As omicron variant of COVID-19 triggers travel warnings, U.S. scientists on watch for first case

Though not a single case has yet been detected in the United States, a new variant of the virus that causes COVID-19 has raised concerns around the world and has Arizona analysts working through the holiday week to watch for it.

First flagged in South Africa two days ago, genomic tests showed the variant the World Health Organization has dubbed omicron was spreading rapidly in South Africa in November. The strain, officially called B.1.1.529, has also been identified in other countries including Belgium, Israel and Hong Kong.

While the new variant rockets into headlines and triggers public health alerts and travel bans — the White House has implemented new restrictions on flights from eight African countries as a precautionary measure — experts say the effects of this variant are still uncertain.

The concern about how much this strain has changed compared with other versions of the novel coronavirus puts greater focus on long-term questions about the trajectory of the pandemic. Scientists and health officials have been on high alert for any mutations that might allow a new version of the virus to evade COVID-19 vaccines, which are currently the most effective tool to keep the disease at bay.

That’s already happened to a certain extent with the Delta variant, which has proven more adept at evading immune defenses and caused surges across the U.S since the summer. Now scientists are watching to see whether omicron will enter the scene.

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“We have not seen any B.1.1.529 in Arizona and none have been found in the U.S. or the Western Hemisphere to date,” said David Engelthaler, director of the pathogen and microbiome division at the Translational Genomics Research Institute (TGen). In partnership with state and tribal public health partners, Arizona State University, University of Arizona and the Centers for Disease Control and Prevention, TGen analyzes positive COVID-19 tests in Arizona to monitor for new and emerging variants.

The omicron variant — which some experts briefly referred to as “Nu” before the WHO made its official designation — “has a large number of mutations, and some of these mutations have some worrying characteristics,” said Maria Van Kerkhove, the COVID-19 technical lead with the WHO Health Emergencies Program, in a video posted by the WHO.

The WHO said in a statement that the mutations may have the potential to increase the risk of reinfection. But “we don't yet know how (the mutations) act together, or how a virus with so many changes will behave,” said Jeffrey Barrett, director of the COVID-19 Genomics Initiative at the Wellcome Sanger Institute, in a tweet.

Efrem Lim, an assistant professor at the Arizona State University Biodesign Institute and a virologist whose lab helps sequence SARS-CoV-2 genomes to track variants, said that the unusually high number of mutations in omicron is of particular cause for concern. Most variations of the Delta variant demonstrate at most between five and 10 mutations across the whole genome, but omicron has almost 30, Lim said.

How so many mutations arose at once is a mystery that’s still developing in real time, according to Lim. “We will probably try to pinpoint exactly how (the mutations) arose,” Lim said. “In the past, we've seen cases where, particularly (in immunocompromised) people that have prolonged infections ... the virus accelerated (its) mutation rate. (But) we don't know for sure.”

Changes in transmissibility, clinical presentation and ability to evade immunity “are going to be the three key pieces to look for as more is learned about the variant in the next several weeks,” said Dr. Joe Gerald, an associate professor of public health at the University of Arizona. He emphasized that even with a dominant Delta strain, Arizona is already seeing hospitals pushed back to capacity.

“We've got problems aplenty as it is moving into the Christmas holidays,” Gerald said.

The White House has issued a statement imposing air travel restrictions on flights coming from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi. President Biden also urged unvaccinated individuals to get vaccinated and for those eligible for booster shots to take them.

Gerald said that there may be a short-term benefit to travel restrictions, since they may offer scientists more time to understand differences between omicron and existing strains like Delta. However, he emphasized that the U.S. is vulnerable to global spread of new COVID-19 variants due to high levels of international travel.

“If this virus is in fact more transmissible than Delta, there's just no way to contain it,” he said. “We have enough historical precedent to understand you could delay (the spread of a new variant but) you can't prevent (it).”

Gerald added that although vaccine companies like Pfizer and Moderna have been evaluating whether to update vaccines and booster doses to more precisely address new variants of COVID-19, it would likely take them three to six months before they could roll out enough new doses to make an impact.

Lim and Gerald both noted that more time is needed to see whether the variant is more transmissible or more likely to dodge vaccines. And if it can evade vaccines, Gerald is waiting to see the consequences of breakthrough infections.

“If vaccine immunity or prior infection immunity is still keeping people out of the hospital, then that should give us a little bit of a sigh of relief. If it doesn't, then we're going to be in a little bit more difficult situation,” Gerald said.

Though the new strain was first reported in South Africa, that doesn’t necessarily mean it originated there. South Africa has a robust variant surveillance program, which probably contributed to the country’s ability to report the omicron variant. But public health officials are calling for increased access to vaccines around the globe, particularly in developing countries.

“Vaccine inequity (and) health inequities are huge, pervasive, persistent problems ... I think this just illustrates one more example of where we could and should do more to try to create a will to close the gap,” Gerald said. “We're all in this together, and the better prepared developing countries are to surveil, monitor and respond to these infections, including having access to vaccines, the better off we all are.”

In the meantime, Lim said he put aside Thanksgiving celebrations to come to work on monitoring cases in Arizona.

“That is our job, to be vigilant (and) keep looking out for these new variants,” Lim said.

Independent coverage of bioscience in Arizona is supported by a grant from the Flinn Foundation.

Melina Walling is a bioscience reporter who covers COVID-19, health, technology, agriculture and the environment. You can contact her via email at mwalling@gannett.com or on Twitter @MelinaWalling.

This article originally appeared on Arizona Republic: COVID-19 omicron variant in Arizona: Here's what you need to know