Last summer, Walensky launched a reorganization of the CDC, acknowledging that its “performance did not reliably meet expectations” during the pandemic.

She said she wanted to modernize the agency and rehabilitate its reputation.

In a statement, Biden said, “Walensky leaves CDC a stronger institution, better positioned to confront health threats and protect Americans.”

In an internal email announcing her departure, Walensky wrote that she would step down on June 30.

She gave no specific reason for the decision to resign, writing that “at this pivotal moment for our nation and public health, having worked together to accomplish so much over the last two-plus years, it is with mixed emotions that I will step down.”

Walensky touted the administration’s Covid response, the CDC’s decision to declare racism a serious public health threat and its efforts to contain mpox among the accomplishments on her watch.

“I have never been prouder of anything I have done in my professional career,” she wrote.

Walensky had earlier this year notified top White House aides, including Chief of Staff Jeff Zients, that she planned to leave, an administration official granted anonymity to discuss her departure said. The two ultimately settled on making the decision public around the end of the Covid public health emergency.

Still, her resignation blindsided many health officials throughout the administration, many of whom had expected her to stay on at least through the end of the year — if not the end of Biden’s first term.

And Walensky in her email offered little in the way of a transition plan, writing only that “more information will be shared with you about next steps for CDC.”

Georges Benjamin, executive director of the American Public Health Association, said Walensky’s departure will not adversely impact the government’s transition out of the public health emergency.

“But it’s more turmoil for the agency, it’s always unfortunate when a leader leaves,” Benjamin said. “I think she did a good job and I’m sorry to see her go.”

‘The need for change’

Walensky’s supporters point to her success in overseeing the vaccination of millions of Americans against Covid, the successful effort to control the mpox outbreak of 2022, and her efforts to improve the CDC.

But her critics, including many Republicans in Congress, see Walensky as responsible for confusing public health messaging that didn’t help end the pandemic, but did reduce trust in the government.

And public trust in the CDC has dropped dramatically since April 2020. Scores of lawsuits have been filed by critics of its pandemic performance challenging the agency’s authority, raising the very real question of whether Americans will listen to federal health officials’ recommendations the next time a national health crisis rolls around.

Walensky sought to regain lost ground by being more forthcoming about the CDC’s failings in recent months.

“The agency recognizes — and it’s been very public — that we haven’t been able to be as nimble as we’ve needed to be,” Walenksy told POLITICO in an interview in October. “I think people within the agency recognize the need for change.”

A year ago, she ordered a review of the agency’s Covid response and structure, and in August, she introduced a spate of reforms to improve its ability to move faster during an outbreak, communicate better with the public and be better prepared for the next public health emergency.

Walensky walked into an “impossible job,” said Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota.

Both the state of the pandemic at the time, the institutional challenges of her agency, and the disjointed national public health system created challenges anyone would have struggled with, he said.

“I don’t know who could have been the director of CDC at this time and been seen as a good steward of public health,” he said. “If they put you as a driver going down the side of the mountain and you realize halfway you don’t have brakes, good luck. I don’t care how good a driver you are.”

‘The CDC alone can’t fix this’

Walensky was appointed in December 2020 by then-President-elect Biden. As the head of Massachusetts General Hospital’s infectious disease division and a professor of medicine at Harvard Medical School, Walenksy was widely respected in public health circles for her work, including decades of HIV research.

But her lack of experience navigating a federal agency — let alone one in the fight of its life — raised concerns.

“She didn’t really come from a more traditional public health background and she didn’t have a lot of experience in government,” said Marcus Plescia, chief medical officer at the Association of State and Territorial Health Officials.

She took over the agency from Robert Redfield at a deeply fraught moment. One year into the pandemic, the CDC had been beset by devastating testing failures, confusing communication and health guidance and disruptive political meddling by Trump-era political appointees, among other problems. Morale inside the agency’s ranks was low, and Americans’ distrust of its work was already growing.

Walensky said at the time that her work during the AIDS crisis had prepared her for the challenge and pledged to combat the pandemic with “science and facts.”

But during her first year on the job, she, too, quickly came under fire, particularly for her communication and messaging. The agency was not holding regular Covid briefings, and Walensky did not hold a solo news conference until about a year into her directorship.

She also faced backlash over the agency’s Covid public health guidance, which was criticized by both those who felt the agency wasn’t doing enough to protect the public and those who felt it was doing too much and overstepping its mandate.

During the height of the Omicron wave, in which hundreds of thousands of new cases and thousands of deaths were reported each day, the CDC changed its isolation guidelines, saying people who tested positive but had no symptoms needed to isolate at home for only five days, down from the previous 10. A few months later, the agency revised its masking guidance, moving away from basing it on case numbers to giving more weight to how much pressure hospitals were under.

In an interview with POLITICO at the time, Walenksy said it was not solely the CDC’s responsibility to battle the pandemic. “The CDC alone can’t fix this,” Walensky said. “Businesses have to help, the government has to help, school systems have to help. This is too big for the CDC alone.”

As Covid cases began to decline in the spring of 2022, Walensky soon faced another unexpected test: Mpox. Though the federal government was better prepared for the unprecedented outbreak — both an FDA-approved vaccine and treatment already existed — than it had been for Covid, the agency’s early response again faced problems.

The CDC’s testing process for the rare virus was clunky and hard for doctors to use, leading to an undercount of cases in the outbreak’s early days. Then, as cases started to rise rapidly in July, the administration’s outbreak response was beset by vaccine shortages and slow distribution, a pivot to an emergency vaccine administration method that confused patients and inequitable vaccine distribution among different racial and ethnic groups.

“After almost three years of the Covid pandemic, you would think that the public health agencies responsible for our preparedness and response would be prepared for anything,” said then-Sen. Richard Burr (R-N.C.) during a September HELP Committee hearing. “By every measure, the response from the Biden administration on the monkeypox crisis has been a catastrophic failure.”

By late October, however, new daily mpox cases were in the single digits, down from hundreds at their summer peak. Though the agency’s own analysis says the virus could continue to circulate among certain groups, some observers credit Walensky and the CDC for containing the crisis.

“We’re sitting on a public health success,” said Kathleen Hall Jamieson, director of the Annenberg Public Policy Center at the University of Pennsylvania. “It’s very difficult to get the public to quickly learn something. And when we see jumps — big jumps — in numbers in a matter of months on a public health issue, that means they did a good job.

“Sometimes when we’re looking at the public health world, we forget successes,” she added. “We just look at the failures.”

Restoring confidence

Both the Covid and mpox crises raised fundamental questions about the way the CDC functions within the federal government.

Allegations from lawmakers that the nation’s premier public health agency has been compromised by political pressure did not end with the Trump administration, they just started to come from Republicans.

At the same time, public health experts, including hundreds of Walenksy’s former colleagues at Mass General, were incensed over the Biden administration’s decision to continue to use a CDC public health order called Title 42 to turn away migrants at the U.S. border, despite the agency’s own scientists being against it.

It will end when Biden ends the Covid public health emergency on May 11.

At the same time, a string of lawsuits has challenged the CDC’s authority to impose its guidance on Americans. A year ago, a Trump-appointed federal district court judge in Florida ordered an injunction against the CDC’s mandate that people wear masks on public transportation, saying the order was outside the agency’s authority.

The administration appealed the case, which is still in the courts, a move aimed less at preserving the mandate under the current pandemic circumstances than preserving the agency’s powers to make public health rules in future health emergencies.

Walensky’s reform agenda for the agency, launched in August, is ultimately designed to not just help the agency function better, but to restore confidence in the CDC in Washington, the U.S., and the world.

She laid out plans to speed up data delivery, make public health guidance easier to understand, build up the CDC’s communications team, strengthen the CDC’s national laboratory system and shift internal incentives for staff away from publishing in scientific journals and toward making practical policy recommendations, among other measures.

She emphasized the need to share research and data sooner and be more open with the public about what agency scientists do — and don’t — know.

But she told POLITICO that the CDC’s inability to compel states to share information about disease outbreaks is getting in the way of that effort and the agency needs both broader authority to collect that data and more money from Congress to draw in new talent and train the public health workforce to speed up the information flow to the public.

Public health experts agree that isn’t likely to happen this year given Republican control of the House.

A law enacted in December will require future CDC directors, starting in 2025, to receive Senate confirmation.

But under current law, Biden will be able to appoint a new CDC leader without worrying about a bruising confirmation battle ahead of the 2024 election.

David Lim and Shawn Zeller contributed to this report.