Ministers knew in 2016 that “even a moderate pandemic would overrun the system” and the government’s emergency response function would be “very rapidly overwhelmed” by a major disease outbreak, the UK Covid-19 public inquiry has heard.

A meeting of the Department of Health and Social Care board – which included the permanent secretary, Sir Chris Wormald, and the then chief medical officer, Dame Sally Davies – concluded “there would be significant issues if it became necessary to track or quarantine thousands of people”, newly disclosed documents revealed.

But the civil servant who subsequently took charge of emergency preparedness and health protection at the DHSC, Emma Reed, said “there was no discussion with me about quarantining” and “there was no discussion with me about track and trace”.

At the start of the third week of the inquiry’s investigation into the UK’s preparedness for a pandemic that claimed more than 220,000 lives, Reed, who took charge of the health system’s emergency preparedness directorate in February 2018, said she had been aware of the risk of “system overload”.

But the inquiry heard how some attempts to strengthen the system were shelved: in 2016 a decision to fund high-end quarantine facilities was “deferred by ministers”, documents revealed. Meanwhile, as a no-deal Brexit loomed in November 2019, the government deprioritised key projects to prepare for a pandemic that was just around the corner.

The inquiry also heard how Matt Hancock, the health secretary from July 2018, requested a briefing note on emergency preparedness when he took office. He was told of plans to cope with “an additional 800,000 bodies” in the event of a flu pandemic, the note showed.

But there was no mention of the fact that the 2016 Exercise Cygnus, a major cross-government flu pandemic exercise, found that the UK’s pandemic preparedness and response plans and capabilities were not sufficient to cope with a severe outbreak. Hancock is due to give evidence on Tuesday.

By June 2020 only 8 of the 22 work streams based on the recommendations from Cygnus had been completed. DHSC’s pandemic flu readiness board didn’t sit at all between November 2018 and November 2019 as a result of the threat of a no-deal Brexit.

The government was also accused of sidelining nurses and other healthcare groups in the run-up to the pandemic, including those who had worked closely on outbreaks of Ebola in west Africa and Middle East respiratory syndrome in Saudi Arabia. Rosemary Gallagher, the Royal College of Nursing’s professional lead in infection prevention and control, told the inquiry it had been “a mistake” not to include nurses in Exercise Cygnus. Before Covid the government made engagement with stakeholder organisations less of a priority, she said.

During Reed’s evidence the inquiry revealed internal DHSC documents relating to a November 2019 pandemic preparedness meeting that showed “areas of work not prioritised” included boosting adult social care and community care during a pandemic, the public health communications strategy and refreshing the 2011 pandemic flu strategy to ensure it was “accurate and up to date”.

The pandemic flu strategy was the UK’s only pandemic plan and envisaged the possibility of 800,000 deaths.

“My view that time was preparing for a no-deal exit took precedent over completion of some of these pieces of work for a short period of time,” Reed said.

Hugo Keith KC, counsel to the inquiry, challenged Reed over the priorities. He said that given a significant number of care home residents would probably die in a flu pandemic, “why did no one say we cannot afford to stop the pandemic preparedness?” She said no-deal Brexit had been a “real and present and credible threat” while a pandemic was “the risk of a threat”.

The inquiry also heard from Reed that “there was no overarching assessment of the impact of the pandemic preparedness strategy on inequalities” since the publication of the 2011 flu pandemic strategy.

The inquiry continues.

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