England’s chief medical officer and chief scientific adviser during the Covid pandemic have faced the UK’s public inquiry for the first time.

Chris Whitty, the chief medical officer (CMO), and Patrick Vallance, who was chief scientific adviser (CSA) between 2018 and 2023, frequently flanked Boris Johnson and Matt Hancock during daily Covid briefings. Both said today that the UK did not have sufficient capacity to scale up testing and treatment programmes when the pandemic struck.

Whitty, giving evidence this morning, said: “We had a very good capacity to do a very small amount of diagnosis really quickly [but] we did not have the ability to scale up – and I could repeat that across multiple other domains.”

Vallance, echoing this, said: “I think scaling up is really, really important.”

The former CSA added: “When we started looking at vaccines in January 2020, it was obvious that the industrial vaccine base in the UK had pretty much gone.” He clarified that this “was not an active decision” but a matter of “benign neglect”.

Whitty also used his time on the witness stand to criticise “the level of abuse and in some cases threat to people who volunteer their time”, referring to attacks – including on himself – during the initial waves of the pandemic. He said the phenomenon was “extremely concerning” and posed a risk to the UK’s ability to rely on scientists during future emergencies.

Heather Hallet, chair of the inquiry, condemned the abuse, saying it was “wrong for so many reasons”.

Both men also expressed the need for health inequalities and disparities to be factored into pandemic planning for the future.

Vallance said: “All pandemics feed off inequality, and drive inequality. That’s the way they behave and that is the tragedy that needs to be understood and is relevant.”

He added that thinking about health disparities needed “to be embedded right from day one”.

It came after Hugo Keith KC, counsel to the inquiry, had earlier put to them that “the government systems on preparedness, and the policy, and the guidance and structures paid absolutely no regard to disparities in health”.

Last week the inquiry heard from Michael Marmot and Clare Bambra who revealed that almost no emergency planning reports had so much as referred to health inequalities.

The first witness to appear this morning was Roger Hargreaves, director of the COBR unit, who made the case for better government transparency around civil protection.

Hargreaves who is director of the Civil Contingencies Secretariat in the Cabinet Office and was responsible for preparing for, responding to and learning lessons from major emergencies.

“It’s also important… that there is transparency about what government does, so government can be held to account,” he said, before adding: “I think there may be room to take it [transparency about civil contingency planning] more seriously.”

Exchanges between Hargreaves and Keith were frequently tetchy. At one point, Keith grilled the official over his lack of knowledge regarding a report by the independent National Preparedness Commission that highlighted “serious weaknesses” in the UK’s national resilience plans, adding they were “not fit for purpose”.

“I think there’s a lot of that which I’d agree with,” Hargreaves said in response.

The inquiry continues.