When a close ally of Donald Trump stepped down from his role at the US health department this week, it blew the lid open on simmering tensions between the president’s political operatives and public health officials in charge of the country’s coronavirus response.

Michael Caputo announced on Wednesday he was standing aside as head of communications at the department for two months, after coming under fire for a Facebook live session he hosted on Sunday, in which he accused scientists at the US Centers for Disease Control and Prevention of being part of a criminal conspiracy to undermine the president and help his Democratic rival Joe Biden.

Mr Caputo, a staunch ally of Mr Trump, said he was taking the leave of absence while he underwent “necessary screenings” for an unspecified lymphatic condition that he blamed for putting him under stress.

However, several senior officials told the Financial Times that Mr Caputo’s video outburst and subsequent stepping aside were just the most visible signs of how relations between Mr Trump’s political appointees and his administration’s career scientists have deteriorated as the election approaches.

With less than 50 days until the election, the president has hit the campaign trail more regularly, and is keen to reassure his supporters that the threat of the disease — one of his main political vulnerabilities — is subsiding. This has sparked a fresh round of arguments in Washington, where his allies in government wants to ensure official public policy reflects his optimistic stance.

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“It is chaos right now,” said one career civil servant at a top public health agency. “It seems that with the election coming up, Trump’s people are desperate to make sure the government response tallies with what he is telling voters about Covid-19, rather than what the situation is.”

Another said: “Tensions are worse now than they have been for a while. They will not let the scientists speak freely. They are trying to police everything we do and say.”

Ashish Jha, professor of global health at Harvard University, said: “It is undoubtedly clear that meddling by Trump appointees has got much worse recently. The pandemic is going badly, but the president is desperate to put it behind him, and the public health agencies are not fully co-operating.”

Mr Trump clashed with the US scientific community from the beginning of the pandemic, openly disagreeing with his own government officials over how serious the virus was, how it should be treated and how many tests were needed.

Michael Caputo took a leave of absence after accusing government scientists of participating in a criminal conspiracy to damage the president © AP

The president gave a glimpse of those tensions on Wednesday night, when he publicly rebuked Robert Redfield, the head of the CDC, for comments Dr Redfield had made earlier in the day.

Dr Redfield had told members of the Senate health committee he thought a vaccine would not be in wide circulation until late 2021, adding that a mask might prove more beneficial for fighting the virus than an immunisation. Hours later, Mr Trump — who has insisted a vaccine will be widely available this year — said of one of his most senior scientific officials: “I think perhaps he made a mistake.”

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Officials say this was merely the latest in a recent series of attempts by Mr Trump and his appointees to undermine public health officials.

Last month Alex Azar, the health secretary, announced that laboratory-developed coronavirus tests would no longer need to be approved by the Food and Drug Administration, which the department oversees. Officials within the FDA told the FT that Mr Azar made this decision despite concerns from Stephen Hahn, FDA director, who feared that inaccurate tests could flood the market.

“Alex Azar is desperate to make sure he does not get the blame for there not being enough tests,” said one ally of Dr Hahn.

The health department did not respond to a request to comment.

But while Mr Azar has been keen to make sure enough tests are being manufactured, his department has also been accused of leaning on the CDC to make sure that fewer people seek them out.

The CDC changed its guidelines on testing last month to recommend that people who had been exposed to the virus but did not have symptoms did not need a test. The agency then referred all queries about that decision back to the health department, its parent organisation.

Robert Redfield was rebuked by Donald Trump after saying masks might be more effective than a vaccine at stopping the spread of the virus © Getty Images

Insiders said they believe Mr Azar was trying to help reduce the number of tests carried out in order to comply with Mr Trump’s stated wish to have fewer tests as a way to bring down the official case count.

The health department has also clashed with scientists at the CDC over the organisation’s regular scientific reports, known as Morbidity and Mortality Weekly Reports. Political appointees have been trying to change parts of these reports since the early summer, when the CDC began warning about a worrying surge in cases, according to people inside the agency.

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Dr Redfield defended the scientific integrity of those reports on Wednesday, insisting he would not allow them to be compromised “under my watch”. But he also admitted he had been “deeply saddened” by Mr Caputo’s outspoken attack on his staff.

Several government scientists told the FT the biggest problem has been heavy handed interference by communications officials such as Mr Caputo who do not want senior officials to speak freely to the media.

Emails obtained last week by Politico show Paul Alexander, a health professor hired as an adviser by Mr Caputo, instructing officials on how Anthony Fauci, the director of the National Institute of Allergy and Infectious Diseases, should answer media questions. The health department on Wednesday announced that Mr Alexander was leaving.

An official at another health agency said that Mr Alexander’s attempt to collar Dr Fauci was typical of the approach of Mr Caputo and those around him.

“They want to muzzle us,” the person said. “They know that the greatest power we have is the ability to speak directly to the public and tell them the truth about coronavirus.”

Via Financial Times