CDC still working on goal of doubling coronavirus sequences to expand the hunt for mutations

Earlier this year, a senior CDC official told CNN he hoped over the next two weeks the agency would more than double the number of coronavirus genomes sequenced in the United States per week. Although the number of streaks increased in those two weeks, it has not doubled.

The United States has been criticized for having a lackluster sequencing program. According to an analysis by the Broad Institute of Harvard and the Massachusetts Institute of Technology using data from GISAID, an independent data-sharing initiative, the United States ranks 33rd in the world for sequences per 1,000 cases of Covid-19, behind countries that have much less resources, such as Senegal and Burkina Faso.

“We’re not even 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.

Then-President-elect Joe Biden last week said he would increase funding for coronavirus surveillance efforts once he was in office.

White House coronavirus coordinator Jeff Zients told reporters on Wednesday that funding must come from Congress. He said the nation’s ranking in the world in terms of genomic sequence testing was “clearly unacceptable”.

In order to keep up with mutations as they occur and to respond quickly, sequencing in the United States must increase dramatically, experts tell CNN.

“They don’t need to double their efforts. They need to at least 10-fold their efforts, ”said David Montefiori, virologist at Duke University Medical Center.

Acceleration of sequencing in the United States

Scientists are looking for coronavirus mutations by taking samples of the virus from patients’ noses and analyzing their genetic sequences.

The CDC performs genetic sequencing in its own labs and also funds sequencing in public health labs nationwide and commercial labs.

Dr Gregory Armstrong, director of the CDC’s Office of Advanced Molecular Detection at the National Center for Emerging Infectious and Zoonotic Diseases, told CNN earlier this year that over the next two weeks, the agency hopes to increase the number of coronavirus genomes being sequenced each week, from about 3000 to about 6500. This represents an increase of 3500 sequences per week.

In an email to CNN on Jan. 10, Armstrong said that “we are aiming to have commitments” for the additional footage.

The number of sequences has increased since the start of the year, but not by 3,500 per week. Instead, the number increased from 2,250 to 2,650 per week, according to figures Armstrong provided to CNN on Sunday. This means that the United States missed its sequencing target of 850 to 1,250 samples.

“They come in deeply small, and it’s tragic. And it’s costing Americans lives,” Hotez said. “Until they can find a way to modernize and do great things, we will never solve this 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 per week.

“These accelerate over the next 2 weeks (it takes time to set up the systems to get samples from all over the country and to fix the issues that inevitably arise on startup),” Armstrong wrote to CNN. . “One of the main advantages of these 5,000 per week is that, compared to what CDC got, they are much more representative of the United States – covering all states, providing both a sharper and more precise picture. of what’s going around here. ”

Armstrong said in December that the CDC had invested $ 15 million in state and local public health labs and that state labs pledged to make an additional 750 per week.

CDC expects thousands of extra footage per week

Armstrong noted that this additional sequencing “will not go live immediately.”

He said the commercial labs “hope to be fully operational in 2-3 weeks. We depend on the entrepreneurs for this, who have informed us that they need more time to develop. But we are very happy with the quality. . of the date they provide. ”

Armstrong wrote that public health labs “hope to be mostly at full capacity by January 25 (dealing with 64 jurisdictions scattered between the eastern United States and the western Pacific, there will almost certainly be delays in some jurisdictions). ”