U.S. steps up search for Omicron variant in domestic COVID-19 cases

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A sign advertises coronavirus disease (COVID-19) testing ahead of the Thanksgiving holiday at Logan International Airport in Boston, Massachusetts, U.S., November 22, 2021. REUTERS/Brian Snyder

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CHICAGO, Nov 29 (Reuters) - The United States is enhancing its COVID-19 surveillance to distinguish domestic cases of the Omicron variant from the still-dominant Delta, the head of the association of state-run public health laboratories told Reuters on Monday.

The new variant, first identified in southern Africa last week, has since been detected in 10 other countries. U.S. officials say it is only a matter of time before it turns up in the country.

Omicron has prompted new alarm due to an unusual number of mutations that suggest it may reduce vaccine protection, though much remains unknown. Countries worldwide are scrambling to understand the prevalence of the new version of coronavirus within their borders.

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"I'm confident we'll see it," said Scott Becker, chief executive of the Association of Public Health Laboratories (APHL). "My assumption is we're going to see it in the next couple of days."

On Friday, members of the group made up of state and city public health laboratories met with White House officials for a briefing on the variant and U.S. efforts to identify it, Becker said. An additional meeting with the U.S. Centers for Disease Control and Prevention is set for later on Monday.

"I can assure you that our public health officials here are in very close touch daily and in ongoing calls with all state health officials and public health partners," White House press secretary Jen Psaki told reporters.

One of the first steps will be to increase use of a ThermoFisher Inc (TMO.N) COVID-19 molecular test to help identify potential cases, said Becker.

Other countries, including Belgium and Israel, have said they are using the ThermoFisher test. Its design allows it to detect a genetic mutation within the S gene, which can distinguish the Omicron variant from Delta, which currently accounts for more than 99.8% of coronavirus cases.

Detecting COVID-19 cases in which the S-gene appears to drop out alerts lab officials that such samples should undergo additional sequencing to confirm the presence of Omicron.

"It gives us a signal, and then those specimens that have it will immediately go for sequencing," Becker said.

Of the 68 public health labs doing sequencing in the United States, 56 have done a test run with the ThermoFisher system, and 35 are already using it.

"I expect the other 21 will be using it as of today," Becker said.

Currently, the United States runs sequences on 93,000 COVID-19 tests a week, up sharply from 3,000 a week at the beginning of 2021, Becker said. Public health labs run between 15,000 and 20,000 of those per week, he said.

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Reporting by Julie Steenhuysen; additional reporting by Francesco Guarascio in Brussels and Maayan Lubell in Jerusalem; Editing by Michele Gershberg and Nick Macfie

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