As of October 1, 2025, the federal government entered a lapse in appropriations, resulting in an immediate shutdown of many operations across the Department of Health and Human Services (HHS) and its divisions. HHS has released its FY26 Lapse in Funding Contingency Plan, alongside division-specific updates for key agencies including the National Institutes of Health (NIH), Advanced Research Projects Agency for Health (ARPA-H), Administration for Strategic Preparedness and Response (ASPR), Agency for Healthcare Research and Quality (AHRQ), Centers for Disease Control and Prevention (CDC), and Food and Drug Administration (FDA). While essential services and those funded by multi-year appropriations or user fees will continue, most routine research and administrative functions are suspended until appropriations are restored.
Key Details: The National Institutes of Health
According to HHS’s NIH contingency plan, NIH has paused new grant reviews, awards, and most administrative and intramural research activities. The NIH Clinical Center has suspended new patient admissions and protocols, although essential patient care and animal welfare services remain active.
In its Notice NOT-OD-26-004, NIH clarified the impact for the extramural community. Institutions may continue drawing funds from existing awards through the Payment Management System, though restrictive terms or system edit checks may block certain transactions. Grant applications should still be submitted according to posted deadlines through Grants.gov or ASSIST; however, NIH will not process them until operations resume. Peer review meetings and Advisory Council reviews are suspended and will be rescheduled. NIH staff are unavailable during the funding lapse, and central email inboxes are not monitored.
The eRA Commons system remains accessible with limited support; applicants encountering technical issues are advised to submit a ticket to document problems, which NIH will consider once operations resume. For active grants, work may continue, but recipients should anticipate delays in the issuance of new Notices of Award, RPPR reviews, and no-cost extension processing. The Office of Laboratory Animal Welfare (OLAW) is fully shut down, and institutions should delay Assurance submissions and reporting until after the lapse, while maintaining their own animal welfare oversight.
Other Agency-Specific Updates:
Advanced Research Projects Agency for Health (ARPA-H):
Unlike other HHS divisions, ARPA-H operations continue during the shutdown because the agency is supported by multi-year appropriations. This allows ARPA-H to move forward with ongoing high-risk, high-reward research and innovation projects despite the funding lapse.Administration for Strategic Preparedness and Response (ASPR):
ASPR, which leads the nation’s health preparedness and emergency response efforts, is operating under a reduced workforce, limited to excepted activities necessary to protect life and property. Essential emergency preparedness and response operations continue, but routine programmatic activities are paused until appropriations are restored.Agency for Healthcare Research and Quality (AHRQ):
AHRQ has scaled down to minimal staffing levels, with only excepted activities continuing. The agency’s core mission of improving health care quality and safety is on hold during the shutdown, including most grantmaking, peer review activities, and research dissemination efforts.Centers for Disease Control and Prevention (CDC):
The CDC remains operational only for critical public health functions. Essential activities include protecting the health and safety of the public, such as monitoring and responding to disease outbreaks, maintaining laboratory operations that are necessary for public health, and operating programs that protect human life. Non-essential programs and research projects are paused until funding is restored.Food and Drug Administration (FDA):
The FDA is continuing activities that are funded by user fees already collected or those deemed excepted for public health and safety. Approximately 86% of FDA staff are retained due to this funding structure. However, the FDA is not accepting new submissions that require FY26 user fees during the lapse. Work related to review of previously submitted applications supported by prior-year fees continues, as do food safety inspections and certain enforcement functions.
Resources for USC Researchers
For USC researchers and research administrators, the most important steps are to continue submitting proposals on time, plan for delays in reviews and awards, and coordinate with SPA regarding Payment Management System drawdowns. Non-urgent communications with NIH and other agencies should be delayed until the shutdown concludes. In the rare case of an emergency involving human participant safety in NIH-funded research, contact information is provided within NOT-OD-26-004. A list of agency-specific contingency plans can also be found below:
Agency Contingency Plans:
- HHS Department-wide FY26 Contingency Plan
- NIH Contingency Plan
- ARPA-H Contingency Plan
- ASPR Contingency Plan
- AHRQ Contingency Plan
- CDC Contingency Plan
- FDA Contingency Plan
The Department of Contracts and Grants will continue to monitor federal updates closely and will provide additional guidance as new information becomes available.