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Omicron is in America: What happens next?


U.S. health officials on Wednesday identified the first case of the omicron variant in the country—detection that was largely possible due to increased genomic sequencing and other surveillance efforts.

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The U.S. finds its first omicron case

According to CDC, the first case of Covid-19 due to the omicron variant was detected in an individual from California.

"The individual was a traveler who returned from South Africa on November 22," CDC said. "The individual, who was fully vaccinated and had mild symptoms that are improving, is self-quarantining and has been since testing positive. All close contacts have been contacted and have tested negative."

The case was confirmed by CDC, as well as the California and San Francisco Departments of Public Health, through genomic sequencing conducted at the University of California at San Francisco, CNN reports.

How genomic sequencing helped detect omicron

Significant improvements in the U.S.' surveillance system may have helped health officials quickly detect the omicron variant, Politico reports. According to Politico, since the beginning of the year, the United States has significantly improved its surveillance efforts, going from sequencing fewer than 1% of all positive coronavirus samples to now sequencing between 5% and 10% of all positive samples.

According to CDC Director Rochelle Walensky, around 80,000 samples are being sequenced per week, which represents around one out of every seven positive samples.

"Throughout the pandemic ... CDC has continuously monitored variants and vastly expanded our capacity for genomic sequencing over the past nine months," Walensky said. "We are actively putting systems in place with local and state laboratories to make detection and sequencing even faster."

Walensky added CDC is increasing testing at four major international airports—Atlanta, Newark, New York, and San Francisco—to detect Covid-19 cases more quickly among travelers arriving to the country.

"CDC is evaluating how to make international travel as safe as possible, including pre-departure testing closer to the time of flight and considerations around additional post-arrival testing and self-quarantine," Walensky said.

How the U.S. can track omicron as it spreads

Now that the omicron variant has been detected in the United States, public health experts have recommended different ways to detect new cases and track the variant as it inevitably spreads, NPR reports.

1. Use PCR testing for early detection

According to NPR, the omicron variant exhibits an "S gene target failure" on certain PCR tests, a characteristic that makes it stand out from the dominant delta variant and potentially more identifiable even without genomic sequencing.

"One of the things about this variant is that there is a tell in laboratory tests, so you don't even have to do the full genetic sequencing," said David Kessler, chief science officer for the federal Covid-19 response. Labs that can identify that characteristic in their PCR tests have "an ability to do an early, quick analysis," he said, and then prioritize those tests for full sequencing.

Currently, around 56 state public health labs can identify this omicron marker on their PCR tests, and other labs with similar capacity are being asked to use this specific test for the next two weeks, NPR reports.

2. Ramp up sequencing efforts, especially in areas with less testing

The United States has significantly increased its genetic sequencing, but many public health experts say it is also important to ensure that sequencing is not focused on just one particular region with a large population.

"If you're focusing on that sequencing in very limited or few populations, you can get 10,000 sequences a day from New York City and doesn't tell you what's happening in the rest of the country," said Rick Bright, CEO of the Pandemic Prevention Institute at the Rockefeller Foundation.

Similarly, Scott Becker, CEO of the Association of Public Health Laboratories, said that in areas where there's less testing, "you're going to see less specimens coming through the surveillance system and therefore we won't be sequencing as many from those parts of the country."

He added, "It's important that all states work with CDC to conduct the surveillance and ramp it up if necessary."

3. Improve communication between CDC, labs, and clinicians

Even with labs processing more PCR tests, detecting new cases of the omicron variant could still be slow if the labs do not notify CDC about what they are finding, NPR reports.

The "silos of our public health surveillance system" have kept the United States from quickly detecting variants throughout the pandemic, said Kavita Patel, a non-resident fellow at the Brookings Institution.

"The labs that the states run or the labs that the academic centers run are in isolation of where clinical work is happening," she said. "So the two just don't speak."

Bright agreed, saying, "We have a lot of capability and different public health labs across the United States, but we're not fully leveraging all of the sequencing capability in our academic sectors and our private sectors, and we're not yet linking all of that together to get as much information as possible."

4. Track all breakthrough infections

According to Kessler, an increase in breakthrough infections could be a sign that the omicron variant is spreading widely in the United States and evading vaccine immunity.

"[I] would predict that we would see an increase in breakthrough cases [after omicron's arrival in the United States]," Kessler said, although he noted that it's "still up in the air" whether these cases would lead to more severe Covid-19.

Currently CDC only tracks limited information on breakthrough infections, focusing on those that cause hospitalizations and death instead of all cases.

Without data on all breakthrough cases, Bright said that "we're missing the opportunity to look at the changes in those viruses that could be leading to those severe cases and stopping it before it gets there."

"There's a lot of information being left on the table by not looking into those [breakthrough] cases," he added. (Chappell, NPR, 12/1; Rabin et al., New York Times, 12/1; Howard et al., CNN, 12/1; AP/Modern Healthcare, 11/30; Lim, Politico, 11/30; Stein/Wroth, "Shots," NPR, 11/30)


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