Medical experts have warned for months that the United States is lagging far behind other countries in research on the evolution of the coronavirus, both in speed and scope of approach. In early December, the discovery of a more rapidly spreading variant of COVID-19 in the UK made the need for genetic sequencing urgent that will help determine whether treatment and vaccine regimens remain effective against new mutations of the virus.
In the USA, 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 probably spreading here unseen, a victim of the country’s delayed COVID-19 sequencing campaign, and warned that other new locally grown variants may also be mutating without anyone’s knowledge.
The United States is estimated to be behind more than 30 nations in its sequencing effort, according to an analysis by the Broad Institute of the GISAID Initiative’s global database.
But Colorado, where the first case of the fastest-spreading British variant was found in the United States, is racing to reverse that trend. The state expanded its public health team and equipment to accelerate its efforts. Its laboratories have identified the genetic sequencing of 1,400 samples so far and intend to sequence about 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 to track the spread of specific variants of the disease. Although mutations are common and often harmless, variant B.1.17 appears to spread more easily than previous strains. Both Pfizer and Moderna said they believed their vaccines would still be effective against it.
Even before the Colorado case was identified, state health department labs were running diagnostic tests that could immediately signal potential samples with one of the UK’s variant’s characteristic mutations. He was also training the team on 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 fortunate” that the sample from the UK’s first case in the United States came to her laboratory.
“We don’t have all the samples across the state of Colorado, so the sample came to us and we were looking for some sort of luck,” said Travanty.
Some states have struggled to follow suit. The increase in coronavirus cases has forced laboratories to choose between diagnostic testing of the local population and sequencing of the virus, a process that requires many resources and can take days.
“More than anything else, sequencing was all about people,” said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories (APHL). She said APHL had heard of labs frustrated with “incredibly tight” supplies used for sequencing and other lab work.
Researchers at the University of California at Los Angeles were among those who abandoned their sequencing work last year amid a peak in COVID in southern California.
“We just didn’t have the capacity,” Omai Garner, director of clinical microbiology for the UCLA Health System, told CBS News.
“The people I would use for this sequencing are the same people who were doing the diagnostic test,” added Garner.
As the Trump administration comes to an end, senior officials in the Biden transition say that stepping up sequencing work will be a key priority in funds requested from Congress as part of the president-elect’s COVID-19 bailout proposal.
In November, the Center for Disease Control and Prevention announced that it was expanding its own capacity to collect and sequence coronavirus samples from health officials across the country. Samples sent to CDC laboratories identified the first cases of B.1.1.7 in several states, including Texas, Indiana and Pennsylvania, state public health officials told CBS News.
This month, Illumina and LabCorp announced new CDC contracts to sequence samples of SARS-CoV-2, the virus that causes COVID-19. Illumina has already identified 51 of the first 54 cases of variant B.1.1.7 in the country.
The CDC also announced in December that it was releasing about $ 15 million in funding to support local sequencing efforts through the Epidemiology and Laboratory Capacity (ELC) program, which has spread to some public health labs 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 went to new employees, equipment and supplies. In Utah, officials said that funding for the CARES Act and an ELC grant of about $ 176,000 helped the state increase its sequencing capacity to about 3,000 samples per day. And in Arkansas, a spokesman said the ELC money should “arrive soon”.
“They, like us, are growing,” said Travanty of the CDC. She says the CDC has now doubled the number of samples it has asked the states for its strain surveillance program.