The rapid spread of Covid makes it “inevitable” that children will be infected and have their education disrupted, making a strong case for vaccinating those aged 12 and over, the government’s leading medical advisers told MPs.

Prof Chris Whitty, the chief medical officer for England, rejected suggestions from one Conservative MP that “white boys” who have previously contracted Covid should be exempt from vaccination, saying that discrimination on that basis wasn’t practical or desirable.

Whitty and Prof Jonathan Van-Tam, the deputy chief medical officer, appeared before the Commons education committee over the decision to offer Covid vaccines to 12- to 15-year-olds, after the Joint Committee on Vaccines and Immunisation (JCVI) had said the benefits were too small.

Vam-Tam told MPs that “lower [risk] does not mean anything close to zero” for children in the age group because of the Delta variants higher infectiousness.

“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 at some point.

“The point of infection, if left to happen, is not of their choosing, and may be at a point in their educational careers, thinking particularly of GCSEs and A-levels when it is extremely inconvenient to be laid low, albeit for a short number of days, with cough, fever, and respiratory symptoms,” Van-Tam said.

Whitty told MPs said any time in school missed through being inoculated should be balanced against the longer period lost to those who were infected. “You’re not comparing a child being vaccinated against nothing happening, you’re comparing a child being vaccinated against a near-certainty that child will get Covid,” Whitty said.

The appearance by the medical leaders, including Prof Wei Shen Lim of the JCVI, came after new figures showed that Covid infections have spread rapidly inside England’s schools, following the government’s decision to end the use of preventitive measures such as masks, social distancing and self-isolation.

Robert Halfon, the Conservative MP who chairs the committee, asked if the witnesses acknowledged there was “low transmission” of Covid among the 12-15 age group.

Whitty replied: “That is not true, there is definitely substantial transmission happening in this age group. In fact the age group we are talking about is the one in which the highest rate of transmission is currently occurring, as far as we can tell.”

He added that it was a “reasonable stab” to estimate that 50% of children in England had already had Covid, leaving many still at risk, and noted that children in deprived areas were at the greatest risk of seeing their education disrupted.

Caroline Johnson, the Conservative MP for Sleaford and North Hykeham, asked: “Why not vaccinate just those children? We know that children from black and ethnic minoroity groups are more at risk from Covid.”

Whitty responded: “I’m not convinced that feels to me like an effective public health intervention,” adding that such discrimination would not be desirable.

But Johnson – a medical doctor – went on to ask Whitty if the risks to some “white boys” from vaccination made it justified.

“Just to be really clear on this, if you’re a parent in a rural area with relatively low levels of Covid disruption so far, who is white, male, and already certainly had Covid and tested positive for Covid before, is the vaccine still, for that child, in their benefit?” Johnson said.

Whitty said trying to differentiate between children was difficult: “It’s not obvious to me what gain you get from this, given that even at an individual level, benefits marginally exceed harms, as the JCVI laid out.

“So I think if you tried to design a programme where you actually said, ‘the government refuses to vaccinate the following people,’ if you actually wrote it down I think you’d find it quite difficult to put something out that both made sense and was actually deliverable.

“At a certain point, public health is about pragmatism and about saying, what is to the benefit of the people who are the most disadvantaged, which is our starting point.”