How HHS Budget Cuts And Vaccine Hesitancy Threaten Clinical Trial Operations — And What Leaders Can Do
By Stacey B. Lee, JD, professor of law and ethics, Johns Hopkins Carey Business School and Bloomberg School of Public Health
What happens when the two pillars of U.S. clinical research — regulatory oversight and public trust — start to erode at the same time? Trial sponsors and CROs are confronting dual challenges in 2025: significant staffing reductions at the Department of Health and Human Services (HHS) and escalating public distrust in vaccines and clinical research. These factors are poised to disrupt trial timelines, complicate recruitment efforts, and necessitate strategic adjustments from clinical operations leaders.
Consequences For FDA And NIH Oversight
The FDA is set to lose 3,500 staff members, and the NIH will see a reduction of at least 1,200 positions. These agencies are pivotal in ensuring the safety, efficacy, and scientific integrity of the clinical research pipeline. With reduced personnel, clinical operations teams should anticipate the following:
- Extended review times for INDs, protocol amendments, and marketing applications.
- Decreased frequency of site inspections, potentially impacting data integrity verification.
- Limited agency guidance on complex trial designs and novel endpoints.
For instance, the recent termination of NIH-funded research on vaccine hesitancy has already led to significant job losses in research labs. These challenges are particularly concerning as sponsors strive to incorporate decentralized trial designs, enhance diversity in recruitment, and implement digital health tools — all initiatives that rely heavily on active agency engagement.
When Public Trust In Vaccines Undermines Trial Recruitment
Vaccine hesitancy now extends well beyond COVID-19 and is increasingly affecting other areas of preventive medicine. In March 2025, the NIH abruptly terminated over 40 grants supporting vaccine communication research. One high-profile example is UCSF Professor Dr. Nisha Acharya’s NIH-funded shingles vaccine study, which was halted midstream, resulting in layoffs and the suspension of outreach efforts targeting underserved older adults.
For clinical operations teams, this disruption is more than academic. When trials are forced to shut down mid-recruitment — particularly those relying on community partnerships — the cost is measured not just in lost data but in lost trust. This is especially damaging in populations where medical skepticism is already high.
Operationally, vaccine hesitancy and canceled research funding impact:
- recruitment rates, especially for preventive trials
- retention and protocol adherence
- site selection strategies
- community engagement models.
These shifts challenge clinical teams to adopt more localized trust-building strategies — for example, working with faith-based leaders or community health workers to co-host information sessions, tailoring materials to regional health literacy levels, or embedding local advocates in trial education efforts and require contingency planning for trials that may suddenly lose public or institutional support.
A Talent Crisis In Public Health Research
The intersection of budget cuts and growing public skepticism also affects the pipeline of clinical investigators and research sites. Trials focusing on marginalized populations or relying on local health infrastructure often face the first setbacks when federal grants decrease.
Additionally, the termination of vaccine communication research may discourage early-career researchers from pursuing public health-focused clinical science. Over time, this creates expertise gaps in critical areas such as community engagement, diverse trial participant recruitment, and ensuring uptake of approved therapies.
What Clinical Operations Teams Can Do
Given the high risk of delays and recruitment shortfalls, clinical operations leaders should consider the following approaches:
- Strengthen Cross-Sector Partnerships
- Form industry-academic collaborations to access established research infrastructure.
- Join consortium efforts to share recruitment resources across complementary studies.
- Develop relationships with research-intensive healthcare systems to streamline site activation.
- Advocate for Research and Transparency
- Engage with professional associations to quantify and communicate the impact of regulatory delays.
- Participate in public forums addressing the value of clinical research.
- Develop educational materials that clearly explain trial processes to potential participants.
- Invest in Community Trust
- Allocate additional resources to community engagement, especially in regions with lower research participation.
- Develop site-specific strategies for addressing vaccine and research hesitancy.
- Partner with community-based organizations to rebuild trust in the research enterprise.
- Build Internal Resilience
- Revise timeline projections to account for extended regulatory reviews.
- Enhance training for site teams on evolving regulatory expectations.
- Implement flexible protocols that can accommodate potential disruptions.
- Develop contingency plans for recruitment challenges in hesitancy-prone regions.
Resilience Isn’t Enough — We Need Strategic Investment
The clinical research industry has demonstrated remarkable resilience during global crises, but resilience alone is insufficient. HHS and its agencies play a foundational role in maintaining research integrity, participant safety, and scientific progress. As their resources contract, the risks to trial operations grow.
Yet within this disruption lies opportunity. The clinical trials community has proven again and again that it can adapt in the face of adversity. By embracing collaboration across sectors and leaning into innovation, clinical leaders have a chance not only to stabilize the research ecosystem but to strengthen it for the future. Clinical leaders can reassert the value of research not only to regulators and funders but also to the communities we serve. By implementing the strategies outlined above with clarity and purpose, operations teams can mitigate the impact of today's challenges while building a more robust and trustworthy research infrastructure for the future.
About The Author:
Stacey B. Lee, JD, is a professor at the Johns Hopkins Carey Business School and the Bloomberg School of Public Health, specializing in healthcare regulatory issues and their impact on clinical research operations. She advises pharmaceutical companies and clinical research organizations on regulatory strategy and compliance. Professor Lee is the author of Transforming Healthcare Through Negotiation (Routledge, 2025) and serves as CEO of Praxis Pacisci, where she trains healthcare and research leaders in strategic negotiation. Her insights on healthcare regulation have been featured in USA Today, Bloomberg Law, NPR, and CGTN America.