Labs are on the hunt for cases of omicron

With the nation’s first case of omicron identified in California, public and private labs nationwide are scouring virus samples to learn how far the new coronavirus variant has traveled.

While omicron, first identified in South Africa, its neighboring countries and Europe, has spread rapidly, scientists are analyzing thousands of positive COVID-19 samples to find 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 effective 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 efforts of coronavirus lagged 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.

This year, less 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 Rochelle Walensky said at Tuesday’s White House COVID-19 briefing 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 one in seven positive PCR tests.

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

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

With the federal funding, state health departments have bolstered surveillance efforts 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.

Cases of omicron are rapidly increasing in South Africa, and have surfaced in the United Kingdom, several other European Union nations, as well as Australia, Canada and Israel.

The first 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.

The case was identified through genomic sequencing at the University of California, San Francisco, and the sequence was confirmed at CDC.

Public health labs are prioritizing samples with a marker known as “S gene dropout” that differentiates 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 find 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 confirmed, 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, of the Association of Public Health Laboratories.

The emergence of omicron “underscores the incredible importance of surveillance, which we do a relatively poor job of,” said Dr. Bruce Walker, professor at Harvard Medical School and Massachusetts Institute of Technology.

Walker praised the surveillance efforts in South Africa, the United Kington and Israel.

“We need that sort of capacity in the U.S. as we look to our collective future, co-existing with this,” he said.

David Engelthaler, head of the infectious disease branch at Phoenix-based TGen, a private research lab that tracks and sequences virus samples under a contract with the Arizona Department of Health Services and the CDC, said U.S. surveillance is improving.

“We weren’t gathering intelligence on this pathogen by having a cohesive strategy across the country for sequencing,” he said. “But that’s changing.”

California Gov. Gavin Newsom lauded the state’s “large-scale testing and early detection systems” in the hunt for the omicron variant in the Golden State.

California will ramp up testing at airports for arrivals from countries where cases have been identified, according to California Department of Public Health officials.