US rushes to catch up with other countries in COVID sequencing research

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Medical experts have been warning for months that the United States is far behind other countries in research into the evolution of the coronavirus, both in speed and comprehensiveness of approach. In early December, the discovery of a faster-spreading variant of COVID-19 in the UK urgently needed genetic sequencing that will help determine whether treatment regimens and vaccines remain effective against new mutations in the virus. .

In the United States, 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 was already spreading here unseen, a victim of the country’s delayed COVID-19 sequencing campaign, and have warned other new local variants could also mutate without anyone knowing.

The United States is estimated to be more than 30 countries behind in its sequencing effort, according to Broad Institute analysis from the GISAID Initiative’s global database.

But Colorado, where the first case of the faster-spreading British variant was found in the United States, is rushing to reverse that trend. The state has expanded its public health personnel and equipment to speed up its efforts. Its laboratories have identified genetic sequencing of 1,400 samples to date and aim to sequence some 200 samples per week.

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

Even before the Colorado case was identified, state health department labs were running diagnostic tests that could immediately flag potential samples with one of the mutations characteristic of the British variant. He also trained staff on the new procedures to speed up the search for the fast-growing bug.

Emily Travanty, scientific director of the Colorado Department of Public Health and Environment, said “it was really a bit of luck” that the sample from the first British case in the United States entered her laboratory.

“We don’t have all of the samples all over the state of Colorado, so the sample came here for us and we were on the prowl, it was kind of lucky,” 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 take days.

“More than anything else, sequencing comes down to staffing,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories (APHL). She said the APHL had heard from labs frustrated by the “insanely tight” supplies used for both 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 spike in southern California.

“We just didn’t have the capacity,” Omai Garner, director of clinical microbiology for UCLA’s health system, told CBS News.

“The people I would use for this sequencing are the same people who performed the diagnostic tests,” Garner added.

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

In November, the Centers for Disease Control and Prevention announced they were expanding their own coronavirus sample collection and sequencing capacities with health authorities nationwide. Samples sent to CDC labs 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 contracts with the CDC to sequence samples of SARS-CoV-2, the virus responsible for COVID-19. Illumina has since identified 51 of the first 54 cases of B.1.1.7 variant in the country.

The CDC also announced in December that it is providing some $ 15 million in funding to support local sequencing efforts through the Epidemiology and Laboratory Capacity (ELC) program, which has spread to some labs. of public health on the front line of the pandemic.

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

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