The hope was to sequence an additional 3,500 coronavirus samples per week. But only 2,250 to 2,650 additional samples have been sequenced, according to CDC numbers, with more expectation coming soon, as private labs recently went online to help with the effort.
Hunting for new mutations is a critical part of combating the spread of the virus. Although most mutations are harmless, some can spread more quickly, be more deadly, or be resistant to coronavirus vaccines.
“We are not doing as well as Ouagadougou,” said Dr. Peter Hotez, an infectious disease specialist at Baylor College of Medicine, referring to the capital of Burkina Faso.
Last week, then-elected President Joe Biden said he would increase funding for coronavirus surveillance efforts as soon as he took office.
On Wednesday, White House coronavirus coordinator Jeff Zients told reporters the funding needs to come from Congress. He said the country’s ranking in the world in terms of genomic sequence testing was “clearly unacceptable”.
To track mutations as they happen and respond quickly, sequencing in the U.S. needs to increase dramatically, experts say to CNN.
“They don’t need to double their efforts. They need at least 10 times their efforts,” said David Montefiori, a virologist at Duke University Medical Center.
Increasing sequencing in the U.S.
Scientists look for mutations in the coronavirus by taking samples of the virus from patients’ noses and analyzing their genetic sequences.
CDC performs genetic sequencing in its own laboratories and also funds sequencing in public health laboratories across the country and commercial laboratories.
Dr. Gregory Armstrong, director of the Office of Advanced Molecular Detection at the National Center for Zoonotic and Emerging Infectious Diseases, told CNN earlier this year that, in the next two weeks, the agency hoped to increase the number of coronavirus genomes being sequenced to each week, from about 3,000 to about 6,500. This is an increase of 3,500 sequences per week.
In an email to CNN on January 10, Armstrong said that “we intended to have commitments” for the additional sequences.
The number of sequences has increased since the beginning of the year, but not by 3,500 per week. Instead, the number increased between 2,250 and 2,650 per week, according to figures provided by Armstrong to CNN on Sunday. This means that the US missed its target of sequencing in 850 to 1,250 samples.
“They are extremely small and this is tragic. And it is costing American lives,” said Hotez. “Until they can find a way to modernize and do great things, we will never solve that problem.”
Armstrong said the CDC now has contracts with three private labs – Quest, Labcorp and a partnership between Illumina and Helix – to make a total of 5,000 sequences a week.
“This is increasing in the next 2 weeks (it takes time to get systems up and running to get samples from all over the country and solve the problems that inevitably arise during startup),” wrote Armstrong to CNN. “One of the main advantages of this 5,000 a week is that, compared to what the CDC has been getting, they are much more representative of the US – covering all states, providing a more granular and more accurate picture of what is circulating here.”
Armstrong said in December that the CDC invested $ 15 million in state and local public health labs, and the state labs pledged to make 750 more a week.
CDC expects thousands more sequences a week
Armstrong noted that this additional sequencing “will not be online immediately”.
He said the commercial labs “expect to be fully operational in 2-3 weeks. We depend on contractors for this, who have notified us that they need more time to expand. But we are very pleased with the quality of the date they are providing.”
Armstrong wrote that public health labs “expect to be mostly at full capacity by January 25 (when dealing with 64 jurisdictions spread across the eastern United States and western Pacific, there will almost certainly be delays in some jurisdictions)” .
John Bonifield Amanda Sealy of CNN contributed to this report.