A pharmaceutical contractor under scrutiny for its ties to former government officials could be one of the bottlenecks holding up the production of millions of Johnson & Johnson COVID-19 vaccines.

Emergent BioSolutions, the U.S. company making “drug substance,” the active ingredient in the vaccines, is still awaiting regulatory authorization, according to a company official familiar with the process. Emergent-made doses were not included in the paperwork Johnson & Johnson submitted to the Food and Drug Administration. That means that the material Emergent makes would not be available to be used for vaccines that can be administered in the United States now.

Johnson & Johnson is due to deliver 20 million doses by the end of March, but just 4.7 million had been delivered as of March 25, according to the Centers for Disease Control and Prevention.

Emergent spokesman Matt Hartwig said the company is capable of producing drug substance to support more than 1 billion doses annually.

“We are on track and meeting all of our commitments to Johnson & Johnson and Astra Zeneca,” said Hartwig.

The FDA declined to respond to questions, directing questions to Johnson & Johnson.

“We expect to ship 20 million doses by the end of March,” Johnson & Johnson spokesperson Jake Sargent said in an email, declining to share details on when supply will begin to ramp up and to what degree the delay is related to Emergent.

[Johnson & Johnson under pressure to deliver promised vaccine doses to states]

The apparent challenges come amid increased scrutiny of the firm’s Washington connections, including to top Trump pandemic response official Robert Kadlec, and its outsize influence on the Strategic National Stockpile.

The White House canceled a trip to the company’s Baltimore plant earlier this month.

A Johnson & Johnson executive told Congress in February the company could deliver 20 million U.S. doses by the end of the month, but said that was “assuming necessary regulatory approvals relating to our manufacturing processes.”

The delay also raises questions about Operation Warp Speed, the Trump administration initiative to invest billions in vaccine manufacturing in order to ensure millions of doses were ready to ship immediately upon an FDA green light.

Operation Warp Speed awarded Emergent $628 million in June 2020 to scale up.

Still, Emergent stated in a regulatory filing to the Securities and Exchange Commission in December that it could not guarantee timely delivery of doses.

“The manufacturing processes for our CDMO [contract development and manufacturing organization] COVID-19 programs are under development and will be complex,” the company states. “As a result, there can be no assurance that we will be able to produce any significant quantity of these products in a timely basis or at all.”

The filing also states that negotiating further commitments under existing contracts to manufacture COVID-19 vaccines “could adversely affect our business, financial condition, operating results and cash flows.”

Experts in pharmaceutical manufacturing say the apparent delay with Emergent could indicate that FDA has unresolved concerns with its facilities.

“Most of the FDA’s publicity is focused on the clinical trials, but they also want to be comfortable with the fact that the manufacturing operations will reliably produce consistently high quality product,” he said.

“It most likely means the FDA has some questions about their manufacturing operations,” Mark Witcher, a pharmaceutical manufacturing expert and former executive at Amgen, a Johnson & Johnson competitor, said in an email.

“The current manufacturing sites likely have a good manufacturing track record. New manufacturing sites like Emergent may not have a track record with FDA and would require additional effort to assure they are capable of reliable production of high quality material,” he continued. “It is not uncommon when a contract manufacturer takes on a manufacturing process in a new location (e.g. to help increase production) for it to take some time to stand up and validate the process and then to be inspected and ok’d by FDA.”

Other experts expressed surprise, given that Johnson & Johnson entered into a $480 million deal with Emergent to make use of its existing facility in the Bayview neighborhood of Baltimore nine months ago.

“That’s very surprising to me as Emergent signed a 5-year work order with J&J back in July 2020,” bioprocessing expert Kim Nelson said in an email. “That should have resulted in the Emergent Bayview site being listed in the EUA when it was filed.”

Emergent’s Baltimore facility is a Center for Innovation in Advanced Development and Manufacturing, a public-private partnership meant to quickly scale up in a public health emergency. It has been inspected by FDA for years.

“The [Good Manufacturing Practice] systems … should all have had any potential inspection issues worked out long ago,” he said.

Hartwig, the Emergent spokesman, said the pre-pandemic designation during the Obama administration and subsequent government partnerships are what made it possible for the company to be able to produce 1 billion doses of vaccine annually.

Emergent’s ties to former Trump administration officials came under scrutiny when a whistleblower complaint by former Biomedical Advanced Research and Development Authority Director Rick Bright raised concerns about cronyism impacting multi-million dollar government contracts.

Kadlec, the assistant secretary for preparedness and response in the Trump administration, served as a consultant to Emergent Biosolutions until 2015. From the time Kadlec was confirmed to his federal post in 2017 to the 2020 deal to manufacture COVID-19 vaccines, the biodefense company received more than $1.2 billion from the division Kadlec oversaw.

Purchases of Emergent’s anthrax vaccine comprised more than 40 percent of the stockpile’s budget from 2010 to 2018, The New York Times reported. That left fewer resources for pandemic supplies like N95 masks.

Kadlec has been tapped by Senate Health, Education, Labor and Pensions Committee ranking member Sen. Richard M. Burr, R-N.C., to shape legislation meant to prepare the U.S. for the next pandemic, STAT reported Thursday. Kadlec is a former aide to the committee and to Burr.

If Johnson & Johnson does not deliver 20 million doses on time, the U.S. government can pass on buying them, according to the terms of its $1 billion contract.