Earlier this month Trump announced he wanted former rival Robert Kennedy Jr to run the US health department. Kennedy’s vaccine scepticism has alarmed the medical community, though his calls for stricter regulation of food ingredients have won praise.

In a statement Trump said Bhattacharya would work with Kennedy to “restore the NIH to a Gold Standard of Medical Research as they examine the underlying causes of, and solutions to, America’s biggest Health challenges, including our Crisis of Chronic Illness and Disease”.

Bhattacharya posted on X, formerly Twitter, that he was “humbled” to be picked.

“We will reform American scientific institutions so that they are worthy of trust again and will deploy the fruits of excellent science to make America healthy again!” he wrote.

On Tuesday the president-elect also nominated Jim O’Neill – a former federal health official and close ally of conservative donor Peter Thiel – as deputy secretary of the health department.

But it is Bhattacharya who’s more widely known after he challenged the public health establishment’s response to the Covid outbreak four years ago.

In October 2020, Bhattacharya co-authored an open letter known as the Great Barrington Declaration, calling for an alternative to lockdowns, recommending that the focus should instead be on protecting vulnerable groups such as elderly people.

He remains a vocal critic of how Anthony Fauci – a former director of the US National Institute of Allergy and Infectious Diseases, a division of NIH – handled the pandemic.

Then-NIH director Francis Collins said at the time the Great Barrington Declaration, which came before Covid vaccines were available, was dangerous, dismissing the authors as “fringe experts”.

Bhattacharya is not the only Trump nominee to have criticised the response of US public health agencies to the pandemic.

Trump has also picked Marty Makary, a Johns Hopkins surgeon who opposed the Covid-19 vaccine mandate, to run the Food and Drug Administration (FDA).

Dave Weldon, a physician and former Republican congressman who has also cast doubt on vaccine safety, was picked to run the Centers for Disease Control and Prevention (CDC).

Kennedy and O’Neill’s department of health would oversee the agencies run by Makary, Weldon and Bhattacharya, but all five need to be confirmed by the Senate.

Last week Trump also nominated TV personality Dr Mehmet Oz to be the Centers for Medicare and Medicaid Services administrator.

While Trump’s picks for US public health agencies have broadly been welcomed by his allies, not all of them have won a positive reception from conservatives.

He has also nominated Dr Janette Nesheiwat, a Fox News medical contributor, to become the next surgeon general.

But her previous comments opposing abortion restrictions and in support of masking schoolchildren during the pandemic have riled some Trump supporters.