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Ministers were warned coronavirus could kill as many as 3,500 people in prisons – but later chose to publish revised guidance that put the figure at just 100.
Prison charities have put justice secretary Robert Buckland under pressure after making the revelation on Wednesday.
Public Health England had originally sounded the alarm over inmates and prison staff in late March, saying the worst case scenario for the prison system was as many as 3,500 deaths from Covid-19.
But a month later, Buckland published updated guidance from PHE that estimated a dramatically lower 100.
It is not yet clear why the estimate changed, but the documents have been published amid shortages of personal protective equipment (PPE) for frontline staff and concerns the virus can easily spread indoors.
The Howard League for Penal Reform and the Prison Reform Trust were sent the documents after they threatened the Ministry of Justice with legal action for failing to release more low-risk prisoners when the virus began to peak.
As of 5pm on Monday, a total of 19 prisoners and six prison staff are known to have died after contracting Covid-19. Data also show 362 prisoners across 74 jails, and 401 workers in 67 prisons, have tested positive.
The MoJ has released a number of pregnant prisoners and some other low-risk prisoners early, meaning the prison population has been reduced by around 3,000. There are thought to be about 81,000 remaining prisoners in England and Wales.
Halting of the majority of court cases has meant few new inmates – which experts viewed as the most likely source of an outbreak.
Prisoners have also remained locked up in self-isolation for long periods to avoid contagion, something charities say is “neither sustainable nor humane”.
As Boris Johnson prepares to begin to ease the lockdown from next week, however, both charities have called from more transparency from ministers.
Frances Crook, chief executive of the Howard League, said civil society must hold government to account, adding: “The documents that we are publishing today would never have seen the light of day were it not for our legal intervention. Transparency is essential in a time of crisis.
“We also have a responsibility to keep probing, to hold ministers to their promises, and to call for action. That is what we are doing now.”
Peter Dawson, director of the Prison Reform Trust, said containment of the disease in prisons “rests on the most fragile of foundations” and said a “more generous” release scheme was needed.
He said: “Sticking to the current regime of almost universal bang-up simply isn’t sustainable for the next 12 months. And without government intervention, the prison population is bound to return to previous levels as courts come back into action.”
A statement released by the government last week said modelling by PHE and HM Prison and Probation Service found measures taken by government were successfully limiting deaths and containing the outbreak.
Prisons minister Lucy Frazer thanked prison staff and celebrated “positive signs that our carefully implemented approach is limiting the impact of this initial phase of the pandemic – actual cases and deaths so far are much lower than originally predicted”.
She added: “We will continue to do everything possible to make sure this remains the case.”
HuffPost UK has contacted Public Health England for comment.
A prison service spokesperson said: “We have robust and flexible plans in place to keep staff, the public and prisoners safe. These are based on the latest public health advice, and there are positive early signs that these are proving effective.”