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Scientists are combing through coronavirus samples to see how widespread omicron is

MARY LOUISE KELLY, HOST:

The search for the omicron variant is on. Yesterday, the first case was found in the U.S., a person from California who had recently traveled internationally. Now, today, more cases, one in Minnesota. That person had recently attended a convention in New York City. And another case in Colorado. Scientists say it is not a surprise that cases are turning up in the U.S., but the coming days will be critical for understanding just how widespread omicron is. NPR's Will Stone reports.

WILL STONE, BYLINE: Dr. Charles Chiu suspected the sample being sent to his lab might be omicron. It was 3:00 p.m. on Tuesday, and Chiu, who is a virologist at UC San Francisco, had just received an email from the local health department. It said that a positive COVID-19 case had been identified in someone who had recently traveled to South Africa.

CHARLES CHIU: They wanted to get an answer very quickly. I realized that there was certainly a possibility that this is a case of omicron.

STONE: Chiu's lab does genomic sequencing to understand what variants are circulating in the Bay Area.

CHIU: We managed to get the sample in the laboratory by 6:00 p.m. We did actually two analyses simultaneously.

STONE: The first was a PCR test, what's generally used by labs to diagnose a COVID-19 case. Except this particular PCR test happens to be good at screening for omicron because it can pick up what's called a spike gene dropout.

CHIU: The idea behind spike gene dropout is that, PCR tests, they typically look for multiple targets on the virus. One common target is a spike gene. But what's interesting about omicron is omicron has a deletion, specific deletion in the spike gene.

STONE: That deletion causes the PCR tests to look different. This is the result of a mutation in omicron.

CHIU: We are fortunate in that at least spike gene dropout is a very good screening tool, but it doesn't prove that it's omicron.

STONE: You still have to sequence it, which can take a bit more time. For that, Chiu used a small, pocket-sized sequencer, and by close to midnight, he had confirmed his suspicions.

STONE: It's very likely that this is the tip of the iceberg.

STONE: Scientists in the U.S. already had a sense of how to look for omicron, thanks to an early heads-up from South Africa and Botswana. Earlier in the pandemic, the U.S. had struggled to ramp up its surveillance for variants. But Alexandra Phelan at Georgetown Center for Global Health Science and Security says the country is definitely in a better place now.

ALEXANDRA PHELAN: We've actually had quite a significant increase in our capability to conduct the genetic sequencing and then to be tracking what's going on with variants. But right now, this is really, I guess, the first full test we have of that system being up and running.

STONE: This week, the CDC director said about 1 in every 7 positive PCR tests are now being sequenced in the U.S. That's a big increase. But Phelan says one challenge is that not everywhere in the country is doing the same amount of it. Some places, like California, are doing a lot of sequencing, but in others...

PHELAN: In some states we're sequencing, you know, less than 1%. Getting a bit more consistency across the nation will be critical.

STONE: The more testing that's done, the better positioned the U.S. will be to track the spread of omicron. But the testing is a mix of PCR tests and rapid antigen tests. Dr. Alex Greninja at the UW Medicine Clinical Virology Lab in Seattle says these rapid tests are great and convenient.

ALEX GRENINGER: At the same time, they're not as good at that next portion. They don't get reported to public health as much, they don't get sequenced. And so as that grows as a growing share of testing in the United States, that's an area that we're sort of dark to.

STONE: No one wants omicron to be in the U.S., but Dr. Chiu at UCSF says there's a silver lining to finding it here. We can now study it more easily.

CHIU: Whether it's more infectious, whether it's more transmissible, whether it may affect vaccine protection.

STONE: And that is critical for figuring out what needs to be done to stop it. Will Stone, NPR News. Transcript provided by NPR, Copyright NPR.