CDC still working on goal to double coronavirus sequences to expand hunt for mutations

The US Centers for Disease Control and Prevention did not meet a goal to quickly ramp up surveillance for possibly dangerous coronavirus mutations, according to numbers from the federal agency.

At the beginning of the year, a senior CDC official told CNN he hoped over the next two weeks that the agency would more than double the number of coronavirus genomes being sequenced in the US per week. While the number of sequences did increase over those two weeks, it did not double.

The hope was to sequence an additional 3,500 coronavirus samples per week. But only 2,250 to 2,650 additional samples were sequenced, according to CDC numbers, with more expected soon as private labs have recently come online to help in the effort.

Hunting for new mutations is a critical part of combatting the spread of the virus. While most mutations are harmless, some might be able to spread more quickly, be more deadly, or prove resistant to coronavirus vaccines.

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

“We’re not even doing as good 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-President-elect Joe Biden said he would increase funding for coronavirus surveillance efforts once he was in office.

“We simply do not have the kind of robust surveillance capabilities that we need to track outbreaks and mutations,” according to Biden’s American rescue plan issued last week. “Tracking the way the virus is changing and moving through the population is essential to understanding outbreaks, generating treatments and vaccines, and controlling the pandemic.”

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

In order to track mutations as they happen and respond quickly, sequencing in the US needs to increase dramatically, experts tell CNN.

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

Ramping up sequencing in the US

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

The CDC does genetic sequencing in its own labs, and it also funds sequencing at public health labs across the country and at commercial labs.

Dr. Gregory Armstrong, director of the CDC’s Office of Advanced Molecular Detection at the National Center for Emerging and Zoonotic Infectious Diseases, told CNN at the beginning of the year that over the next two weeks, the agency hoped to increase the number of coronavirus genomes being sequenced each week, from about 3,000 to about 6,500. That’s an increase of 3,500 sequences per week.

In an email to CNN on January 10, Armstrong said “we were targeting 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 by between 2,250 and 2,650 per week, according to numbers Armstrong supplied CNN Sunday. That means the US missed its sequencing goal by 850 to 1,250 samples.

“They come up profoundly small, and that’s tragic. And it’s costing American lives,” Hotez said. “Until they can figure out a way to modernize and do big 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 do a total of 5,000 sequences each week.

“Those are ramping up over the next 2 weeks (it takes time to get the systems in place to get samples from all over the country and to work through issues that inevitably arise during startup),” Armstrong wrote to CNN. “One of the main advantages of these 5000 per week is that, compared to what CDC had been getting, they’re much more representative of the US — covering all states, providing both a more granular and more accurate picture of what’s circulating here.”

Armstrong said in December, the CDC put $15 million out to state and local public health labs and the state labs have made a commitment to do 750 additional per week.

CDC expects thousands more sequences per week

Armstrong noted that this additional sequencing “isn’t coming online immediately.”

He said the commercial labs “hope to be fully up in 2-3 weeks. We’re dependent on the contractors for this, which have notified us that they need additional time to scale up.  But we’ve been very pleased with the quality of date they’re providing.”

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