In this edition of AcademyHealth’s Situation Report, we highlight the recently reached deal in the Senate to end the longest government shutdown in history and fund the government through January 2026. However, the deal does not address ACA subsidies and leaves many feeling uncertain about the future of health care coverage. We also offer further updates on legal and policy shifts related to research funding, indirect costs in NIH grantmaking, as well as calls to disband the Advisory Committee on Immunization Practices (ACIP) and overturn their decisions because new ACIP appointees lack necessary credentials and experience to make vaccine-related recommendations. Given these recent developments, we offer ways health services researchers can take action and ways Situation Report readers can support our work.
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In today’s issue:
- Congress Finds a Path Out of the 42-Day Government Shutdown
- What the Shutdown-Ending Deal Could Mean for Federal Workers
- An Award for AcademyHealth’s Advocacy Efforts and a Call to Action for the Future
- NIH Indirect Cost Dispute Reaches Federal Appeals Bench
- Lawsuit Calls to Disband CDC Vaccine Panel
- Senate Democratic Caucus Warns FDA, HHS Against Baseless Limits on Mifepristone
Congress Finds a Path Out of the 42-Day Government Shutdown
On Sunday night, eight Senate Democrats broke with party leadership to advance a Republican measure that would end the nation’s longest government shutdown. The Senate passed the deal Monday night by a vote of 60-40. The deal includes a continuing resolution (CR)—a short-term funding bill—that would fund most of the government through January 30, 2026. The bill reverses the President’s mass firings of federal workers that occurred during the shutdown and would ensure backpay for all federal employees. The deal also includes a “minibus” of three appropriations bills that would provide funding through September 30, 2026, for military construction, veterans’ affairs, the legislative branch, the Food and Drug Administration (FDA), and the Department of Agriculture, which administers Supplemental Nutrition Assistance Program (SNAP). However, the deal does not address the expiration of Affordable Care Act (ACA) subsidies at the center of the appropriations standoff. In return for their support, Senate Democrats received a promise from Senate Republicans that the Senate would vote by mid-December on whether to extend the health care subsidies. Democrats who oppose the deal voiced their concerns, calling the promise “vague” and the agreement “a policy and political disaster.” Even if a bill extending the health care subsidies passes in the Senate, its future in the House is uncertain since House Speaker Mike Johnson has not committed to a vote in the House.
While the deal’s passage in the Senate signals an end to the shutdown, the measure needs to survive a vote in the House and President Trump’s approval. On Monday, Speaker Johnson called members back to Washington to vote on the package as early as Wednesday. Speaker Johnson stated that President
Trump is expected to sign the measure, providing the first clear path out of the shutdown.
What the Shutdown-Ending Deal Could Mean for Federal Workers
The Senate is advancing a shutdown-ending agreement that would keep agencies funded through at least through January and reverse recent federal layoffs. Specifically, this bill will undo the more than 4,000 layoffs the administration issued during the shutdown. These reductions in force (RIFs) affected many federal health agencies, notably the CDC. While these RIFs were currently paused by a federal court, it was unclear whether the administration would seek to move forward with the RIFs once the government reopened—if this bill passes in the house, the legislation would prevent all agencies from carrying out any RIFs through January. Moreover, the legislation also aims to protect guaranteed back pay for all federal workers who were furloughed, something the administration suggested may not happen. Given these provisions, this potential shutdown-ending deal will help restore some key functions in federal health agencies, such as CDC offices pertaining to injury prevention, respiratory disease surveillance, and chronic disease, all of which were largely impacted by the October RIFs.
An Award for AcademyHealth’s Advocacy Efforts and a Call to Action for the Future
AcademyHealth has been selected by Research!America to receive the Paul G. Rogers Distinguished Organization Advocacy Award, recognizing our leadership in advocating for the Agency for Healthcare Research and Quality (AHRQ) and strengthening the field’s collective voice through our Situation Report series. As home to the Friends of AHRQ, AcademyHealth has long championed the agency’s essential role in supporting evidence-based improvements in health care quality, safety, and equity.
“This award reflects not just our advocacy, but the collective effort of a community that understands how vital AHRQ is to better care, smarter spending, and improved health,” said Josh Caplan, Director for Government Affairs at AcademyHealth.
The Paul G. Rogers Distinguished Organization Advocacy Award honors a public or private organization that has made exceptional contributions to advancing medical and public health research. AcademyHealth will be formally recognized at Research!America’s 2026 Advocacy Awards in March. Read the full announcement here.
This recognition is a testament to what our community can achieve together when we speak with one voice for evidence. But the challenges ahead demand that we keep building momentum. That’s why, as we celebrate this milestone, we’re also looking forward, inviting our members and partners to sustain and strengthen this work.
This Giving Tuesday, we’re calling on our community to power what comes next. Philanthropic gifts provide AcademyHealth the flexibility to respond quickly to emerging threats, elevate trusted voices in the media and policy arenas, and invest in the infrastructure that keeps evidence at the center of decision-making. We are thrilled to welcome Colleen Marfione, AcademyHealth’s first Development Director, who will lead this new chapter in philanthropic growth, starting with our Giving Tuesday campaign, and help build the diversified, sustainable support that our field needs. Learn more about Colleen here.
Giving Tuesday is December 2, 2025. Whether you can make a one-time donation, a monthly donation, or simply share our campaign with your network, you are supporting the future of evidence. You can donate here. Want to participate in a friendly fundraising challenge? Our CEO and Board Chair are competing to see who can rally more champions for science! Join Team Aaron or Team Rasu to ensure that evidence continues to lead the way toward better health and health care for all.
NIH Indirect Cost Dispute Reaches Federal Appeals Bench
During a hearing on Wednesday, questions and remarks from federal appeals court judges indicated that they might have doubts concerning several key arguments presented by the Trump administration in a lawsuit contesting dramatic cuts to research overhead payments. In February, the National Institute for Health (NIH) announced that it would decrease support for indirect or overhead costs from the previous range of 30 to 70 percent to 15 percent. The proposed policy change would result in some academic medical centers and universities losing over $100 million a year, ceasing biomedical progress, according to a STAT analysis and researchers. In response, three lawsuits were filed the day the cap was to go into effect, collectively representing 22 organizations and states including hospitals, academic medical centers, and private and public universities. In April, a federal judge blocked the policy after issuing a permanent injunction, to which the Trump administration quickly appealed claiming that the case was out of the judge’s jurisdiction— an argument current judges seem to be skeptic of.
The legal battle over indirect costs in grantmaking continued when the Senate Appropriations Committee endorsed a bill proposing a NIH budget increase and using language meant to prevent the administration from changing negotiated indirect costs. In September, however, House appropriators advanced legislation that included an overhead cap for high income private colleges and universities. Similarly, President Trump signed an executive order in August that would change the grantmaking ecosystem to systematically favor institutions with lower overhead costs, a move experts argue could jeopardize the quality of research.
Several of the organizations and institutions, such as the Association of American Universities and Association of American Medical Colleges, who sued the administration area looking for compromises. One coalition led by former Trump advisor Kelvin Droegemeier, for example, offer up a new model that would permit research institutions two methods to receive reimbursement for indirect costs: (1) a fixed percentage of the total project budget dedicated to overhead costs; or (2) a cumbersome accounting process that would change many overhead costs to direct costs. While some senators were seemingly interested in this model and its proposed transparency, others have expressed concern that it could further increase indirect costs paid by the federal government.
Health services researchers can communicate the importance of covering overhead costs to producing high quality research to their representatives, notably House representatives. The proposed cuts would negatively impact universities in conservative states, which might also be leveraged when tailoring communication to certain lawmakers.
Lawsuit Calls to Disband CDC Vaccine Panel
Last Wednesday, the American Academy of Pediatrics (AAP) and five other medical groups updated their lawsuit against HHS Secretary Robert F. Kennedy Jr. to call for the disbanding of the secretary’s new Advisory Committee on Immunization Practices (ACIP), the overturning of their decisions, and for ACIP to be reconstituted under court supervision. The lawsuit explains that the new ACIP appointees lack the necessary credentials and experience and posits that their votes should be nulled and voided. While there is no precedent for the panel to be reconstituted under court supervision, the lead counsel on the lawsuit is hopeful about the possibility. The original lawsuit, filed in July, sued the secretary and HHS for changing COVID-19 vaccine recommendations without evidence. In AAP’s press release on the updated lawsuit, they call out specific concerns with ACIP policy decisions such as a recommendation against a vaccine preservative that has been found to be safe as well as a recommendation for separate instead of combined shots for the measles, mumps, and rubella, and varicella vaccines.
Health services researchers play a critical role in evaluating the impact of vaccine recommendations and ensuring that policy decisions remain grounded in transparent, reproducible evidence.
Senate Democratic Caucus Warns FDA, HHS Against Baseless Limits on Mifepristone
In a letter sent to the FDA and HHS, Senate Democrats warned the administration against imposing additional restrictions on access to abortion pills, following the FDA’s announcement that they would perform their own review of the evidence on the safety and effectiveness of mifepristone, one of the drugs used for medication abortions. The caucus warned the agencies to not “cherry-pick junk science,” noting that the administration’s review of mifepristone seems to be based on a recent report by the right-wing Ethics and Public Policy Center. Experts explain that this report was authored by individuals with no medical training, distorted data, and lacked methodological rigor and data transparency, noting that it overstates risk by relying on broad and undisclosed diagnosis codes and events not clearly tied to the drug.
Mifepristone, used alongside misoprostol to end pregnancies, has been approved as safe and effective by the FDA since 2000 after a thorough review of the evidence. Last month, a federal court in Hawaii ruled that the current risk evaluation and mitigation strategy for mifepristone is unlawful because abortion pills are safe and effective. Health services researchers can continue to uplift the evidence on the safety and efficacy of mifepristone to their local, state, and federal policymakers.
Previous Editions
This is the latest in a series of Situation Report updates from AcademyHealth. You can find prior issues here.
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