CDC Steps Up Tracking of Virus Variants After Months of ‘Flying Blind’

The Centers for Disease Control and Prevention is investing $200 million in a new genome-sequencing pilot program to ramp up surveillance of COVID-19 variants, the administration announced Wednesday. The move comes months after the mutated viruses began spreading overseas—months in which the U.S. was “flying blind,” according to one expert.

The initiative will be run out of and overseen by the federal agency but will rely on partnerships with other academic and scientific institutions, officials said. National Testing Coordinator Carol Johnson said the program will attempt to scale the agency’s existing sequencing from 7,000 samples per week to about 25,000 a week, stressing the $200 million would kickstart a “pilot” program but was not enough to support sequencing efforts long term. More funding is needed through the president’s American Rescue Plan, she said.

“We remain in the midst of a very serious pandemic. The continued spread of variants… could jeopardize the progress we have made in the past month,” CDC Director Rochelle Walensky told reporters Wednesday, adding that it is unclear how long it will take the agency to scale up to sequencing to 25,000 samples a week.

“I don’t think this is going to be a light switch,” she said. “It is going to be a dial.”

Since the beginning of his time in office, President Joe Biden’s top COVID-19 advisers and health officials have warned about the spread of new variants. Over the last several weeks, more than 1,200 COVID-19 cases across 42 states have been reported as having been caused by a variant that originated in the United Kingdom (B117). Dr. Anthony Fauci, Biden’s chief medical officer, told reporters last week that he believed the variant would become dominant in the U.S. by the end of March. A variant that originated in South Africa (B1351) is also concerning health officials, though only 17 cases have been reported in the U.S., according to data collected by the CDC.

Experts say those case numbers are likely higher and that more sequencing needs to be completed in order for the administration to understand where and how the variants are being transmitted.

“The fact that we don’t know how much B117 is circulating means we are making all of our policy decisions… about opening restaurants and bars and other places … we’re doing it all blind,” said Dr. Ashish Jha, dean of Brown University’s School of Public Health.

“The timeline around B117 becoming dominant should also be a timeline where we need to get high-risk people vaccinated. But we’re coming up with totally different estimates of when [the variant] is going to come up and where. We’re… guessing on little bits of data here and there. We need to have much more thoughtful projections. The big lesson from last year… flying blindly does not land you where you want. It leads to crashes,” Jha added.

According to Professor Larry Gostin, director of the O'Neill Institute for National and Global Health Law at Georgetown University, “we should assume the worst” when it comes to the continued spread and variation of coronavirus strains, “irrespective of our ability to sequence.”

“The CDC and the states and localities have not developed the capacities of systematically sequencing viruses,” Gostin said. “We also do not have the data systems that enable us to monitor ongoing mutations.”

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Gostin called the lag behind sequencing efforts in the United Kingdom symptomatic of longer-term neglect of investing in public health infrastructure, both federally and on the part of states.

“States and localities, in particular, don't have the technical or laboratory capacity to sequence large numbers of viruses and we have no centralized data system to monitor incidence of new mutations,” Gostin said. “President Biden has promised to increase our genomic surveillance capacities, but that takes considerable funding and time. It requires investments in a skilled workforce, laboratories, and integrated data systems. We are far behind and we need to catch up quickly. Viral mutations are likely to be a major concern, not just for COVID-19 but also for a wide variety of novel diseases.”

According to Dr. Arnold Monto, a professor of epidemiology and global health at the University of Michigan and a former adviser to the World Health Organization, part of the problem is that until recently, sequencing work was being performed by evolutionary biologists, “and not to inform epidemiologic or vaccine studies.”

“The problem is that this has not been prioritized for surveillance purposes in the U.S.,” Monto told The Daily Beast. “This is changing now with the new emphasis but [it] will take time… This is just part of the national problem of the gap in broad pandemic planning.”

Fauci and other top health officials say the vaccines available to Americans, namely the Pfizer and Moderna vaccines, protect against the B117 variant, though a recent study shows a new mutation could make the vaccines less effective. Data gathered by the Novavax and Johnson & Johnson clinical trials in South Africa suggest their vaccines are less effective against the variant spreading rapidly in that country. And South Africa recently said it was halting the rollout of the Oxford/AstraZeneca vaccine because evidence from clinical trials suggested it did not work well against the variant.

Wednesday’s announcement comes after intense conversations inside the CDC and with the White House coronavirus task force about how to better track new mutations and their spread in the U.S. Officials have in recent days discussed the ways in which the federal government can expand its partnership with state health agencies and labs to scale up sequencing.

Speaking in his first major public event since he was sworn into office last month, President Joe Biden on Tuesday evening told a town-hall audience in Wisconsin that while there are an indeterminate number of variants circulating in the United States, there is “no evidence” that the current crop of vaccinations do not provide protection.

Biden did, however, caution that the vaccines may not be as effective at preventing certain strains—a major concern as the B117 variant is expected to become the dominant strain in the country.

“It may be that a certain vaccination for a certain strain may reduce from 95 percent to a lower percentage of certainty,” Biden said. “It may not be as effective.”

Still, Biden said the scientific consensus is that “if you’re eligible, if it’s available, get the vaccine”—no matter what the concerns about efficacy against novel variants.

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In November 2020, the CDC began receiving COVID-19 samples from states for sequencing through the National SARS-CoV-2 Strain Surveillance (NS3) system. The system scaled up slightly over the following months. By the end of January, the CDC was processing just 750 samples per week. This month, Walensky said the agency aimed to analyze as many as 6,000 virus genomes per week by the middle of February. But the agency has struggled to build up that effort in part because there has been little coordination between various labs and universities with the capacity to sequence and surveil, according to two Biden officials familiar with the matter.

For example, Washington University in St. Louis, which originally sequenced the human genome more than 20 years ago, is set up to sequence 1,000 COVID-19 samples per week, according to a recent report by Science magazine. But so far, the lab has only received 100 samples. The CDC program will attempt to create a national surveillance system by diverting samples to a select group of labs and institutions to complete the sequencing.

One of the main impediments to scaling sequencing is a lack of funding. Biden health officials said Wednesday that the $200 million dedicated for the CDC sequencing program is not enough—that surveillance of COVID-19 variants will require additional funding through the stimulus package currently being negotiated on Capitol Hill. House Democrats on the Energy and Commerce Committee have proposed a $1.75 billion bill dedicated to surveilling new variants, including through genome sequencing. That bill will likely be tied up on Capitol Hill for the next several weeks, a Democratic aide told The Daily Beast.

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