Medical experts have been warning for months that the US is lagging far behind other countries in research into the evolution of the coronavirus, both in speed and in completeness of action. In early December, the discovery of a faster-spreading variant of COVID-19 in the UK created urgency for the need for genetic sequencing that will help determine whether treatment regimens and vaccines remain effective against new mutations of the virus.
In the US, the first case of the British variant B.1.17 was discovered in Colorado in December, and at least 15 states have since identified cases of the strain. Public health experts say it probably already spread here unseen, a victim of the country’s delayed COVID-19 sequencing campaign, and warned that other new homegrown variants could also mutate without anyone knowing.
According to a Broad Institute analysis of the global GISAID Initiative database, the US is estimated to be behind more than 30 countries in sequencing.
But Colorado, where the first case of the faster-spreading British variety was found in the US, is rushing to reverse this trend. The state has expanded its public health workforce and equipment to speed up its efforts. The laboratories have so far identified the genetic sequencing of 1,400 samples and aim to sequence some 200 samples per week.
The sequencing process 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 certain variants of the disease. Although mutations are common and often harmless, the B.1.17 variety seems to spread more easily than previous species. 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 health department labs were running diagnostic tests that could immediately mark potential samples with one of the British variant’s characteristic mutations. It also trained personnel 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 it was “really lucky” that the sample from the first British case in the US got into her lab.
“We don’t have all the monsters in the entire state of Colorado, so the monster came to us here and we were looking forward to some luck,” Travanty said.
Some states are struggling to follow suit. The increase in coronavirus cases has forced laboratories to choose between diagnostic testing of the local population and sequencing the virus, a resource-intensive process that can take days.
“Sequencing has come down mostly to personnel,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories (APHL). She said APHL has heard of labs frustrated by “incredibly tight” supplies used for both sequencing and other lab work.
Researchers at the University of California Los Angeles were among those who quit 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 at UCLA Health System, told CBS News.
“The people I would use for that sequencing are the same people who did the diagnostic tests,” added Garner.
As the Trump administration draws to a close, senior Biden transition officials say intensifying sequencing work will be a key priority in the funds requested from Congress as part of the president-elect’s COVID-19 bailout 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 across the country. 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 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 that it was releasing approximately $ 15 million in funding to support local sequencing efforts through the Epidemiology and Laboratory Capacity (ELC) program, which has trickled down to some public health laboratories on the front lines of the pandemic.
A spokesman for the Massachusetts State Public Health Laboratory said the agency had received $ 3.4 million in ELC funds, which were spent on new personnel, equipment and supplies. In Utah, officials said CARES Act funding and an ELC grant of about $ 176,000 had helped the state increase sequencing capacity to about 3,000 samples per day. And in Arkansas, a spokesperson said their ELC money would come “soon.”
“They are growing, like us,” Travanty said of the CDC. She says the CDC has now doubled the number of samples it has requested from states for its pedigree surveillance program.