The consequences of the order will be felt immediately. Fortune can no longer distribute funds to her collaborators at other universities and she must cease using federal money for any purpose related to the study. That means scientists may have to be laid off.

Researchers may also have to kill macaques, a type of primate, being used in a vaccine study at the University of Pittsburgh that is funded by the Harvard contract. Killing the animals may be necessary, Fortune said, because they are no longer allowed to use federal funds to feed and care for them.

“The macaques, can you believe, they’re so precious. It’s such a heavy responsibility to work with them and to just be asked to kill them halfway through the study…” Fortune said, trailing off.

“Anybody who has animal studies ongoing…is looking at killing the animals” if funding is cut, Fortune said.

When the antisemitism task force announced on March 31 it was reviewing nearly $9 billion of federal grants and contracts tied to Harvard, it said those funds were destined for the university itself and also its affiliated institutions, such as research institutes and Boston-area teaching hospitals.

That left many researchers and hospital leaders at institutions such as Mass General Brigham and Boston Children’s Hospital wondering if their research funding would be affected. But on Tuesday, a Department of Education spokesperson, Madison Biedermann, said, “The hospitals were not impacted in the freeze.”

That appears to mean that the $2.26 billion of frozen funding was destined only for Harvard University itself, not its affiliated institutions.

Fortune is a researcher at the Harvard T.H. Chan School of Public Health, which is part of the university. Her NIH contract was the first one listed in a government memo describing funding that was targeted in the task force’s review.

In an interview last week, Fortune described the multi-site tuberculosis research as the most significant work of her career. Joel Ernst, chief of the division of experimental medicine at the University of California San Francisco and a member of an external board that advises the NIH on tuberculosis research conducted under Fortune’s contract and two others, called the work “unparalleled research” that “very quickly translates to designing vaccines to provide protection and immunity to control the global tuberculosis pandemic.”

That research is now at risk. Nevertheless, Fortune said she supported the decision of Harvard’s leaders to defy the Trump administration’s demands. “I feel better about going down on the right side of this action,” she said.

According to the letter Fortune received from the NIH, the stop-work order will remain in effect for 90 days “unless Harvard University and the [NIH] mutually agree to a further period.”

Spokespeople for the Department of Education, one of the agencies leading the task force, declined to comment on the stop-work order. A Harvard spokesperson referred the Globe to an open letter from Harvard president Alan Garber yesterday.

In the letter, Garber said a decades-long partnership between universities and the American government “has led to groundbreaking innovations across a wide range of medical, engineering, and scientific fields.”

“For the government to retreat from these partnerships now risks not only the health and well-being of millions of individuals but also the economic security and vitality of our nation,” he said.

Mike Damiano can be reached at [email protected].