The abrupt termination last month of nearly half a billion dollars in US government contracts for mRNA vaccine research rattled scientists working inside and outside industry. The cuts raised alarm about the country’s commitment to the Nobel-prizewinning technology, which is credited with saving millions of lives during the COVID-19 pandemic and is regarded as essential for fighting viruses in the future.
Yet not all large-scale research into mRNA vaccines in the United States is being dismantled. Nature has learnt that, even as the US Department of Health and Human Services (HHS) — led by vaccine critic Robert F. Kennedy Jr — pulls back, the country’s military continues to bankroll parts of the same research.
Among the beneficiaries are programmes developing vaccines against some of the world’s deadliest pathogens, including the virus that causes Crimean–Congo haemorrhagic fever (CCHF), a tick-borne disease that kills up to 40% of those infected. In the United States, the government considers such research crucial because these pathogens not only threaten soldiers deployed abroad, but could also ignite a global outbreak.
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“A lot of us are at least relieved the Department of Defense [DoD] is not abandoning mRNA research,” says Amesh Adalja, an infectious-disease specialist at the Johns Hopkins Center for Health Security in Baltimore, Maryland.
Still, he cautions that the HHS’s rejection of the technology, combined with broader policy fractures across the government, threatens to hobble national — and global — readiness for emerging infectious threats.
“The whole biodefence structure is completely derailed,” Adalja says. “I’ve never seen it be disconnected like this.”
Turbulent times
Peter Berglund learnt that his company’s federally backed vaccine programme was being cut the same way that many other affected firms did in a 5 August notice from the HHS’s Biomedical Advanced Research and Development Authority (BARDA), which ordered an immediate shutdown of ongoing studies. For Berglund, chief scientific officer at HDT Bio in Seattle, Washington, the news was a gut punch, as he told colleagues at a conference on RNA-based therapeutics in Boston, Massachusetts, this month.
HDT had been developing a next-generation CCHF vaccine based on a form of RNA that can copy itself inside cells. The company had secured tens of millions of dollars in federal contracts, which it used first to test a shot in mice and monkeys, and then to begin a human trial in Texas this July. The BARDA memo brought everything to a halt the very next month.
But “that was mommy”, Berglund says. “Then daddy calls.”
Within days, HDT executives heard from project managers at the DoD’s Joint Program Executive Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense, which had been co-funding the CCHF vaccine research. HDT was told to restart its trial, with the JPEO pledging support through at least this first phase of clinical evaluation.
“It’s been so turbulent,” Berglund says. The DoD funding, although substantial, is less than what had originally been pledged in conjunction with BARDA. “But, at least now we can advance it through phase I” and worry about the rest later, he adds.
A ‘restructuring’ of resources
Others with projects co-funded by the JPEO also learnt of funding cuts and a “restructuring of collaborations” in the 5 August notice. But their situation is less clear.
Earlier this month, AstraZeneca, a pharmaceutical company headquartered in Cambridge, UK, began a human trial of two mRNA vaccines, despite the notice. Each is designed to protect against a different strain of avian influenza. Clinical-trial registries still list both BARDA and the JPEO as collaborators.
An AstraZeneca spokesperson declined to comment on the US government’s role in funding the trial against bird flu — which has been infecting US poultry and dairy cattle and raising the spectre of a leap into humans. The JPEO did not respond to requests for comment.
In a statement, HHS press secretary Emily Hilliard disputed suggestions that withdrawing from joint projects would weaken the nation’s pandemic preparedness, writing that “BARDA is prioritizing evidence-based, ethically grounded solutions.”
The JPEO and BARDA had also been jointly funding a preclinical-stage vaccine programme for biotechnology firm Moderna in Cambridge, Massachusetts. The mRNA shot is aimed at Marburg virus — a close but even deadlier relative of Ebola — which caused an outbreak earlier this year in northwest Tanzania, resulting in ten deaths. Neither Moderna nor its collaborator, the University of Texas Medical Branch in Galveston, responded to e-mails from Nature seeking comment on the project’s funding status.
Not every mRNA project has fared so well: those lacking joint DoD support have been brought to a standstill.
At Emory University in Atlanta, Georgia, for instance, biomedical engineer Philip Santangelo had been using CRISPR gene editing to develop an inhalable flu therapy, delivered to the lungs through mRNA. The DoD, through its Defense Advanced Research Projects Agency (DARPA), had provided more than US$20 million to support early-stage development, but that funding ran out last year. A follow-on contract from BARDA was meant to underwrite the design and testing of a dry-powder formulation that would be easy to administer in emergency settings. With the BARDA money frozen, Santangelo says that he’s been forced to pursue funding from foundations, non-profit organizations and other non-governmental entities.
Patchwork support
Santangelo is hardly alone in seeking ways to keep mRNA research on track. Other academics, navigating a minefield of uncertainty over whether US funding agencies will continue to financially support such work, still submit grant proposals — but the term ‘mRNA’ is often scrubbed out, replaced by phrases such as ‘nucleic-acid-based medicines’ to sidestep scrutiny.
A few glimmers of hope remain, however. A spending package advanced this month by a US House of Representatives committee directs BARDA to support mRNA-vaccine research. And the DoD’s Defense Threat Reduction Agency (DTRA) solicited applications this year for its Reimagining the Next Generation of Biodefense Vaccines programme. According to Karl Ruping, chief executive of Tiba Biotech in Cambridge, Massachusetts, DTRA programme managers told him that the agency is open to supporting mRNA vaccines so long as they advance the goal of more-resilient biodefence tools.
Outside the defence establishment, the US Department of Agriculture is maintaining support for mRNA vaccine development as well, awarding grants for projects targeting respiratory viruses that affect pigs, chickens and cows.
Taken together, these programmes reflect commitment — but only in pockets of government, exposing a troubling absence of coordination, says Michael Osterholm, an infectious-disease researcher and biosecurity specialist at the University of Minnesota in Minneapolis.
For now, researchers can take comfort knowing that agencies outside Kennedy’s direct control are charting a different course. But the HHS leader’s influence remains strong, and many worry that he could soon shape policy across the entire federal agenda, including at the DoD. “I’m not sure that it’s the safe haven for mRNA research that some associate with it,” Osterholm says.
This article is reproduced with permission and was first published on September 24, 2025.
