Adds Makary comments in paragraph 7, background in paragraphs 3-6 and 13-15, analyst comment in paragraph 17

By Bhanvi Satija

July 30 (Reuters) - The U.S. Food and Drug Administration's top vaccine official, Vinay Prasad, has left the agency after just three months as Director of the Center for Biologics Evaluation and Research, a government spokesperson said.

Prasad, an oncologist who was a fierce critic of U.S. COVID-19 vaccine and mask mandates, had been appointed in May by FDA Commissioner Marty Makary. Together they had promised to speed regulatory action and pilot new review pathways.

In recent days, criticism of his tenure has intensified around the agency's handling of a gene therapy for Duchenne muscular dystrophy from Sarepta Therapeutics SRPT.O.

The FDA-approved therapy played a role in the death of two teens who had advanced disease, and after a third death in a separate experimental gene therapy from the company, the FDA on July 18 asked Sarepta to stop all shipments of the approved DMD therapy, saying it had safety concerns.

Laura Loomer, a far-right activist and President Donald Trump ally, on July 20 posted a blog in which she called Prasad a "progressive leftist saboteur" who was undermining the agency's work. Loomer critiques earlier this year led to the ouster of national security officials.

On Monday, the Wall Street Journal's opinion section ran two pieces criticizing Prasad, one of which called him a Bernie Sanders acolyte in MAHA drag, referring to the Trump administration's "Make America Healthy Again" movement. Both said he was not basing regulatory decisions on whether drugs helped patients, but on price.

"When he saw some of these sort of smear pieces, he didn't want to be a distraction," Makary said of Prasad's departure in an interview with CNBC on Wednesday.

Prasad, whose departure was announced late on Tuesday, did not immediately respond to a request for comment.

The FDA on Monday changed course on Sarepta and said shipments to the main group of patients for the drug could restart.

Other changes under Prasad, who was also the agency's chief medical and science officer, included a new policy limiting the approval for COVID-19 vaccines, and his FDA division also rejected therapies from Replimmune REPL.O and Capricor Therapeutics CAPR.O.

Shares of Replimmune nearly doubled in value, while those of Sarepta and Capricor gained 11% and 18%, respectively on Wednesday.

Endpoints and STAT news first reported Prasad's departure.

Prasad was a physician who joined the agency from the University of California, San Francisco. He has had stints at the National Cancer Institute and the National Institutes of Health.

The Department of Health and Human Services, which oversees the FDA, did not immediately respond to a request for comment on when Prasad's successor could be announced.

The FDA and other health agencies have seen multiple shakeups in recent months, under the leadership of U.S. Health Secretary Robert F. Kennedy Jr.

Prasad's predecessor and longtime vaccine official at the FDA, Peter Marks, was ousted earlier this year, followed by gene therapy head Nicole Verdun.

"While another vacancy and another potential new face add uncertainty, we still think Prasad’s departure is a net positive for the sector as many of our conversations have been overwhelmingly focused on regulatory risk and what he may or may

not do," said Leerink analyst Joseph Schwartz.

(Reporting by Gnaneshwar Rajan, Shivani Tanna and Bhanvi Satija in Bengaluru; Editing by Caroline Humer and Bill Berkrot)

((Gnaneshwar.Rajan@thomsonreuters.com;))