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The nation’s efforts to develop and stockpile key medicines for guarding against public health threats are underfunded by some $35 billion, the Biden administration warned Congress on Monday, forcing officials to make risky trade-offs that could leave the U.S. unprepared for the next emergency. 

Over the next five years, the Department of Health and Human Services estimates that the U.S. will need $64 billion overall to fund the work of an array of agencies tasked with “medical countermeasures” for threats ranging from COVID-19 to nuclear attacks.

That means, at funding levels that had been laid out by Congress last year, the National Institutes of Health, Administration for Strategic Preparedness and Response, and Food and Drug Administration say they will together be billions short of what they need to sustain their pipeline of emergency medicines.

The estimates released Tuesday are the first of its kind given to Congress since authorities dug deep into the nation’s stocks for responses to COVID-19, mpox, and Ebola. While the exact math of the shortfall could be slightly smaller after the latest budget passed by Congress, officials say there remains a wide gap between their needs and available money.

Since the last of these annual reports, a combination of new needs and inherited shortfalls from previous budgets add up to a substantial increase. By contrast, in December 2019, the same so-called Public Health Emergency Medical Countermeasures Enterprise projected needing just $28.8 billion.

“As the first PHEMCE multiyear budget released since the start of the COVID-19 pandemic, it will serve as a useful tool for Congress to gauge ASPR’s funding levels to provide the country protection against whatever comes next,” Assistant Secretary for Preparedness and Response Dawn O’Connell said in a statement.

The largest of the new funding buckets identified by HHS is to pay for $16.7 billion worth of “multidisciplinary efforts” at the Biomedical Advanced Research and Development Authority. 

Citing lessons learned from COVID-19, which relied on pivoting mRNA vaccine technology initially developed for other diseases, BARDA hopes to fund products that can be deployed to counter a variety of different pathogens.

“The multidisciplinary line really wasn’t a big deal, and now, the threat-agnostic work there at BARDA, that’s going to change the game. That’s where you’re going to see the biggest investment,” a senior administration official told CBS News.

Pandemic influenza remains the biggest standalone need in the report, totaling $8.8 billion – up from the $5.7 billion from the 2019 budget. Among their goals, officials hope to use the money to speed production of emergency vaccines and develop alternatives to needles and syringes.

Not every threat has seen their funding needs climb, the Biden administration says. 

For example, anthrax is estimated to need just $1.7 billion, down from the $2.3 billion in the 2019 report. Money would go to supporting ongoing efforts to support a new kind of anthrax vaccine and treatment.

The official cited shelf life extensions for anthrax stockpiles as part of why needed costs have declined, as well as a growing reliance on multipurpose antibiotics.

“We’re trying to think more strategically about having things across the portfolio. If an antibiotic is good enough for anthrax, we can have it on the shelf for the plague as well,” the official said.

Congress has historically not fully funded the budgets laid out by federal officials in these reports to Capitol Hill, since they first began under the Obama administration. 

Officials acknowledged in a Government Accountability Office report from October that the White House’s budgets did not always fully reflect the stockpile’s needs, due to “competing priorities and tradeoffs” in the budget process. 

This year, the Biden administration hopes Congress can enshrine pandemic preparedness needs as mandatory funding, akin to military defense spending. Department officials have previously warned about challenges restocking supplies depleted for the mpox response, which used drugs and vaccines initially saved up for a potential smallpox attack.

“Mandatory funding says we are confident enough that this is where we need to be headed for defense, for security purposes. That we think that, no matter what else is happening in the world, this is money that deserves to be spent,” the official said.

Supporters say there is a bipartisan appetite among members of Congress for the funding boost.

“With some members, there’s definitely some COVID fatigue that will make it a little challenging on the Hill. But I think that, especially from the defense and national security standpoint, there are members that are very interested in this,” says Taylor Sexton, executive director of the Medical Countermeasures Coalition.

Sexton’s organization lobbies on behalf of a broad range of groups that get federal funding to sustain their pandemic preparedness work, including biotech companies and universities developing drugs and vaccines that end up in the stockpile.

He cited previous threats, like the September 11 attacks and Hurricane Katrina, that led to Congress upping its spending for emergency preparedness.

“If we don’t continue to fund these agencies, all the stuff that we’ve been building is going to atrophy over time. We’ll be back where we started before,” said Sexton.

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