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The coronavirus epidemic is now “concentrated” in hospitals and care homes, which is pushing up the overall rate of infection, one of the government’s scientific advisers has said.

The reproduction, or “R”, rate of the virus has actually risen over the last two weeks despite a decline in community transmission under lockdown, according to professor John Edmunds of the London School of Hygiene and Tropical Medicine.

This is because the epidemic is showing fewer signs of slowing down in hospitals and care homes where there is a “big problem”, and so the average is higher, he said.

Edmunds, who sits on the government’s scientific advisory group for emergencies (Sage), said the most recent estimates put the R rate between 0.75 and one, or just below one, with London at the lower end.

There was confusion as foreign secretary Dominic Raab told the Downing Street briefing that the R rate was lower – between 0.5 and 0.9, the lowest government estimate yet.

But national statistician Sir Ian Diamond then told the same briefing he would “not demur” from Edmunds’ estimate, admitting the R rate had risen.

He said: “It’s probably gone up just a little bit from these last estimates and that is driven by the epidemic in care homes, he [Edmunds] would say, and I would not demur from that.

“That is a real challenge to reduce the epidemic in care homes.”

The government is using the R number, which sets out how many other people one person with Covid-19 infects on average, to determine how far and how fast to lift the lockdown.

Ministers must keep the R rate below one or risk a rapid increase in the spread of the virus.

“It’s a big problem that we have in hospitals and care homes, but I think what’s happened is that the community epidemic has come down and that epidemic is now being concentrated in these settings,” Edmunds told the Commons science committee.

“Our data are not really good enough to give us any certainty about what the reproduction number really is in hospitals and it’s probably variable between one hospital and another, and care homes is even worse.”

Edmunds said the epidemic in the community had shrunk “really considerably” under lockdown, so “what we’re seeing is this continuing epidemic in hospitals and care homes”.

“What we are now measuring as the reproduction number is […] to a significant proportion this residual reproduction, this residual transmission in these settings.”

Earlier, Diamond told the committee that the ramping up of Covid-19 tests in care homes should be used to build a study of the transmission and prevalence of the virus in those settings.

“I do believe that the epidemic in care homes is not going to go away in the short-term,” he said.

Shadow health secretary Jon Ashworth said the rising R rate showed the government had failed to implement infection control at care homes.

He said: “Many warned care homes were highly vulnerable calling for a credible strategy to protect residents and care workers with PPE and accessible, regular testing.

“If ‘R’ now increasing because of social care surely exposes government failures to implement infection control in social care.”