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U.S. races to catch up with other countries in COVID-19 sequencing research

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Medical experts have warned for months that the U.S. is falling far behind other countries in research on the evolution of the coronavirus, in both speed and comprehensiveness of approach. In early December, the discovery of a faster-spreading variant of COVID-19 in the U.K. lent urgency to the need for genetic sequencing that will help determine whether treatment regimens and vaccines remain effective against new mutations of the virus.

In the U.S., the first case of the U.K. variant B.1.17 was discovered in Colorado in December, and since then, at least 15 states have identified cases of the strain. Public health experts say it was already likely spreading here unseen, a casualty of the country's delayed COVID-19 sequencing campaign, and warned that other new homegrown variants could also be mutating without anyone's knowledge.

The U.S. is estimated to lag behind more than 30 nations in its sequencing effort, according to an analysis by the Broad Institute, from the global GISAID Initiative database.

But Colorado, where the first case of the faster-spreading U.K. variant was found in the U.S., is rushing to reverse this trend. The state has expanded its public health staff and equipment to speed its efforts. Its labs have identified the genetic sequencing of 1,400 samples so far and aim to sequence some 200 samples a week. 

The process of sequencing involves extracting and analyzing the unique genetic information in a virus sample to look for mutations. These findings help public health researchers track the spread of particular variants of the disease. While mutations are common and often harmless, the B.1.17 variant appears to spread more easily than previous strains. Both Pfizer and Moderna have said they believe their vaccines will still be effective against it.

Even before the Colorado case was identified, the state's health department laboratories were running diagnostic tests that could immediately flag potential samples with one of the U.K. variant's characteristic mutations. It was also training staff on new procedures to speed the search for the fast-moving bug.

Emily Travanty, scientific director with the Colorado Department of Public Health and Environment, said it "was truly a bit of luck" that the sample of the first U.K. case in the U.S. came into her lab.

"We don't have all of the samples in the whole state of Colorado, so that the sample came here to us and that we were on the lookout for it was sort of a bit of luck," Travanty said.

Some states have struggled to follow suit. The surge in coronavirus cases has forced labs to choose between diagnostic testing of the local population and sequencing the virus, a resource-intensive process that can last for days.

"More than anything else, the sequencing has come down to staffing," said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories (APHL). She said APHL has heard from labs frustrated with "incredibly tight" supplies used both for sequencing and other laboratory work.

Researchers at the University of California Los Angeles were among those to abandon their sequencing work last year, amid a COVID spike in Southern California.

"We just didn't have the capacity," Omai Garner, director of clinical microbiology in the UCLA Health System, told CBS News.

"The people I would use for that sequencing are the same that were doing the diagnostic testing," added Garner.

As the Trump administration comes to an end, senior Biden transition officials say stepping up sequencing work will be a key priority in the funds requested from Congress as part of the president-elect's COVID-19 rescue proposal.

In November, the Centers for Disease Control and Prevention announced it was expanding its own capacity to collect and sequence coronavirus samples from health authorities around the country. Samples sent to CDC labs identified the first cases of B.1.1.7 in several states, including Texas, Indiana, and Pennsylvania, state public health officials tell CBS News.

This month, Illumina and LabCorp both announced new CDC contracts to sequence samples of SARS-CoV-2, the virus that causes COVID-19. Illumina has since identified 51 of the first 54 cases of the B.1.1.7 variant in the country.

The CDC also announced in December it was releasing some $15 million in funding to support local sequencing efforts through the Epidemiology and Laboratory Capacity (ELC) program, which has trickled out to some public health labs on the front lines of the pandemic.

A spokesperson for the Massachusetts State Public Health Laboratory said the agency had received $3.4 million in ELC funds, which had gone to new staff, equipment, and supplies. In Utah, officials said CARES Act funding and an ELC grant of some $176,000 had helped the state boost sequencing capacity to some 3,000 samples a day. And in Arkansas, a spokesperson said their ELC money was expected to be "coming soon."

"They, like us, are ramping up," Travanty said of the CDC. She says CDC has now doubled the number of samples it has requested from states for its strain surveillance program.

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