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In a typical year, several thousand samples from flu patients around the world arrive at the U.S. Centers for Disease Control and Prevention. They're crucial for understanding the virus's evolution and help form the bedrock of the World Health Organization's effort to design the next annual flu shot.

But this year, the flow of that data has come "pretty much to a grinding halt," says Demetre Daskalakis, who led the National Center for Immunization and Respiratory Diseases at CDC until he 

From February through July, he says CDC received only 427 samples, 60 percent fewer than the same time period last year. Only 12 countries had sent CDC samples by then, down 65 percent compared with 2024. CDC did not respond to NPR's request for comment.

"When those viruses are not coming in, we don't know what to put in the vaccine, and you're going to have less effective vaccines," says Daniel Jernigan, former director of the CDC's National Center for Emerging and Zoonotic infectious diseases in Atlanta, who also resigned in August.

Seven labs around the globe — CDC included — form a network of "WHO collaborating centers" that together make sense of all the virus samples sent in from National Influenza Centers in over 150 countries. But shipments to that whole network are also down so far this year, says Maria Van Kerkhove, interim director of the department of epidemic and pandemic threat management at WHO.

WHO typically foots the bill for the shipment of many of these samples around the globe. But on January 20, President Trump pulled out of the organization, accusing it of being "owned and controlled by China." The move blew a roughly billion-dollar hole in the organization's budget, and the fund to pay for shipments shrank. WHO is working to find other funding for the shipments, says Van Kerkhove. "We are committed to ensure that our ability to monitor and assess [flu] is not dependent on one member state."

But if this trend continues, scientists could have a patchier picture of influenza's evolution, says Kanta Subbarao, a flu researcher at Laval University who used to run one of those collaborating centers in Melbourne, Australia. "A reduction in the ability of national influenza centers to share samples will be a huge blow to influenza surveillance."

Less data could mean a less effective flu shot

In February and September each year, scientists from these WHO collaborating centers meet to decide what influenza strains next year's flu shot should target for the northern and southern hemisphere flu seasons.

"Because we can't predict exactly which virus will dominate in the next season, the vaccine contains multiple strains to try to protect the population against what will come," says Subbarao.

Picking those strains is a bit of a gamble, but one made less risky by the work of more sophisticated labs, like CDC.

"What we do is work up those viruses. We sequence them. We do tests in ferrets," says Daskalakis. "We do all this stuff to be able to sort of say this virus has a higher pandemic potential, this is a virus that is going to totally circulate next season for flu."

Fewer samples will make those analyses harder, says Arnold Monto, an epidemiologist at the University of Michigan. "It reduces the amount of data that the decision can be made on."

WHO officials declined to share precisely how much less data is getting shared with collaborating centers. And there's still time before February's meeting for countries to send in more samples. But Daskalakis worries that the slowdown at CDC could be harder to reverse, as countries may be wary of sharing data with the U.S. after its withdrawal from WHO.

If CDC becomes increasingly out of the loop, Daskalakis says it'll make the U.S. less prepared for a possible flu pandemic. In addition to getting thousands of influenza virus samples from around the world, CDC typically receives about a dozen "candidate vaccine viruses" from the WHO network that serve as the raw material for mass producing flu vaccines in eggs.

"By the time I left CDC at the end of August, we had received two, not a dozen," says Daskalakis, which could make it harder to scale up a response to a potential pandemic flu outbreak.

CDC's view of other dangerous pathogens, from COVID-19 to polio, is becoming dimmer too, Daskalakis says. That makes it harder for the agency to find concerning variants of any virus that might spark the next big outbreak.

"The system is designed to be able to find needles in the haystack if it gets fed enough, if it gets enough data," says Daskalakis. "If it doesn't get fed enough, it's going to take longer to find the needle in the haystack."

And as Daskalakis learned during the COVID-19 pandemic, that time can cost lives.

"Every day that we delayed, every day we had less coordination, was a day that tens, hundreds, thousands of people were going to die," he says. If a similar virus hits as the U.S. continues to isolate itself, he foresees a repeat.

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Jonathan Lambert

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