The chief medical officer said the “great majority” of those aged 12 to 15 who were unjabbed were likely to catch the virus “at some point” in the future.
But the senior medic said that those schoolchildren who refuse to get vaccinated should not be stigmatised or excluded from classroom activities.
Appearing before MPs on the Education Select Committee, Professor Whitty urged those who were invited to be vaccinated to do so, saying the benefits of inoculation “outweigh the risks”, although he conceded this was only by a “small margin”.
He said: “The great majority of children who have not currently had Covid are going to get it at some point.
“It won’t be necessarily in the next two or three months but they will get it sooner or later because this is incredibly infectious ... vaccination will reduce that risk.”
For those who refused to take up the offer of a vaccine, he said the “views of families should be respected and no one should be stigmatised in either direction”.
Dr Camilla Kingdon, president of the Royal College of Paediatrics and Child Health, who was also answering questions from MPs, added: “Whatever choice a child makes or a family makes there should be no judgment attached to it.
“We would expect that children and families who decided not to take up this offer are able to participate in a full range of activities.”
Professor Whitty said there was “substantial transmission happening” in the 12-to-15 age group. “In fact, the age group we’re talking about is the one in which the highest rate of transmission is currently occurring, as far as we can tell,” he said.
Given the low risks posed by the virus to children, the Joint Committee on Vaccination and Immunisation (JCVI) had originally said that the individual advantage of vaccinating children against Covid was “marginal”, and asked the CMOs to assess the wider public health benefits.
But Professor Whitty and his counterparts concluded in advice issued on 13 September that the vaccination of this age group would help to reduce Covid-19 transmission in schools and minimise educational disruption.
Under the CMOs’ recommendation, children are being offered just one dose. The JCVI will be consulted next spring, when more data is available internationally, to determine if a second dose is needed.
Doses will be largely administered within schools, health officials said, and children considered competent will be given the final say on whether they want to be vaccinated.
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