Two weeks before the start of the summer half-term holiday, Haslingden High School in Rossendale, north-west England, recorded almost no cases of Covid-19.

That Monday, two students tested positive for the virus and were sent home. Two became ten. By Friday, there were 35 cases reported in the school. Within a week the number had grown to 70.

“I just sat there watching the emails pinging through,” said headteacher Mark Jackson, who reluctantly made the decision to close the school and move all lessons online just days before the start of half term on May 27.

“It [coronavirus] definitely was being passed around in school,” he said. “The contact tracing was just becoming overwhelming.”

Haslingden is one of many of schools struggling to contain the rise of a new coronavirus variant that has ripped through parts of the country in recent weeks. Pupil populations, which remain unvaccinated, have been disproportionately hit leading teachers to call on government for clearer guidelines on safety, testing and vaccination for young people.

The proportion of pupils in England absent from school because of Covid nearly doubled in the week leading up to the start of half-term, rising from 1 per cent to 1.8, and accounting for more than 140,000 pupils, according to government data.

Paul Whiteman, general secretary of the National Association of Head Teachers, a union, said high levels of absence were causing unavoidable disruption to education “particularly in those hotspot areas”.

In places where the Delta variant first identified in India has taken hold, the spike is sharpest. In Bolton, 31 per cent of secondary school pupils were off for Covid-related reasons, while in Blackburn and Darwen, which borders Rossendale, 13 per cent were absent, in the same period.

As cases of the Delta strain, which is 40 per cent more transmissible than the previously dominant Alpha variant continue to rise, teachers fear the situation will grow worse.

Chart showing that the Delta variant has rapidly out-competed the Alpha variant in the UK, sending cases surging

At Haslingden High, children are back after the holiday. But staff fear more will have to be sent home following results of their PCR tests this week. “We feel like we’re waiting for it to happen again,” Jackson said.

In Manchester, Samantha Offord headteacher at Birchfields primary school, is concerned the disruption will further set back pupils already hit hard by the pandemic, often living with high levels of deprivation. “It’s really been awful,” she said

“It’s not so much the learning, it’s their attitude to learning, their resilience [that is affected],” Offord said. “We’re just feeling like we’ve got on top of it and then you send 90 children home.”

Since schools returned to in-person teaching on March 8, the government has advised all secondary pupils and teachers to test themselves for Covid at home twice a week using lateral-flow devices which give a result within half an hour.

It said it was taking “additional measures” where the Delta variant was spreading, “including increasing testing for staff, pupils and families”.

Professor Russell Viner, a paediatric professor at University College London and adviser to government’s SAGE committee, said high levels of testing in schools meant more cases were being recorded than other parts of society, adding that school infections mirrored those in the community, rather than driving rates of transmission.

“We opened schools [in March] and, contrary to what people suggested, cases continued to fall. That tells us very clearly that this isn’t just about children in schools,” he said.

But some scientists warn that lateral-flow tests miss many cases, and that schools, which are already struggling with the administrative burden of running test-and-trace programmes, are unsure students are conscientiously taking them.

“It’s difficult to know,” Andy Byers, headteacher at Framwellgate School in Durham, said. “We only require them to tell us if they’ve tested positive.”

Some school leaders are calling on government to urgently improve safety standards in schools.

The National Education Union, which represents teachers, and Unison, which represents support staff, have called for face coverings to be mandatory in all areas of schools, and vaccinations for all children aged 12 and over.

This week Matt Hancock, health secretary, signalled he is drawing up plans to offer Covid vaccines to children later in the summer. The government lifted previous guidance that pupils wear masks in school settings on May 17.

Byers is among many school leaders who distrust the government’s guidance and are taking decisions into their own hands. In the absence of a clear framework for what would happen in the event of an outbreak, he has decided safety precautions, including masks, should continue.

Line chart of Share of pupils absent due to the coronavirus, state schools only (%) showing School pupil absences due to Covid-19 increase in England

Precautions, he said, have helped keep cases at the school low. But rising case rates in nearby Newcastle are a worrying reminder of the disruption that could come.

“We’ve had no real communication all the way through, which is why we took the measures we took ourselves,” he said. “I can see us keeping this until the end of term.”

Union chief Whiteman urged the government to address what he called an “explanation deficit” which has left schools unsure of what will happen in the event of a local outbreak.

He said educators feared a repeat of the “disastrous” last term, when the government closed schools a day after children returned from the Christmas holidays after insisting for weeks they were safe to reopen.

At Haslingden High, Jackson is anxious about what is to come.

“If we have another September where you’re isolating close contacts students will really suffer,” he said. “It has honestly been a really tough 15-16 months . . . we’ve coped, but it’s getting to the point where it’s getting difficult to cope.”