A researcher works in the stem cell lab on the Stanford University campus in Palo Alto, Calif., in 2012. (Paul Sakuma/AP)

The Trump administration has thrown into doubt a multimillion-dollar research contract to test new treatments for HIV that relies on fetal tissue — work targeted by antiabortion lawmakers and social conservatives aligned with the president.

The turmoil over the National Institutes of Health contract with the University of California at San Francisco is part of a building battle between conservatives opposed to research using fetal tissue and scientists who say the material is vital to developing new therapies for diseases such as AIDS and Parkinson’s.

The researcher who runs the UCSF laboratory was given a 90-day extension on the contract, rather than another year’s $2 million installment, as had been routine. A few days earlier, she had been told the money would be cut off immediately, according to a virologist familiar with the events.

Almost every drug for treating or preventing HIV infection has been tested at the UCSF laboratory and an affiliate through this method, which involves incubating human T cells in mice. Scientists say there is no substitute to assess drugs at that early stage of development. The National Institutes of Health contract has provided all the funding for the lab’s HIV work.

The sudden uncertainty about the future of the laboratory on the West Coast has erupted as health officials in Washington are reconsidering whether the government should alter its support of research involving fetal tissue “in light of the serious regulatory, moral, and ethical considerations involved,” as they announced the review in September.

In recent weeks, Health and Human Services Department officials have held sessions with patient advocates, scientific societies, ethicists and leading abortion opponents to hear their views. HHS officials insist they have not made a decision, saying publicly only that they want to expand alternatives.

“This is a pro-life, pro-science administration,” HHS Assistant Secretary for Health Brett Giroir wrote in mid-November to Rep. Mark Meadows (R-N.C.), leader of the House’s conservative Freedom Caucus.

Since President Trump took office, congressional conservatives and antiabortion activists have ratcheted up pressure on the administration to stop government support of fetal tissue research. They contend that such studies use what they characterize as “body parts” from “unborn babies” and that alternatives exist.

The tissue comes from elective abortions. Researchers say its use has not led to an increase in the prevalence of abortion and has spurred scientific advances that could not have been made otherwise.

Irving Weissman, a pioneer in stem cell research at Stanford University, said the research method used by the UCSF lab “is absolutely essential. There is no substitute today.”

The UCSF research has been a particular target of opponents’ ire. Several dozen lawmakers signed a letter asking the administration to cut its funding. And in recent weeks, a columnist for the conservative website CNSNews.com wrote repeatedly that the administration had not canceled the contract. The board of the site’s parent company, called the Media Research Center, includes conservative Rebekah Mercer, the leader of a family super PAC that poured money into Trump’s election.

The UCSF contract is the second pot of federal money affected by the conservative crusade. In September, the Food and Drug Administration ended a small $16,000 contract with a California-based nonprofit organization, Advanced Bioscience Resources, for fetal tissue that was to be implanted into mice for research into immune responses to drugs.

The UCSF contract was due to expire Wednesday. The virologist familiar with the events said that a contracting official from NIH’s AIDS division at the National Institute of Allergy and Infectious Diseases gave the principal researcher preliminary notice in early October that the government would extend the contract, which began in 2013, for the next year. Government officials confirm that happened.

Accounts differ, however, on what happened next.

According to the virologist, the principal investigator was told in a telephone conversation with an NIH employee last Wednesday that the AIDS division was exercising its discretion to discontinue the contract. A university spokeswoman, speaking on the condition of anonymity because she had no authorization to discuss the matter, confirmed the university was informed last week the contract was not being extended.

The virologist said the NIH employee “made it clear it was not an internal NIH decision,” and said the decision was “coming from the highest levels.” The employee, a contracting official representative, also said that the UCSF work was supported within the AIDS division and that staff had spent weeks answering questions about the contract, the virologist said.

Five days later, the university received a letter from the AIDS division saying the government would continue the contract until March 5, with no forecast of its prospects, according to an individual with knowledge of the letter.

Lawrence Tabak, NIH’s principal deputy director, said in an interview that “there was never any intention to indicate we intend to terminate the contract.” After conferring with contracting officials, he said, “I have no indication such a call was made.”

Tabak and HHS spokeswoman Caitlin Oakley both said the contract’s future will remain uncertain until the administration completes its reconsideration of fetal tissue funding.

“No final decision has been made,” Oakley said.

Even so, the principal investigator is preparing to shut down the lab, according to the individual familiar with Monday’s letter from NIH to the university’s business office. The Washington Post is not identifying the investigator, who has been involved with HIV research since the mid-1990s. The investigator and university colleagues in AIDS research have been subject to demonization and occasional threats for their work over the years.

Though the letter promises payment prorated for 90 days, sections of it sound like instructions for an orderly closing of a research enterprise. The letter instructs the investigator to “finish ongoing studies as planned,” not to produce new animals for studies and to be ready, if requested later, to return lab animals and equipment to the government.

The contract supports the full-time equivalent of six employees, and university rules require 60 days’ notice before anyone is laid off.

The laboratory is part of the UCSF Department of Medicine’s experimental medicine section. The government pays the lab to provide a central testing platform for assessing in animals the effectiveness and safety of chemical compounds that seem promising for HIV prevention, treatment and cure from earlier stages of development by drug companies and other academic researchers.

The lab does this testing on what are known as humanized mice. These are mice that start out with deficient immune systems. Tissue from the thymus glands of aborted fetuses is implanted into a capsule in the connective tissue under the mice’s kidneys. In four months, that tissue grows into the equivalent of a human thymus, the site of the body that produces T cells, which become depleted in people — or such mice — infected with HIV.

Using this animal model, the UCSF lab — and the affiliated institute, which had similar NIH funding earlier — has evaluated more than 100 chemical compounds from five dozen drug classes.

In some instances, the testing discovered that substances to prevent or treat HIV that seemed promising in a test tube were too toxic in animals. In others, the testing showed great promise, such as a drug that appears likely to block infection for as long as a year that pharmaceutical company Merck is now developing.

If the administration halts UCSF’s work, Stanford’s Weissman said, “this is . . . cutting off a line of research that has been in the past and is likely to be in the future [helpful] to solve the AIDS epidemic.”

Lenny Bernstein and Alice Crites contributed to this report.