One of the country’s top scientists received “extremely hateful messages” during the pandemic, including threats to his family about “having their throats cut”, the UK Covid inquiry has heard.

Professor Sir Jonathan Van-Tam said the hate mail, which led to the police getting involved, made him consider stepping down from his role as England’s deputy chief medical officer.

Sir Jonathan, who left the post at the end of March last year, said on Wednesday that while his job involved huge workloads and stress, he “did not expect my family to be threatened with having their throats cut”.

He added: “I did not expect the police to have to say: ‘Will you move out in the middle of the night or in the middle of the evening, whether you might move out for a few days, while we look at this and potentially make some arrests?’”

However, the family did not make the move in the end because they “didn’t want to leave the cat”.

Sir Jonathan also spoke about this workload during the early days of the pandemic, saying he was working seven days a week, and it was “horrendous for all of us”.

At the end of his evidence, inquiry chairwoman Baroness Heather Hallett told Sir Jonathan: “In relation to the abuse and threats that you described earlier, I’ve come across that kind of extraordinarily awful behaviour in another context and I know the impact it can have upon the recipients, victims and the victims families, even if they don’t receive threats, which by the sounds of it yours may have done.

“It’s just too awful to contemplate.

“I just want you to be reminded, you probably don’t need reminding but just in case you do, the vast majority of the population abhor such conduct, and we are enormously grateful to you and your colleagues for the way in which you have served the public of this country, of the whole of the United Kingdom, in a time of national emergency.

“So please ignore the violent criminal, idiot element and remember, the rest of us are grateful.”

As well as recalling his personal experience of the pandemic, Sir Jonathan told the hearing that in January 2020 he became seriously concerned about the threat the virus posed to the UK.

It had become clear to him that this was a novel coronavirus, and that human to human transmission was occurring.

Sir Jonathan told the inquiry: “My instincts were telling me that this was going to cause us real trouble and be a pandemic.”

He added that his professional experience, together with reports of the virus spreading in China, helped to form the opinion “that we were in for a bad time”.

In his statement to the inquiry, Sir Jonathan wrote that on January 16 2020, “I absolutely understood in my mind’s eye, that it was a matter of when, not if, things would progress”.

However, he also said chief medical officer Sir Chris Whitty was “entirely right” not to “wake up Sage and wake up Cobra because I was getting a bit excited about something based on instinct”.

Asked about him expressing this view to Sir Chris at this time, Sir Jonathan said: “You get a range of opinions on science, you get a range of opinions on when the data are certain enough to tell you what you’re seeing, and then you have to overlay on top of that personalities.

“Much as Chris and I are great friends and very dear colleagues, and I genuinely mean that, we are different personalities and we both say we’re different personalities – I’m the one who chases the ball, Chris is the one who would look at the ball first and make a more qualified and thoughtful decision about whether it was worth chasing.”

He added: “In any case, I was subordinate to Chris and I respect the chain of command, so I was perfectly content with the response that I received.”

In written evidence given to the inquiry, Sir Jonathan said he was “surprised” that Boris Johnson, the prime minister during the pandemic, was not involved in the first five emergency Cobra meetings about the coronavirus outbreak when “at each meeting, the situation was escalating”.

He also said it was “ill-informed, and rather unhelpful” for the then-British leader to say that he would “continue to shake hands” on March 3 2020 when advice had been published on the same day encouraging the public to adopt alternative greeting techniques.

In an echo of Mr Johnson’s own troubles in accessing his former mobile phone, Sir Jonathan said he could not remember the passcode for his past Government-issued phone and that the WhatsApp messages on the device from the time of the Covid outbreak had since been “inadvertently deleted”.

But he said that the conversations were likely “available from other witnesses” so did not think the lack of access would “prejudice the inquiry’s investigation in any significant way”.

Sir Jonathan also gave evidence on measures taken to control the virus and actions taken by Public Health England (PHE).

He told the inquiry that PHE’s risk assessment “failed us” as Covid-19 began to emerge.

He said: “One of the things that I think where the risk assessment system has failed us is that whilst it may be extremely accurate, and I’m absolutely not calling into question the judgment of any of my PHE or wider health protection colleagues about the risk assessment, the problem is that it relates to the current moment.

“That unfortunately, when you then try and say, well, what does it mean for the future? You get into massive uncertainty, and that’s part of the problem.”

Sir Jonathan added: “I think it’s very unfortunate that (the risk assessment) can be read as, well, (the risk) is low, just forget about it.”

Sir Jonathan also told the inquiry:

– It is “impossible to tell” if the UK would have avoided mandatory lockdowns if action had been taken earlier.

– The NHS would “inevitably be broken” if Covid-19 infections continued at the same rate during the early months of the pandemic.

– The epidemiological consequences of outdoor sporting events during the Covid-19 pandemic may have been underestimated, and while mass outdoor gatherings have a very limited epidemiological effect, there was more concern about the risk of Covid infection in places such as pubs, bars or restaurants, as well as movement of fans between countries.

– The tier system of restrictions across different parts of the country during the pandemic “did not serve us well”.

– He signed a letter to the Cabinet secretary warning of the risks of reopening the country after the first national lockdown to “leave a mark in the sand”.

– Operation Moonshot – a Government ambition to introduce mass-testing for Covid-19 – “didn’t make any epidemiological sense” and he “couldn’t see it working ever”.