identified variant had also been uploaded to GISAID, an online database for disease variants, by a research team in Hong Kong, followed by more early sequences from scientists in Botswana.

The number of mutations observed with the omicron variant hasn’t previously been seen with other strains, Adalja said. There are concerns that specific mutations to the spike protein could make the omicron variant less vulnerable to the so-called neutralizing antibodies generated by vaccines or natural immunity from previous Covid-19 infections.

"There's a very good chance this variant will be very resistant to neutralizing antibodies, but we can't yet say with any degree of certainty how resistant," said Theodora Hatziioannou, a virologist at Rockefeller University in New York City.

Researchers have been preparing for this possibility.

In lab experiments with a virus that was genetically altered so it didn’t pose a threat to humans, Hatziioannou and her colleagues produced myriad combinations of spike protein mutations and tested how well they were able to evade Covid-19 antibodies.

One of their more worrisome outcomes was observed in a lab-produced spike protein that carried 20 mutations — more than had been observed in any other known variant at the time but fewer than in the omicron variant. It was largely resistant to neutralizing antibodies from both vaccines and natural immunity.

More research is needed to understand how the omicron variant behaves in real-world settings, but Hatziioannou said many of the variant's mutations correspond to the types of changes she and her colleagues studied in the lab.

"Nature essentially reproduced our experiment, only at a much larger scale," she said.

Scientists around the world are racing to characterize the omicron variant, focusing in particular on whether it is more contagious, causes more severe disease or can evade the protection of vaccines. Those open questions may awaken anxieties from early in the pandemic, but Carl Bergstrom, a professor of biology at the University of Washington, said drug therapies and the vaccines still offer crucial advantages.

"We have a whole bunch of tools now that we didn't have before," he said. "But it's disappointing, for sure. There was kind of this general feeling that we're coming off this delta wave, we're triple-boosted, and it could almost be like 2019 again."

Adalja said the emergence of the omicron variant should spur people to get vaccinated or to get booster shots. Countries should also increase testing for Covid-19 to track where — and how quickly — the variant is spreading.

Since omicron was designated a "variant of concern," more than 40 countries have banned travel from southern Africa.

Hatziioannou said such sweeping measures, which may have been a "knee jerk reaction" to the most recent devastating wave of delta infections, are largely ineffective.

"The variant is likely already here," she said. "Closing the barn door after the horses have bolted is useless."

Cases involving the omicron variant have been detected in at least 16 countries. The variant hasn’t yet been confirmed in the U.S., but the country’s leading infectious disease expert, Dr. Anthony Fauci, the director of the National Institute of Allergy and Infectious Diseases, said it's possible that the omicron variant is already spreading in the country.

"When you have a virus like this, it almost invariably is ultimately going to go essentially all over,” he said Saturday on NBC’s “Weekend TODAY."

President Joe Biden, who said Monday that people should get fully vaccinated or get booster shots, tried to allay fears about the threat of the new strain.

"The variant is a cause for concern, not a cause for panic," he said.

Kamil similarly said it's too early to know what impact the omicron variant may have in the U.S. and around the world. He added, however, that it underscores the importance of vaccine equity and the need for wealthy countries to help provide that access.

"A booster shot in America has a far smaller effect of preventing variants than the first dose that someone gets in Chad or Benin or Togo," he said. "If we do not protect other nations, we are all going to sink together."