Despite concerns raised during the presidential transition, the President’s Emergency Plan for AIDS Relief (PEPFAR) seems poised to continue its work. The multi-billion dollar government initiative created by George W. Bush in 2003 has worked with remarkable success to treat and prevent HIV, malaria, and tuberculosis in a number of countries around the world, and is often hailed as his greatest legacy.

The Trump administration decided early last month to keep Obama-appointee Deborah Birx, the U.S. Global AIDS Coordinator and U.S. Special Representative for Global Health Diplomacy, in her position, at least for the time being. Birx, who holds the highest position in PEPFAR, told me she was asked to stay on an interim basis the day before the inauguration. While non-termed presidential appointees typically resign leading up to a transition, the fact that Birx was asked to stay on, avoiding a gap in leadership, suggests a degree of consideration for the initiative.  

As Helene Cooper of The New York Times reported, this came after a Trump transition-team questionnaire posed questions that seemed skeptical of the program, asking: “Is PEPFAR worth the massive investment when there are so many security concerns in Africa? Is PEPFAR becoming a massive, international entitlement program?”

The tone of the questions was perplexing, given Secretary of State Rex Tillerson’s praise of PEPFAR in his confirmation hearing, and Vice President Mike Pence’s support of the initiative when it was first proposed in 2003 and when it was re-authorized for the first time in 2008.  

And, as my colleague Ed Yong wrote after the questionnaire was made public, tragedy would unfold if PEPFAR were eliminated. The initiative funds and maintains a complex web of laboratories, supply chains, and health centers that provide a wide array of health services to millions of people around the world—all enabled by sustained funding and logistical support. As of 2016, the program helped provide life-saving antiretroviral treatment for over 11.5 million people, trained 220,000 health-care workers, and facilitated counseling and testing for over 74.3 million people.

Though keeping Birx in her post seems to demonstrate that the administration values PEPFAR, they may also have endangered its ability to function.

Three days after Birx was asked to stay on, Trump issued a presidential memorandum re-instating the Mexico City Policy, also known as the “global gag rule.” The policy has traditionally blocked NGOs from receiving funds from the U.S. government for family-planning programs unless they promise not to “perform or actively promote abortion as a method of family planning.”

This move was, in a way, expected, said J. Stephen Morrison, director of the Global Health Policy Center at the Center for Strategic and International Studies. Each president since Reagan has instituted or rescinded the policy along party lines. But Trump’s memorandum breaks precedent.

His memorandum calls for “a plan to extend the requirements … to global-health assistance furnished by all departments or agencies.” With the addition of that phrase, the policy goes from affecting $400-$600 million in U.S.-aid dollars to $10 billion, according to Morrison. That includes PEPFAR.

In the past, the Mexico City Policy has applied to funding for family-planning programs, rather than all global-health programs. And, once PEPFAR came into being, former President George W. Bush exempted it from the policy. As Scott Evertz, who served as director of the White House Office of National AIDS Policy under George W. Bush, told Slate, “It would have been impossible to treat HIV/AIDS in the developing world … if the global gag rule were to be applied to the thousands of organizations with which those of us involved in PEPFAR would be working.”

Yet this is not the first time that PEPFAR, which is funded through Congress, has come into conflict with ideology. When Pence advocated for PEPFAR in Congress, he pushed for the allocation of funding to abstinence-education programs. “Abstinence and marital faithfulness before condom distribution are the cure for what ails the families of Africa,” Pence said in a 2003 floor speech. “It is important that we not just send them money, but that we send them values that work.”

But these values, in the end, did not work.

When PEPFAR was first funded in 2003, one-third of its budget for HIV-prevention programs was earmarked by Congress to fund abstinence education, though that amount was reduced in 2008. These interventions—including messages printed on billboards and broadcast over the radio—were shown to be ineffective in reducing HIV risk or changing sexual behavior.

The Mexico City Policy has proven to be similarly counterproductive: It’s been associated with an increase in abortions, including unsafe abortions, in the affected countries. NGOs that cannot access U.S.-government funding due to the gag rule are also key providers of contraception, which is thought to lower abortion rates.

It’s unclear how the new global gag rule will be implemented, and how PEPFAR’s support of other organizations will be affected.

Morrison told me the administration’s actions seem dissonant: Keeping Birx in her position—which he called a “smart decision”—“was the done with the right hand, and the Mexico City order comes with the left hand,” he said.

“It hasn’t been explained,” Morrison added. “We don’t know the true costs will be, how this will be implemented in practice, and we don’t know what the legality is.”

And while abortion is illegal in some sub-Saharan countries where PEPFAR operates, many make exceptions for cases of pregnancies resulting from rape, or when the mother’s health or life may be on the line. Other countries place no such restrictions. For instance, abortion is fully legal in South Africa, a PEPFAR partner country, where 6.8 million people were estimated to be living with HIV in 2014.

Health centers that receive PEPFAR funding provide a wide array of services. So a clinic that includes a family-planning program in a country like South Africa may also receive PEPFAR funding for an HIV-treatment program. Under the new policy, that clinic may now be unable to counsel a pregnant 18-year-old girl who was raped that abortion is an option for her, or the clinic would lose its U.S. funding, even if those family-planning services aren’t funded by the U.S.

“I'm very worried, and I'm not sure that any of this was thought through,” Morrison said, adding, however, that it would be “wrong to jump to catastrophic conclusions.” But, in the continued absence of clear direction from the White House, he believes NGOs may begin to “self censor,” and preemptively cut services for fear of losing funding.

For now, the situation remains unclear, says Morrison. But figuring out “whether the left hand contradicts the right is going to have to happen somewhere downstream soon.”