By Betsy McKay, Brianna Abbott & Jennifer Calfas

Robert F. Kennedy Jr.’s handpicked panel of vaccine advisers had decided at its meeting late last week to restrict use of one shot and was about to vote on another when Dr. Daniel Crawford spoke up.

The panel was acting based on “predetermined ideology,” not science, said Crawford, a past president of the National Association of Pediatric Nurse Practitioners who specializes in treating childhood seizures. And the association, he said during a public comment period of the meeting, had lost trust in the advisory panel, which sets guidelines for the Centers for Disease Control and Prevention.

“Because of the lack of trust in the replacement committee, our organization is now relying on outside experts,” he said.

A growing contingent of doctors and policymakers say they have grown wary of federal health guidance since longtime vaccine skeptic Kennedy became Health and Human Services Secretary—and they are forming a parallel public-health universe outside the U.S. government.

Professional medical societies are releasing guidelines that depart from the government’s stance. Governors and state health officials are changing rules to ensure access to vaccines within their borders.

At the nucleus of the effort is an initiative that Crawford mentioned as a new trusted expert: the Vaccine Integrity Project, a group of public-health veterans and researchers who have banded together to sift through and analyze the latest studies on vaccines.

For years, doctors and public-health officials have been used to vaccine skeptics on the outside demanding changes to standard medical practice. Now the government is the one deviating from the norm, they said.

“It’s vital that providers and the public continue to have vaccine information that they can rely on,” Michael Osterholm, leader of the Vaccine Integrity Project, told doctors and policymakers recently.

President Trump addressed vaccines at an event on Monday, saying he thought that childhood shots should be spread farther apart and taken separately. He also linked taking acetaminophen, the key ingredient in Tylenol, during pregnancy to an increased risk of autism.

Autism researchers and doctors say that the claim is unproven, and that women are safe taking the medicine as needed, in consultation with their physician. “Not a single reputable study has successfully concluded that the use of acetaminophen in any trimester of pregnancy causes neurodevelopmental disorders in children,” said Dr. Steven J. Fleischman, president of the American College of Obstetricians and Gynecologists.

Kennedy said his department is closely examining the potential link between autism and vaccines, and that research on it had been actively suppressed. “It will take time for an honest look at this topic by scientists,” he said.

Organizations including the American Academy of Family Physicians, the Coalition of Autism Scientists and the American Psychiatric Association pushed back, saying that strong evidence shows vaccines don’t cause autism. Linking them is dangerous and distracts from research and resources needed to support people with autism, they said.

The resistance has been building since Trump tapped Kennedy and said he told him to “go wild on health.” In May, Kennedy posted a video on X announcing the removal of a Covid-19 vaccine recommendation for pregnant women and healthy children—a change that CDC leaders who recently resigned said they learned about through the social-media post.

In June, Kennedy removed all 17 members of the Advisory Committee on Immunization Practices, or ACIP—the panel that met last week—and replaced them with a team that includes vaccine skeptics. Distrust reached a boiling point at the end of August, when the Trump administration ousted the CDC’s newly sworn-in director, Susan Monarez, following clashes over vaccine policy with Kennedy.

Last week the new ACIP team—including several members appointed just a few days earlier—dialed back the government’s strong recommendation of the Covid vaccine, advising instead “individual decision-making” with a physician, nurse or pharmacist. The advisers also removed the government’s recommendation of a combined vaccine for measles, mumps, rubella and varicella, or chickenpox, for children under the age of 4, instead recommending the varicella shot be given separately.

Private insurance plans normally use ACIP recommendations to guide their coverage. Some insurers have signaled they would continue to cover vaccines that were recommended before the changes last week.

Doctors and other healthcare professionals protested the vote outcomes and the new ACIP’s departure from traditional procedures for weighing evidence based on a labor-intensive evaluation of the latest research.

The Infectious Diseases Society of America reacted in real-time. “Scientific evidence continues to strongly support broad COVID-19 vaccination,” the group posted on X. It also posted: “.@SecKennedy presents a clear and present danger to the American people and their families.”

The ACIP meeting “promoted false claims and misguided information about vaccines as part of an unprecedented effort to limit access to routine childhood immunizations and sow fear and mistrust in vaccines,” Dr. Susan Kressly, president of the American Academy of Pediatrics, said.

An HHS spokesman said that former health officials, Democrat-led states and “establishment insiders” eroded America’s trust and confidence in the public-health system during the Covid pandemic.

“Secretary Kennedy is restoring transparency, accountability, and evidence-based decision-making at the CDC and ACIP,” said Andrew Nixon, HHS director of communications. “Americans have the right to trustworthy government health guidance that’s based on science and evidence—not ideology or partisan politics.” Kennedy has previously criticized some medical societies for receiving donations from pharmaceutical companies.

Early this month, several states broke with the CDC on vaccine policy. Some formed coalitions to come up with their own public-health guidance.

“We have to step up as governors to do this because the federal government is not a trusted partner right now,” said Gov. Tina Kotek of Oregon, one of four states in a newly formed group they call the West Coast Health Alliance. The alliance issued guidelines for the Covid, RSV and flu vaccines for the fall season a day before the ACIP met.

The Vaccine Integrity Project is run by public-health veterans including Osterholm, who directs the Center for Infectious Disease Research and Policy at the University of Minnesota, as well as Dr. Rochelle Walensky, who was director of the CDC from 2021 to 2023. The vaccine project is a program of Osterholm’s center.

Along with a volunteer medical army of doctors and researchers, and with funding from billionaire philanthropist Christy Walton, they are analyzing the latest data on certain vaccines and helping coordinate and advise policymakers and physicians.

The American Academy of Pediatrics had already been working on its own evidence review when it started collaborating with the Vaccine Integrity Project. The AAP, in a rare divergence, broke with the CDC in mid-August to recommend Covid shots for healthy children.

State coalitions on the West Coast and Northeast took the findings from Osterholm’s group and medical associations into account.

Not all states are following along. On Sept. 3, leaders in Florida announced plans to end the state’s vaccine mandates, including those for schoolchildren, and the establishment of a state commission to implement “Make America Healthy Again” principles across the state.

Some former CDC leaders said a shift away from a central, authoritative voice in public health could cause confusion.

“Having a shadow CDC is maybe something that is sort of an attractive option. But that could become very complicated also for state leaders,” Dr. Jay Butler, the CDC’s former deputy director for infectious diseases, said of broad efforts to replicate the CDC’s work outside the government. He left the CDC earlier this year.

On alert

Osterholm conceived of the Vaccine Integrity Project after Trump picked Kennedy to be his health czar. The outspoken 72-year-old epidemiologist has spent decades working with U.S. and state government leaders in Republican and Democratic administrations on pandemics, bioterrorism and other disease threats, and is known for dire warnings—some of which have come true. He has a new book out on preparing for pandemics called “The Big One.”

The vaccine project isn’t a replacement for the ACIP, Osterholm said. It doesn’t write vaccine recommendations itself. And it doesn’t have access to all the data that the CDC has, including data from vaccine manufacturers.

“We’re not a shadow organization,” he said.

Vaccination is one of public health’s biggest tools for preventing and stopping infectious disease, he said—and given Kennedy’s stance, Osterholm was particularly worried about the ACIP.

This spring, Osterholm emailed Walton, the widowed daughter-in-law of Walmart founder Sam Walton, and her Alumbra Innovations Foundation to ask for support for a project to fill in the gaps that would be left if ACIP were changed or dismantled. Walton’s foundation already supported other work at Osterholm’s infectious-disease center. Walton dedicated $246,000 to initiate the project, which launched in April.

Osterholm and his team canvassed health organizations, medical societies, hospital systems and others, asking: If the CDC and ACIP were to be seriously compromised, what could Osterholm’s group do to help them with vaccine recommendations?

They reviewed the responses with a steering committee made up of public-health leaders, former Republican Gov. Asa Hutchinson of Arkansas and a former Republican congressman. Ultimately, they decided that the best thing they could do was research—the kind the CDC normally provides to these groups.

“We as a medical profession don’t have the bandwidth to have every society, every healthcare provider, every state health official do this on their own,” said Walensky, an infectious diseases physician and professor at Harvard Medical School.

Dr. Caitlin Dugdale is one of more than two dozen doctors and researchers Osterholm tapped for the project’s first priority: to analyze the latest data and studies on the Covid, flu and RSV vaccines ahead of the fall season.

On nights and weekends over the summer, Dugdale and the others combed through more than 1,400 studies that had come out since the last time the ACIP reviewed the three viruses and their respective vaccines, and narrowed them down to over 500 to include in their review.

The 40-year-old infectious diseases physician at Massachusetts General Hospital pulled her first all-nighter since she was a medical resident to pore over papers, and worked into the late hours after her daughter’s second birthday. Another volunteer canceled a scuba-diving vacation.

“It’s very important in this moment as doctors and scientists that we stand up and try to speak for science and speak for our patients,” Dugdale said.

Meanwhile, Osterholm and his team had one-on-one calls with each medical society and invited them to group meetings for updates on their research reviews.

Working with the vaccine project “helped us to focus,” said Dr. Kevin Ault, an obstetrician-gynecologist at Western Michigan University Homer Stryker MD School of Medicine. He was an ACIP member from 2018 to 2022 and helps write recommendations for the American College of Obstetricians and Gynecologists.

Actions Kennedy took in the spring, like removing a recommendation for pregnant women to get the Covid vaccine, had put ACOG on alert, he said. “We realized we need to get our act together very quickly,” said Ault, who was in a meeting with current ACIP members when they learned Kennedy had fired them.

The Vaccine Integrity Project’s data synthesis was critical, said Dr. Naima Joseph, a maternal-fetal medicine specialist at Boston Medical Center who worked on recommendations for two medical societies: ACOG and the Society for Maternal-Fetal Medicine.

“To have recently reviewed data that could have potentially refuted our recommendation was really necessary as we know those can change over time,” Joseph said.

Split recommendations

In August, a virtual audience logged into a webinar to hear the results of the project’s research on fall shots. Doctors and researchers presented their findings.

“What you’re about to hear is an analysis typically done by CDC,” said Osterholm. The webinar now has more than 9,000 views.

Dr. Erica Pan, director of the California Department of Public Health, tuned in to see if there were new safety concerns or other evidence that would warrant the changes HHS had made in Covid vaccine guidance.

She concluded that there weren’t. The West Coast Health Alliance, which includes California, is endorsing the recommendations from the AAP and other medical societies that split from the CDC’s changes, Pan said.

Staff at the Massachusetts Department of Public Health also watched the webinar. Massachusetts has required state insurers to cover vaccines recommended by the health department.

Boards of pharmacy in several states, including New Mexico and Pennsylvania, have changed their guidelines to allow pharmacists to administer the updated Covid vaccines under guidelines other than those issued by ACIP.

Osterholm’s team plans to make its data synthesis for the fall vaccines available to the public on an app this week so that researchers can see it and do more analyses. They’re also looking at which vaccines to evaluate next. The project’s ultimate goal is “to exist for the least amount of time possible,” Osterholm said. “We can’t wait for CDC to be restored to its previous level of excellence.”

Beyond vaccination, other academic researchers have archived federal environmental and health data, re-created searchable data tools, and sent out measles outbreak reports usually distributed by the CDC. Former CDC employees, meanwhile, are amplifying on social-media analyses and investigations that the agency continues to conduct but isn’t publicizing.

At least one cancer group is developing contingency plans in case Kennedy reshuffles another advisory panel, the U.S. Preventive Services Task Force, that determines which cancer screenings and other preventive services most insurers must cover.

Dr. Jennifer Hamilton, a family doctor in Philadelphia, has relied for years on the CDC’s guidance. She said she is particularly dismayed by the change in the Covid vaccine recommendation.

She’s relieved that medical societies are publishing their own recommendations and said she now trusts them more than the government.

“I’m not used to getting my recommendations on tweets from X,” she said.