The Centers for Disease Control and Prevention has historically been the pinnacle of American public health. The agency has been a leading voice for evidence-supported health guidance and a watchdog for deadly disease outbreaks for decades. But in the past year, Health and Human Services Secretary Robert F. Kennedy, Jr. and the Trump administration have stripped CDC of funding, programs, staff, and agency leaders. News and insider reports indicate that these changes have dramatically disrupted operations – and A new report gives an inside look On the consequences for public health. An audit published last week History of Internal Medicine It was discovered that dozens of public CDC databases had gone dark. Thirty-eight regularly updated datasets, most of which relate to vaccines, are on hold until at least spring 2025.
“We believe the federal government’s 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 in terms of consistency, we weren’t seeing it here.”
Now state and local governments and independent organizations are trying to fill the void left by the CDC and other national public health agencies.
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Several (mostly blue) states have banded together to form regional health coalitions that are helping coordinate and curate vaccine guidelines. Governors are uniting to help communicate public health information and strengthen policy and funding across the state. Medical societies are also speaking out in defense of evidence-based health recommendations on topics ranging from vaccines to gender-affirming care.
“Trust in federal health institutions has declined under (Kennedy’s) watch to such an extent that you are now seeing the formation of these different regional coalitions,” says Jerome Adams. US Surgeon General under the first Trump administration and was Indiana’s health commissioner from 2014 to 2017. Adams and other experts say such efforts could help mitigate some of the damage, 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 generally a positive step,” says epidemiologist Jennifer Nuzzo, director of the pandemic center at Brown University. “But make no mistake: This is not going to replace what the CDC did, and Americans will be harmed as a result.”
The CDC hosts thousands of repositories of epidemiological data on everything from infections to death rates and vaccination rates. Real-time information is critical for an effective public health response. In the new report, the authors mark datasets that were not updated within their specified frequency (i.e., weekly or monthly) as well as an additional 30-day observation grace period. They found 38 databases that had been frozen – 34 of which were showing no new data entries for 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 frozen databases — 87 percent — relate to vaccines, such as monthly vaccination rates for COVID, respiratory syncytial virus (RSV) and influenza. A handful of databases addressed emergency department visits related to respiratory illnesses and drug overdose deaths.
The study couldn’t determine exactly why these dataset updates stopped, but experts have several theories. For example, national flu reporting stopped due to the government shutdown from October 1 to November 12, 2025. But Freilich says most delays continued after the shutdown. Maintaining routine data entries may be difficult due to CDC restructuring and staff reductions. There’s also a particularly ominous possibility: “We wondered whether some of this data collection was de-prioritized, especially as it relates to vaccines, and we wondered whether that might be political,” Freilich says.
Department of Health and Human Services spokeswoman Emily Hilliard said. 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 stopped reporting flu, COVID or RSV data. However, he did not respond to questions about data related to the stalled vaccine.
Kennedy has long been vocal about his anti-vaccination views and has taken several steps to roll back access to vaccines since taking the top job at HHS. Recently, the CDC reduced its childhood vaccination program – reducing the number of diseases covered from 17 to 11.
As data disappears and health recommendations loosen, 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 previously recommended by the CDC. Last week, 12 medical societies rejected the CDC’s new schedule and instead AAP’s guidance supported.
Different states have also worked together to strengthen access to the vaccine. State leaders and local public health advisers formed the West Coast Health Alliance and the Northeast Public Health Collaborative to establish regional vaccine recommendations in late 2025, after the Trump administration said healthy adults and children do not need to get COVID vaccines. The coalitions have since rejected other CDC changes to vaccine and health recommendations and instead supported the AAP’s recommendations.
“There is no medically justified reason to reduce recommendations for these dangerous diseases,” said Sean O’Leary, chair of the AAP’s committee on infectious diseases, at a recent press conference. “We have worked enthusiastically (with government agencies),” he said. “Unfortunately, the environment we are 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 directly with insurers to verify this.
The Governor is also moving forward. It is composed of fifteen governors so far from mostly blue states such as California, Illinois and New York state and the US territory of Guam. Governor’s Public Health AllianceAn agreement to support and ensure access to health care at the state level.
These state and territory leaders have long been “chief executives” on the front lines of health issues, says Raj Punjabi, the group’s public health adviser and former senior White House director for global health security and biodefense under the Biden administration.
“Governors are always in the driver’s seat when it comes to responding to health threats like avian flu, Mpox or infectious disease like RSV,” Punjabi says.
Freilich says some paused CDC databases will resume updates starting in December 2025. But any disruption could delay action and lead to loss of lives. When data goes dark, public health officials’ view of a population’s vulnerabilities and disease threats also becomes clouded.
“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 use to create a variety of tools and policy responses,” Freilich says.
During major health threats, states have historically called on the CDC to deploy federal epidemiologists and scientists to help trace sources of infection and deliver tools like vaccines to vulnerable communities. Sharing information about infection rates, symptoms and prevention measures may be important during a multi-state outbreak.
Fortunately, Freilich points out, “a lot of the public health data initially comes from state governments.”
Nuzzo and Adams generally agree that recent state and regional public health efforts have some strengths. Staff power and resources can be maximized by exchanging data and jointly planning response efforts or vaccine rollouts. Local leaders have a deeper understanding of their communities, which can lead to more effective policies.
“Culturally, what works in Boston is not the same thing that will work in Boise,” Adams says.
However, Panjabi emphasizes that these new groups, including the Governors Public Health Alliance, will not replace the federal government. This becomes extremely evident in national—or global—health crises such as pandemics.
Adams agrees. “If we have another pandemic, and there is no central authority that people can trust, who will people go to?” He says. “It doesn’t matter what the policies are in Indiana, if every spring and every autumn, a third of your state is traveling to other areas.”
Adams worries that such a fragmented public health system will ultimately worsen health disparities—that people from marginalized communities and populations will have difficulty accessing care. “You will see different standards of care and practice in different areas of the country,” he says, “and that is extremely worrying.”
Nuzzo shares similar concerns about the growing health divide as Democratic states and governors largely lead the charge: “It doesn’t matter where you live or what political party your governor or legislative representative is from, whether you have access to lifesaving tools like vaccines and information.”
