Government plans to reopen all schools in September were called into question by leading scientists and the head of a major teaching union last night amid signs that cases of Covid-19 are increasing again at an alarming rate.

Despite imposing new restrictions on people meeting indoors in parts of the north of England on Thursday – and postponing plans to allow bowling alleys, casinos, skating rinks and other venues to reopen a day later – ministers insist that reopening schools fully early next month remains a top priority.

But in a sign of growing concern and uncertainty about the strategy, Patrick Roach, general secretary of the NASUWT, which represents more than 300,000 teachers across the UK, said the government needed to take urgent action to convince parents and teachers that schools would be safe.

While insisting he was not calling for a postponement, Roach told the Observer: “In light of recent changes to plans for relaxing lockdown measures, the government needs to provide greater clarity to school leaders, teachers and parents about what this will mean for the reopening of schools in September.”

He added: “The warning from the chief medical officer [Chris Whitty] that a fine balance has to be struck in ensuring public health at this stage of the pandemic, and that the country may have reached the limits to the easing of lockdown, will no doubt prompt questions for many parents as well as for those working in schools.

“If schools are to reopen safely, the government will need to give them clarification about what they need to do to take account of the latest scientific evidence and advice, as well as sufficient time to review and, if necessary, adjust their reopening plans.”

Meanwhile, Paul Hunter, professor in medicine at the University of East Anglia, said it had become clear that there is a link between closing schools and controlling the spread of the virus. “The evidence is clear that schools are important in the spread of Covid-19,” he said. “Our studies show that, across Europe, closing schools was the single factor most strongly associated with drops in infection rates.”

Hunter added that while individual risks to children and teachers were probably low, school transmission was likely to push up general infection rates, so the disease would rise exponentially again. “Would re-opening schools increase the spread of Covid-19 in the population? Yes. I think it would very probably do that.”

The chairman of Sage’s sub-group on pandemic modelling, Graham Medley, said it could come down to a choice between reopening schools and shutting other venues such as pubs. “Most people think that opening schools is a priority for the health and wellbeing of children and that when we do that we are going to reconnect lots of households,” Medley told BBC Radio 4’s Today programme.

However, he cited Whitty’s warning about the limits of reopening society. “So closing some other networks, some other activities may well be required to enable us to open schools,” Medley said. “It’s a matter of prioritising. Do we think pubs are more important than schools?”

Virologist Jonathan Ball, of Nottingham University, also warned about the risks of reopening schools as infection levels are rising. “We don’t yet understand whether children play a major role in transmission either to each other, or to the wider community, though we do know that they can be very good incubators and spreaders of viruses.”

It may well be that there is a quid pro quo to be made and we have to stop going to pubs or restaurants

The fear is that infection rates will start to increase in autumn because coronaviruses are seasonal and levels peak in winter months, he added.

“There is real concern now about how easy it will be to safely open schools without threatening the wider community. It may well be that there is a quid pro quo to be made and we have to stop going to pubs or restaurants. It is not just about educating children and preserving their mental health, after all. It’s also about allowing parents to go to work as well.”

One concern for teachers is the wearing of face masks. While this is compulsory for children of 11 and over in shops and on public transport, the guidance is that masks are not necessary for pupils or teachers in schools. One union source said this “makes no sense at all”, adding that parents would justifiably query apparent inconsistencies in the rules.

A Department for Education spokesperson said: “We have set out the controls schools should use, including cleaning and hygiene measures, to substantially reduce the risk of transmission. This does not include the wearing of face coverings as we believe the system of controls laid out adequately reduced the risk of transmission to both staff and students.”

Another DfE source said ministers remained committed to schools reopening, but added: “In the event of a local outbreak, Public Health England health protection team or local authority may advise a school or number of schools to close temporarily to help control transmission. Schools will need a contingency plan for this eventuality. This may involve a return to remaining open only for vulnerable children and the children of critical workers, and providing remote education for all other pupils.”

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