Dr. Rochelle Walensky, the director of the Centers for Disease Control and Prevention, will step down from her place on June 30, she introduced on Friday, capping a tumultuous tenure on the nation’s main public well being company because it struggled to rein within the Covid-19 pandemic, the best menace to American well-being in a long time.

Her departure comes because the administration contends with main vacancies in its Covid-19 response staff. Dr. Ashish Jha, the White House’s Covid-19 coordinator, plans to depart his place this month, together with different key officers, together with Dr. Nahid Bhadelia, a White House adviser on the worldwide response. A brand new White House pandemic workplace has no chief or staffing.

The administration plans to finish the general public well being emergency on May 11, closing main applications — like entry to free assessments — that had helped maintain Americans by way of the worst days of the pandemic.

But the virus has not disappeared. It continues to be killing roughly 1,000 Americans every week and hospitalizing much more. The management vacuum arrives at a precarious time.

In an agencywide assembly, Dr. Walensky admitted to having combined feelings about her resolution and broke down in tears, in line with individuals who had been on a convention name together with her.

“I took on this role with the goal of leaving behind the dark days of the pandemic and moving the C.D.C. — and public health — into a much better and more trusted place,” she mentioned in a subsequent electronic mail to the company’s workers.

Dr. Walensky didn’t reply to a request for remark. Senior administration officers and out of doors specialists have mentioned that Dr. Walensky struggled with an unwieldy management construction on the Department of Health and Human Services, of which the C.D.C. is part. The company’s relationship with the White House was typically tense, as her recommendation to the general public sometimes seemed confusing or contradictory.

An individual aware of her considering mentioned that Dr. Walensky had additionally wearied of harassment from members of the general public who have been sad with pandemic restrictions and of lengthy commutes between the C.D.C.’s places of work in Atlanta and her residence in Massachusetts.

Andy Slavitt, a key adviser on the White House Covid-19 staff in 2021, praised Dr. Walensky’s efforts to do a job “that’s easy to criticize and tough to do.”

“You show up in an emergency status with a specific job to do,” he added. “It’s almost like a mission, with a beginning and end. Even though she was running an agency, running an agency during wartime is different than running an agency during peacetime.”

Public well being specialists mentioned the information had come as a shock, and a few expressed disappointment that she was leaving.

“I think it is a loss for the C.D.C. and for the nation,” mentioned Dr. Megan Ranney, the deputy dean for Brown University’s School of Public Health. “I know that it has not been easy, not just because of Covid but because of the politicization of science.”

Dr. Ranney mentioned that she had obtained hate mail and private assaults however that what she had skilled was “only the tip of the iceberg” in contrast with how Dr. Walensky had been handled.

Dr. Celine Gounder, a former adviser to the Biden administration who has recognized Dr. Walensky since 2004, mentioned, “Her departure signals to me that the C.D.C. is more broken and the federal government’s commitment to public health is even weaker than I’d thought.”

Dr. Walensky grew up in Potomac, Md., in a household of revered scientists. She skilled in medication at Johns Hopkins University and, in 2001, joined the school at Harvard, the place she developed a status as a rigorous researcher and a beneficiant mentor.

Before her tenure as C.D.C. director, Dr. Walensky led the infectious illnesses division at Massachusetts General Hospital, the place she noticed the pandemic’s devastation firsthand. She was famous for her work on well being care coverage, significantly in H.I.V.

But with little expertise working in authorities and main giant establishments, Dr. Walensky was an surprising option to information an company with a workers of about 11,000 individuals.

Dr. Walensky took the helm of the beleaguered company in January 2021. She had a near-impossible process forward of her: restoring the status of the once-storied C.D.C. when public belief within the company, and science extra broadly, was quick ebbing.

The C.D.C. had been pilloried for the reason that begin of the pandemic for missteps in testing, altering recommendation on masking, and antiquated surveillance and information methods. Trump administration officers hectored the company’s leaders, rewrote its steerage and meddled with its analysis studies, undermining the morale of scientists even because the disaster ballooned.

“She insisted that people act more promptly and in a more focused way, so she stimulated people to do things perhaps a little bit differently than they had,” mentioned Dr. William Schaffner, an infectious illnesses doctor at Vanderbilt University who works carefully with the company.

“Morale within the C.D.C. distinctly improved under her leadership,” he added.

But the pandemic proved to be tough floor even for somebody as revered and well-liked as Dr. Walensky. She was roundly criticized by specialists for advising individuals to cease carrying their masks simply weeks earlier than the Delta variant of the coronavirus pummeled the nation.

And after shortening isolation necessities even because the Omicron variant introduced the nation to a standstill, she was accused of letting financial pursuits outweigh scientific warning.

Anne Sosin, who research well being fairness at Dartmouth, mentioned that Dr. Walensky had typically taken the autumn for Biden administration choices, however that she additionally might have accomplished extra to stage with the general public in regards to the rationales for these choices.

Still, Ms. Sosin added, “From the outside, it has sometimes appeared that Dr. Walensky has lacked the courage to say no to decisions that really undermined public health.”

Republicans in Congress repeatedly requested for her resignation and painted the company as a failed establishment in hearings on the pandemic. But some specialists felt Dr. Walensky had accomplished her greatest with an unattainable hand.

“The public — and even health professionals — wanted consistency in message and messaging that was not possible, because Covid has simply never been a static threat,” mentioned Dr. Jeremy Faust, an emergency medication doctor and well being coverage professional at Brigham and Women’s Hospital in Boston.

Dr. Daniel Pollock, who led Covid surveillance for a number of months in 2020 and retired in November 2021 after 37 years on the company, mentioned: “The timing of this leadership transition is very problematic. I worked at C.D.C. under 10 different directors, and when they leave abruptly, for whatever reason, the ripple effects take a big toll.”

It was not instantly clear who would lead the C.D.C. after Dr. Walensky’s departure. Some scientists mentioned Dr. Walensky’s successor must be a public well being generalist attuned to social issues and easy methods to run a big federal company, not a physician-scientist like Dr. Walensky.

“This has to be a public health person,” mentioned Katelyn Jetelina, an epidemiologist who writes a popular newsletter and has been advising the C.D.C. for the previous yr. “We think about treating millions of people at one time, rather than this initial training of one-on-one physician care.”

Despite the controversy surrounding her tenure, Dr. Walensky’s electronic mail to workers members on Friday advised that she believed she had improved the company’s standing.

“We collectively moved C.D.C. forward, reorganizing the agency and embarking on the necessary work to orient the enterprise toward public health action and foster accountability, timeliness and transparency in our work,” she mentioned.

During her time on the C.D.C., Dr. Walensky famous, the company administered greater than 670 million Covid vaccine doses and offered steerage on immunization, social distancing and masking that “protected the country and the world from the greatest infectious disease threat we have seen in over 100 years.”

Dr. Walensky acknowledged the agency’s failings final yr and promised to reorganize it, remodeling its means to reply rapidly to public well being crises. Some organizational modifications have been introduced, however it’s unclear whether or not any of them have made a cloth distinction within the C.D.C.’s work.

Among different modifications, Dr. Walensky helped create an workplace that’s extra organized and empowered to work with state and native well being developments, mentioned Dr. Joshua Sharfstein, vice dean for public well being observe and neighborhood engagement on the Johns Hopkins University Bloomberg School of Health.

“It puts the agency in a position to have a vision for how the nation’s very convoluted public health system holds together,” he mentioned. “One of the jobs as the director is going to be to take the structure that Dr. Walensky has left and use it.”

Under her management, Dr. Walensky mentioned in her electronic mail to workers members, the company bolstered its public well being infrastructure and secured lots of of hundreds of thousands of {dollars} to modernize the nation’s information infrastructure.

She additionally declared racism a critical public well being menace, she famous, and led the company in its efforts to include a multinational mpox outbreak, in addition to the unfold of Ebola in Uganda.

“We made this world a safer place,” Dr. Walensky mentioned. “I have never been prouder of anything I have done in my professional career.”

Emily Anthes, Sharon LaFraniere and Benjamin Mueller contributed reporting.