US rushes to overtake other countries in COVID sequence investigation

Medical experts have been warning for months that the U.S. lags far behind other countries in research into the evolution of the coronavirus, in terms of its rapid and comprehensive approach. In early December, the discovery of a faster spread of COVID-19 in the UK urgently indicated the need for genetic sequencing that would help determine whether treatment regimens and vaccinations remain effective against new mutations of the virus.

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In the US, the first case of the British 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 has probably spread unnoticed here, an accident in the country’s delayed COVID-19 sequencing campaign, and have warned that other new homemade variants could also mutate without any knowledge.

According to an analysis by the Broad Institute, from the global GISAID Initiative database, America will lag behind more than 30 countries in its sequencing effort.

But Colorado, where the first case of the faster spread of the British variant was found in the US, is rushing to reverse this trend. The state has expanded its public health staff and equipment to accelerate its efforts. The laboratories have identified the genetic sequence of 1400 samples so far and aim to sequence approximately 200 samples per 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 to track the spread of specific 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 vaccinations will still be effective against it.

Even before the Colorado case was identified, state health laboratories performed diagnostic tests that could immediately mark potential samples with one of the characteristic mutations of the British variant. It also trained staff in new procedures to speed up the search for the fast-moving bug.

Emily Travanty, scientific director of the Colorado Department of Public Health and Environment, said she was a little lucky that the sample of the first British case in the US came into her lab.

“We did not have all the monsters in the entire state of Colorado, so the monster came here and we were on the lookout for a little luck,” Travanty said.

Some states have struggled to follow suit. The increase in cases of coronavirus has forced laboratories to choose between diagnostic tests of the local population and the sequence of the virus, a resource-intensive process that can take days.

“More than anything else, the order has come down to staff,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories (APHL). She said APHL had heard of labs being frustrated with ‘incredibly stiff’ supplies being used for sequencing and other lab work.

Researchers at the University of California, Los Angeles were among those who abandoned their sequencing work last year amid a COVID increase in Southern California.

“We just did not have the capacity,” Omai Garner, director of clinical microbiology at UCLA Health System, told CBS News.

“The people I would use for the sequence are the same as the diagnostic testing did,” Garner added.

As the Trump administration comes to an end, senior Biden transition officials say succeeding the succession of jobs will be a top priority in the funds requested by Congress as part of the COVID-19 rescue proposal of the president.

In November, the Centers for Disease Control and Prevention announced that it would expand its own ability to collect and rank coronavirus samples from health authorities across the country. Samples sent to CDC labs have identified the first cases of B.1.1.7 in several states, including Texas, Indiana and Pennsylvania, public health officials told 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 that it would release about $ 15 million in funding to support local sequencing efforts through the Epidemiology and Laboratory Capacity (ELC) program, which ran to some public health labs on the front lines of the pandemic.

A Massachusetts State Public Health Laboratory spokesman said the agency received $ 3.4 million in ELC funds, which went to new staff, equipment and supplies. In Utah, officials said CARES Act funding and an ELC grant of about $ 176,000 helped the state increase the order of capacity to about 3,000 samples per day. And in Arkansas, a spokesman said their ELC money is expected to arrive soon.

“They, like us, are rushing up,” Travanty told the CDC. She says CDC has now doubled the number of samples the countries have requested for its tribal monitoring program.