The Columbus Dispatch

Labs work to track omicron variant cases

US sequencing effort has been ramped up

- Ken Alltucker

With the nation’s first case of omicron identified in California and a case verified in Minnesota, public and private labs nationwide are scouring virus samples to learn how far the new coronaviru­s variant has traveled.

While omicron, first identified in South Africa, its neighborin­g countries and Europe, has spread rapidly, scientists are analyzing thousands of positive COVID-19 samples to find more cases in the United States. Still unknown is whether the new variant will transmit more easily than the dominant delta strain or if existing vaccines will be effective against it.

The search for the variant highlights an important but largely hidden facet of the U.S. coronaviru­s response – sequencing positive samples to detect new and emerging versions of coronaviru­s.

Public health experts acknowledg­e the U.S. genomic sequencing efforts of coronaviru­s lagged behind other nations through the early months of the pandemic. One study last year ranked the U.S. 43rd in the world in surveillan­ce and tracking variants.

Earlier this year, fewer than 1% of positives samples were sequenced and sent to the Centers for Disease Control and Prevention. Now armed with nearly $200 billion from the Biden administra­tion, public and private labs are sequencing 5% to 10% of positive COVID-19 samples.

CDC Director Dr. Rochelle Walensky said at Tuesday’s White House COVID-19 briefing that earlier this year, the agency was sequencing about 8,000 samples a week. Now it has ramped up genomic sequencing and is sequencing 80,000 samples a week, or 1 in 7 positive PCR tests.

“That’s more than any other country,” she said.

The virus is constantly changing, an evolutiona­ry process scientists need to monitor closely by sequencing the virus. Sequencing is the process of finding small changes in the virus’s genetic code. Drugmakers use the data to learn whether a new variant becomes resistant to vaccines, antivirals and monoclonal antibody treatments. Public health officials decide necessary precaution­s such as testing travelers to the U.S.

With the federal funding, state health department­s have bolstered surveillan­ce efforts at public health labs and through contracts with university and private labs. These labs sequence the virus and detect small changes in the evolving virus. Many of these mutations mean little, but a “variant of concern,” such as omicron, has the potential to alter the course of the pandemic.

The first known U.S. case was a traveler who returned to California from South Africa on Nov. 22. The person was fully vaccinated and had mild symptoms, and close contacts of the individual have tested negative, the CDC reported Wednesday.

Public health labs are prioritizi­ng samples with a marker known as “S gene dropout” that differentiates omicron from delta, the dominant strain circulatin­g in the U.S.

The S gene is one of three genes targeted by a common PCR test widely used by public and private labs. The test can detect the other two genes, but fails to find the s gene, in omicron and other non-delta variants. This allows labs to search for samples with this characteri­stic, a shortcut to more quickly identify omicron.

Once cases are confirmed, scientists will further study the samples to learn whether the variant will impact testing, vaccines or other COVID-19 therapeuti­cs, said Kelly Wroblewski, director, infectious diseases, at the Associatio­n of Public Health Laboratori­es.

 ?? FREDERIC J. BROWN/AFP/GETTY IMAGES/TNS ?? Earlier this year, the CDC was sequencing about 8,000 samples a week. Now it is sequencing 80,000 samples a week.
FREDERIC J. BROWN/AFP/GETTY IMAGES/TNS Earlier this year, the CDC was sequencing about 8,000 samples a week. Now it is sequencing 80,000 samples a week.

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