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

after unveiling a national strategy to combat the pandemic today. President Biden Turning to the economic crisis it has wrought, Biden will sign tomb or executive orders today one to help people who are unemployed or struggling to buy food, the second to protect federal workers and contractors. This will set into motion a future executive order, which will require federal contractors to pay a $15 minimum wage and provide emergency paid leave, mirroring the nationwide minimum wage increase Biden is seeking as part of his $1.9 trillion relief package. His preference on priority is a bipartisan package and working with members of both parties to come to agreement. This crisis is dire on. It requires immediate action, and we hope and expect members of both parties to work together to do that. Few congressional Republicans have signed on to Biden's proposal, but House Democrats say they want to pass the president's bill as quickly as possible. It's what the people need, what the country needs to crush the virus, put money in the pockets of the American people and honor our heroes. Biden used his first full day in office Thursday to unveil a national strategy to get the pandemic under control. We didn't get into this mess overnight. That's gonna take months for us to turn things around. But let me be equally clear. We will get through this, releasing a nearly 200 page plan and signing 10 executive actions among them. Using the Defense Production Act to increase supplies for vaccines and testing, ramp up production of PPE and extending mask requirements for interstate travel on Busses, planes and trains. Our national plan launches a full scale war time effort to address the supply shortages by ramping up production and protective equipment. Syringes, needles, you name it when I say wartime people kind of look at me like more Time was, I said last night. 400,000 Americans have died, and when pressed about whether his goal of 100 million shots in his 1st 100 days was enough, Biden giving this answer. Come on, give me a break, man. A good start 100 Dr Anthony Fauci, noting the United States is in a very serious situation but also hopeful the new administration will help regain the public's trust. The idea that you could get up here and talk about what you know what? The evidence, What the science is and no, that's it. Let the science speak. It is somewhat of a liberating feeling.

The 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 U.S. 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 U.S. 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 U.S. 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 U.S. 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 USScientists 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 Jan. 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 U.S. — 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 weekArmstrong 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 Jan. 25th (in dealing with 64 jurisdictions scattered between the Eastern U.S. and Western Pacific, there will almost certainly be delays in some jurisdictions)."

The 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 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 U.S. 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 U.S. has been criticized for having a lackluster sequencing program. According an analysis by the of Harvard and the Massachusetts Institute of Technology using data from , an independent data sharing initiative, the U.S. 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 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 U.S. 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 Jan. 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 U.S. — 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 Jan. 25th (in dealing with 64 jurisdictions scattered between the Eastern U.S. and Western Pacific, there will almost certainly be delays in some jurisdictions)."

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