Jonathan Van-Tam has said it is now “inevitable” teenage school pupils will catch coronavirus.
England’s deputy chief medical officer said it is no longer a “theoretical risk” that 12 to 17-year-olds will be infected.
It comes after government figures showed more than 122,000 children – about 1.5% of pupils – in England were out of school last week for COVID-19-related reasons.
Prof Van-Tam told the House of Commons education committee on Wednesday: “Because the Delta variant is so infectious, we are not looking at a theoretical risk of children 12 to 17 becoming infected. I think it is really quite inevitable that they will be so at some point.”
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He also acknowledged the inevitable disruption to pupils’ education, including during exam periods: “The point of infection, if left to happen, is not of their choosing and may be at a point of their educational careers, particularly at GCSE and A-levels, where it is extremely inconvenient to be laid low – albeit for a short number of days.”
Speaking at the same committee hearing, England’s chief medical officer Prof Chris Whitty suggested about half of children have already had COVID and the rest are more likely to get it without a vaccine.
He told MPs: “Let’s make an assumption that the great majority of children who’ve not currently had COVID-19 are going to get it at some point over the next period.
“It won’t be necessarily in the next two or three months but they will get it sooner or later.”
But Prof Whitty added: “Vaccination will reduce that risk.” Jabs have recently become available for over-12s.
The government has been criticised for its schools COVID strategy, with Geoff Barton, general secretary of the Association of School and College Leaders, saying on Tuesday: “We are hopeful that the vaccination programme for 12 to 15-year-olds will help to reduce this level of disruption.
"However, the government must also take more action to support schools and colleges.”
Paul Whiteman, general secretary of school leaders’ union NAHT, said the latest absence numbers reflected changes to policy which now requires fewer pupils to self-isolate when there is a positive case in school.
“We already know of schools that are struggling to keep classes open due to outbreaks occurring," he added.
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