The Centers for Disease Control and Prevention has historically been the pinnacle of U.S. public health. The agency has been a leading voice for evidence-backed health guidance and a sentinel for deadly disease outbreaks for decades. But over the past year, the CDC’s authority has crumbled as the agency has replaced subject matter experts with vaccine deniers and discarded evidence in favor of ideology.
Secretary of Health and Human Services Robert F. Kennedy, Jr., and the Trump administration have stripped the CDC of funding, entire programs, staff and prominent agency leaders. News and insider reports indicate that the ongoing chaos within the hollowed-out agency has interrupted operations dramatically—and a new report gives an inside look at the consequences for public health. An audit published last week in the Annals of Internal Medicine revealed that dozens of public CDC databases have gone dark. Thirty-eight routinely updated datasets, most related to vaccines, have been inexplicably paused since at least the spring of 2025.
“We tend to assume that federal government data is solid. It’s reliable; it’s consistent,” says study co-author Janet Freilich, a Boston University law professor, who has been studying changes in government data in recent years. “At least on consistency, we weren’t seeing that here.”
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Now state and local governments and independent organizations are trying to fill the vacuum left by the CDC and other national public health agencies.
Several (mostly blue) states have joined forces to create regional health alliances that are helping to coordinate and preserve vaccine guidelines. Governors are banding together to help communicate public health information and strengthen policy and funding across state lines. Medical societies are also speaking out in defense of evidence-based health recommendations on subjects ranging from vaccines to gender-affirming care.
“Trust in federal health institutions has plummeted under [Kennedy’s] watch to the extent that you are now seeing the formation of these different regional coalitions,” says Jerome Adams, who served as U.S. surgeon general under the first Trump administration and Indiana’s health commissioner from 2014 to 2017. Adams and other experts say such efforts can help mitigate some of the losses, but they worry that a patchwork public health network could widen health care gaps and have other long-term effects.
“I think the fact that these states are coming together is a generally positive step,” says Jennifer Nuzzo, an epidemiologist and director of the Pandemic Center at Brown University. “But make no mistake: it is not going to replace what the CDC once did, and Americans will be harmed as a result.”
The CDC hosts thousands of repositories of epidemiological data on everything from infection to mortality and vaccination rates. Real-time information is crucial for an effective public health response. In the new report, the authors flag datasets that hadn’t been updated within their designated frequency (i.e., weekly or monthly) plus an additional 30-day observational grace period. They found 38 databases that had been paused—with 34 showing no new data entries in six months or more. In a follow-up analysis on December 2, 2025, only one of the 38 datasets had been updated.
The majority of the paused databases—87 percent—pertained to vaccines, such as monthly vaccination rates for COVID, respiratory syncytial virus (RSV) and influenza. A handful of databases addressed emergency department visits from respiratory diseases and drug overdose deaths.
The study could not determine exactly why these datasets ceased updating, but experts have several theories. The government shutdown from October 1 to November 12, 2025, stalled national flu reporting, for example. But Freilich says most of the delays persisted beyond the shutdown. The CDC’s reorganization and staffing cuts may have made it hard to maintain regular data entries. There’s also a particularly ominous possibility: “We wondered if there was a deprioritization of some of this data collection, particularly as it relates to vaccines, and we wondered if it might be political,” Freilich says.
Department of Health and Human Services spokesperson Emily Hilliard told Scientific American that “changes to individual dashboards or update schedules reflect routine data quality and system management decisions, not political direction.” Hilliard denied that the CDC had stopped reporting flu, COVID or RSV data. She didn’t address questions about paused vaccine-related data, however.
Kennedy has long been vocal about his antivaccine views and has made several baseless moves to roll back vaccines since taking the helm at HHS. Most recently, the CDC scaled back its childhood vaccine schedule—reducing the number of diseases covered from 17 to 11.
As data disappears and health recommendations slacken, independent groups are rallying together to fill the public health data and leadership void.
The American Academy of Pediatrics (AAP) released its own childhood vaccine schedule, which recommends all the shots that had been previously recommended by the CDC. Last week 12 medical societies rejected the CDC’s new schedule and instead endorsed the AAP’s guidance.
Individual states have also teamed up to reinforce vaccine access. In the fall of 2025 state leaders and local public health advisers created the West Coast Health Alliance and the Northeast Public Health Collaborative to establish regional vaccine recommendations after the Trump administration said healthy adults and children don’t need to get COVID vaccines. The alliances have since rejected other CDC changes to vaccine and health recommendations and have instead backed the AAP’s recommendations.
“There’s no medically justified reason to downgrade the recommendations for these dangerous diseases,” said Sean O’Leary, chair of the AAP’s Committee on Infectious Diseases, in a recent press briefing. “We have worked [alongside] government agencies enthusiastically,” he added. “Unfortunately, the environment we’re operating in today is different.”
The CDC has said all vaccines will still be covered by insurance, but the AAP and medical experts are working to verify that directly with the insurers themselves.
Governors are also stepping up. Fifteen governors—so far of mostly blue states, such as California, Illinois and New York State, and the U.S. territory of Guam—formed the Governors Public Health Alliance, a pact to support and ensure access to health care across state lines.
These state and territory leaders have long been “chief executives” on the front lines of health issues, says Raj Panjabi, a public health adviser to the group and a former White House senior director for global health security and biodefense under the Biden administration.
“Governors have always been there in the driver’s seat when it comes to responding to health threats like infectious disease such as avian flu, mpox or RSV,” Panjabi says.
Some of the paused CDC databases have resumed updates since December 2025, Freilich says. But any interruption can delay action and cost lives. When data go dark, so does public health officials’ view of population vulnerabilities and disease threats.
“What we’re seeing now, from this study and previous work, is that the federal government is not always a reliable source of these basic, granular pieces of information that we tend to use to build a variety of tools and policy responses,” Freilich says.
During major health threats, states have historically called upon the CDC to deploy federal epidemiologists and scientists to help trace sources of infection and deliver tools, such as vaccines, to vulnerable communities. Information sharing about infection rates, symptoms and prevention measures can be key during a multistate outbreak.
Luckily, Freilich points out, “a lot of public health data comes from state governments initially.”
Nuzzo and Adams generally agree that the recent state and regional public health efforts have some strengths. Exchanging data and jointly planning response efforts or vaccine rollouts can maximize staff power and resources. Local leaders have a more intimate understanding of their communities, which may lead to more effective policies.
“Culturally, what works in Boston isn’t the same thing that’s going to work in Boise,” Adams says.
Panjabi emphasizes, however, that these new collectives, including the Governors Public Health Alliance, do not replace the federal government. That becomes extremely apparent in national—or global—health crises, such as pandemics.
Adams agrees. “Who do people go to if we have another pandemic, and there’s no central authority that people trust?” he says. “It doesn’t matter what the policies are in Indiana if, every spring and every fall break, a third of your state is traveling to other areas.”
Adams worries that such a fractured public health system will ultimately worsen health disparities—that people from marginalized communities and populations will have a harder time getting access to care. “You’re going to see different standards of care and practice in different regions of the country,” he says, “and that’s deeply concerning.”
Nuzzo shares similar concerns about growing health divides as democratic states and governors largely lead the charge: “It should not matter where you live or what political party your governor or legislative representatives are, whether or not you have access to lifesaving tools like vaccines and information.”