Rick Bright, the virologist who claimed the Trump administration retaliated against him last year by ousting him from his job, has settled his whistle-blower complaint against the federal government and will receive back pay and compensation for “emotional stress and reputational damage,” his lawyer said Monday.

Dr. Bright’s removal last April as head of the Biomedical Advanced Research and Development Agency created upheaval within the Department of Health and Human Services in the earliest days of the coronavirus pandemic.

He said he was removed from his post after he pressed for rigorous vetting of hydroxychloroquine, an anti-malaria drug embraced by President Donald J. Trump as a coronavirus treatment, and that the administration had put “politics and cronyism ahead of science.”

Those allegations are still being investigated by the Office of Special Counsel, which protects federal whistle-blowers. Under Mr. Trump, H.H.S. officials denied any wrongdoing.

The Biden administration confirmed the settlement of the case on Monday in a statement praising Dr. Bright, who advised President Biden during his transition.

“The agency would like to thank Dr. Bright for his dedicated public service and for the contributions he made to addressing the Covid-19 pandemic while he served as BARDA director,” the statement said. “We wish him well in his new endeavors.”

Neither side disclosed details or specifics of the settlement. But Dr. Bright’s lawyer, Debra S. Katz, said her client had been compensated to the fullest extent allowed by the law. She said he will receive back pay, as well as damages to cover the costs of private security and temporary housing that he required after receiving threats. He will also receive compensation, Ms. Katz said, for distress “associated with the disparaging comments and threats” made by administration officials including Mr. Trump, who had blasted Dr. Bright on Twitter as a “creep” and a “disgruntled employee.”

Dr. Bright now works for the Rockefeller Foundation, where he is developing a new institute devoted to pandemic prevention that will function as a hub for scientists in government, the private sector and academia. The goal is to identify new pathogens, he said in an interview. He said he was glad to have the episode behind him.

“Going through the assault that I experienced from the last administration, going through the public criticism from the White House and H.H.S. leadership when I was just trying to do my job, put a lot of stress on me,” he said. “They were trying to find anything they could to disparage me and discredit me.”

After clashing with his bosses, Dr. Bright was assigned to a narrower role at the National Institutes of Health to work on a “Shark Tank”-style program to develop coronavirus treatments. He later went on sick leave because of hypertension, a spokeswoman said at the time. In the interview Monday, Dr. Bright said that at the height of the controversy, he also received a diagnosis of skin cancer.

Ultimately, he quit the government — a departure that Ms. Katz characterized as effectively a termination, because, she said, he had not been given any meaningful work.

Ms. Katz said the settlement was especially satisfying to her. “Many times, whistle-blowers come forward and that’s the end of their career,” she said. But Dr. Bright, she said, has “gone from being persona non grata under the Trump administration to being a respected and important subject matter expert.”

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