The country’s top scientists were never informed about the Eat Out to Help Out scheme, despite Boris Johnson saying they were consulted, the UK Government’s chief medical officer has said.

In potentially damaging testimony, Professor Sir Chris Whitty said he and Sir Patrick Vallance, the Government’s former chief scientific adviser, were never told about the plan, adding: “I think we should have been.”

Whitty said he raised objections to Number 10 about how it was handled, adding “this was aimed at the centre.”

Earlier this week, Vallance told the inquiry he would be “very surprised” if Rishi Sunak, then chancellor, had not learned about the objections to his plan to help the hospitality industry.

In evidence submitted to the inquiry, Sunak said he could “not recall any concerns about the scheme”.

Under questioning from Hugo Keith KC, lead counsel to the inquiry, on Wednesday, Whitty said: “My written statement makes clear there was no consultation.”

Keith said: “I need to put to you that in his witness statement, Boris Johnson says ‘It was properly discussed, including with Chris and Patrick’, do you agree with that?”

Whitty replied: “On this one, neither Patrick nor I can call it and I think we would have done.”

He continued: “I made fairly firmly to Number 10, not to the prime minister, the view that it would have been prudent, let’s put it that way, for them to have thought about discussing it [Eat Out to Help Out] before it was launched.

“And this was aimed at the centre.

“I was unsurprised that the Treasury and many other ministries were coming up with those schemes – it is perfectly legitimate.

“Number 10 held the ring and… so it may well be correct that the Prime Minister was under the impression we had been consulted, but it was not the fact that we were consulted and that difference, I think, is probably worth just highlighting.”

Whitty also said the UK was already in “deep trouble” before the first Covid lockdown, but not everyone in Downing Street understood the “difficult direction” it was going in.

Giving evidence to the UK Covid-19 Inquiry, Whitty also said the debate on herd immunity – which was raised before the restrictions were introduced – was “very dangerous”.

He told the inquiry by the weekend before the first lockdown was implemented on March 23 2020, the UK was already in “deep trouble” and could not afford to wait to see if earlier measures would bring the R number for the rate of infection below 1.

But he said he is not convinced that “all parts of the Downing Street machinery” were “seized of the urgency” of action against coronavirus in early March 2020.

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He added: “What I think people were really not able to conceptualise was how exponential growth would turn from those apparently smaller numbers, still each one a tragedy, but smaller numbers to really very large numbers in an extremely short period of time because of the doubling time.

Elaborating on which part of the “system” may not have fully understood, Whitty said: “I think actually it was a relatively widespread lack of understanding of where we were going ahead.

“I think the people who had been heavily involved in looking at this, and you know certainly Mr [Dominic] Cummings, and many others, I think had realised by now that this was heading in a very difficult direction. But I don’t think everybody in the building did.

He continued: “This was a lot of people really not getting what exponential growth was actually going to mean.”

Whitty also described the debate on herd immunity during the pandemic as “a clearly ridiculous goal of policy” and “very dangerous”.

He told the inquiry that the public debate about this led to “considerable confusion” where there was a “large amount of chatter” by “people who had at best half-understood the issue”.

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The chief medical officer for England said it would have been “inconceivable” to make herd immunity through natural infection as an actual policy goal because “it would have led to extraordinarily high loss of life". 

He said that in his view, the only rational policy response where “you would ever achieve aim to achieve herd immunity is by vaccination”.

Whitty said: “We had no idea whether, even in a theoretical situation, the population would by natural infection even get to the herd immunity threshold.”

He added: “People who’ve got higher risks – older citizens, people with disabilities, people with immunosuppression and so on – [would have] very significant risks of mortality, so the impact of that on mortality would be very severe.”