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Figures from the UK Health Security Agency show a third of under-fives with suspected respiratory syncytial virus test positive.
Dame Ruth told NHS board members: “We’ve got increasing RSV – we see that every year but we are now at highest for 5 years, with critical care at 99 per cent capacity across England.
“We are not yet at the position of seeing RSV numbers go down but we are working hard on it.”
The chief nurse added that wards are so busy children must be transported between hospitals in some areas.
Dr Camilla Kingdon, president of the Royal College of Paediatrics and Child Health, said: “Paediatric teams are exceptionally busy this winter as a result of ever rising demand and staffing issues.
“Some of this increased demand is due to RSV and other respiratory infections, alongside other illnesses and issues.”
The UKHSA said hospital admissions for flu are also highest among children under five.
Official figures show youngsters’ intensive care wards were 90 per cent full last week, with general wards at 82 per cent.
This time last year, intensive care was 82 per cent full and general beds 77 per cent.
Dr Conall Watson, from the UK Health Security Agency, said: “RSV is unfortunately common at this time of the year and can be severe for children under two – particularly for babies and those born prematurely.”
More than 1,000 children were refused admission to intensive care last year because of a lack of beds, the Health Service Journal reported.
Freedom of Information data from 19 NHS hospital trusts revealed 1,345 ICU referrals were turned down last year, with experts blaming staff shortages.