The Biden administration will send $1.7 billion to the Centers for Disease Control and Prevention and local and state governments and other research efforts, starting early next month to find and track coronavirus variants lurking in the United States. Already, the more contagious U.K. variant, B.1.1.7, is now the dominant strain in this country, fueling surges in Michigan and the Northeast.
"Our goal is to get that money out as fast as possible to help states in all the many ways that they need to be able to expand their own sequencing capacity," said Carole Johnson, the White House COVID-19 testing coordinator, in an interview with NPR.
The U.S. has been flying blind in the race between vaccination efforts and the spread of new coronavirus variants that could potentially spark another deadly nationwide surge and reduce effectiveness of the vaccines. U.S. public health officials have been operating with incomplete information because of an inadequate viral genomics surveillance system.
Friday's announcement details how the funds — which were part of the $1.9 trillion COVID-19 relief bill passed last month — will be distributed. The largest share of funds — $1 billion — will go to the CDC, states and cities to bolster their existing surveillance efforts.
The rest will go to longer-term initiatives, including $400 million to create Innovative Centers of Excellence in Genomic Epidemiology, which will be research partnerships between state health departments and academic institutions. An additional $300 million will go to build a "national bioinformatics infrastructure" to handle the flood of data.
Before the coronavirus, genomic sequencing of viruses in the U.S. was aimed largely at tracking foodborne illnesses. The value of genomic sequencing was a "lesson learned" from COVID-19, Johnson said. The pandemic has forced that U.S. system to adapt, and the funding approved by Congress should build up the scientific infrastructure to deal with whatever comes next, she added.
"This is both about today and about building for the long term," Johnson said. "Today's investment ... is about helping us fight COVID but is also about helping us continue to transform how public health works to combat outbreaks of all kinds going forward."
When the U.K. variant first emerged, the viral surveillance system in the U.S. was woefully lacking in resources, especially compared with other countries.
Beginning in 2014, CDC received $30 million per year for a program called Advanced Molecular Detection to build capability and capacity at the agency and the states for laboratory science and epidemiology. "At the time, we thought this was a huge win because it was new money, but in retrospect, it was completely anemic," Scott Becker, executive director of the Association of Public Health Laboratories, said via email to NPR.
In early February, U.S. laboratories were only sequencing perhaps 5,000 to 8,000 coronavirus samples per week. The CDC said the agency has now boosted that to close to 15,000 per week. But many experts estimate the country should be sequencing at least 25,000 per week, if not many more.
Public health experts welcomed Friday's announcement.
"The Biden plan makes sense and is practical," Becker wrote. Not only does it boost surveillance capacity, but it also "looks towards building partnerships across sectors to foster innovations so that we can keep pace with science and technology."
But some question whether this boost in funding is coming fast enough, especially with cases surging in many places and variants spreading quickly.
"With the money going out in May, I'd like to see a timeline of expectations for how quickly sequencing is going up," said Heather Pierce, senior director for science policy at the Association of American Medical Colleges. "There is an urgent need to increase the sequencing by several fold in places where cases are high and rising (like Michigan), and a month or two ramp-up period will put us behind where we needed to be months ago."
Pierce noted that one area that needs immediate attention is the sequencing of every "breakthrough case," which are cases in which people get infected even though they have been vaccinated. The CDC said at least 5,800 such breakthrough infections have been reported so far.
"We need to know whether infection after vaccination is the result of the vaccines, the variants, or some characteristic of the individuals who become infected," Pierce wrote in an email to NPR.
Others said sequencing needs to be focused strategically.
"More is better — but in addition to random sampling we need to do targeted sequencing of hospitalized people, immune-compromised and previously vaccinated people," said Mara Aspinall, a professor of medical practice expert at Arizona State University. "And we have to work globally on this issue."
Still, the funding is an important investment in the CDC, said Gigi Gronvall, a senior scholar at the Johns Hopkins Center for Health Security.
"What I was most worried about in the beginning of this process was that some new entity was going to be created that would analyze genomic information but would be not directly connected to CDC," she said. "That entity would probably fail but take a while and a lot of money with it in the process. This is the time to modernize and strengthen public health, and that begins with strengthening CDC."
The nation needs a "CDC-led national strategy" for sequencing, agreed David Relman, a microbiologist at Stanford University, "where questions are defined at the national level, question-asking coordinated at the state level, and data from states integrated in a strategic manner."
It's important these kinds of efforts continue to receive support going forward, said Jennifer Nuzzo, a senior scholar at the Johns Hopkins Center for Health Security.
"For this to work, there will need to be sustained funding," Nuzzo said. "I am concerned about building up an infrastructure using emergency funds. We have seen over and over again that capacities require sustained investment."
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