Test positivity rates among state-funded secondary school pupils in England increased a fifth over the last two weeks © Oli Scarff/AFP

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Most secondary school pupils in England will return to class later than usual in January to allow for mass coronavirus testing as new data shows a high number of Covid-19 cases among children.

Experts remain divided on whether children are fuelling a wider jump in virus cases, but the rising numbers ensured a chaotic end to term this week with widespread absences and part closures, particularly in London and the south east.

The government on Thursday announced that most secondary pupils will learn remotely until January 11, although there are exceptions for years 11 and 13, vulnerable children and those of key workers. Headteachers will need to set up a rapid testing programme for staff and pupils from the first week of term.

Test positivity rates among state-funded secondary school pupils in England increased a fifth, from 11.3 to 13.5 per cent, over the last two weeks, while the figure for all people across all age groups fell from 6.7 to 6.2 per cent.

Chart showing that positivity rates have been climbing in secondary schools

The latest official data from the Department for Education show that in the week ending December 10, every state secondary school in 10 different local authorities had at least one pupil self-isolating because of Covid-19, and almost a third of pupils were self-isolating in many parts of the south-east.

Separately, the React-1 Study by researchers at Imperial College London found that between November 13 and December 3 the highest rates of coronavirus prevalence were among children, and they appeared to increase more in the second national lockdown compared to the first, when schools were closed.

Professor Paul Elliott, one of the lead authors, said “the mixing of school-age children has corresponded to increased risk [of coronavirus spreading]”, particularly in London.

However, other scientists argued that infection rates in schools are driven by levels in the wider population. In the Schools Infection Study, released on Thursday, researchers from the Office for National Statistics and Public Health England said evidence suggested infection rates in schools “closely mirrored” those in the community.

Chart showing that most European countries arrested and reversed their resurgence in cases while keeping schools open

It found that 1.24 per cent of pupils and 1.29 per cent of staff tested positive for coronavirus in November, similar to the 1.2 per cent in the general population.

Chief investigator Dr Shamez Ladhani said close analysis showed pupils had contracted coronavirus from different sources, with outbreaks in schools mirroring those in the community.

But he admitted that new evidence from London, where rates of coronavirus have continued to rise in schools even as lockdown measures saw cases decline in the wider population, had complicated the picture. “That’s a really odd situation . . . we need to understand that better,” he said.

Chart showing that Many pupils have been absent from school isolating or quarantining in recent weeks

The contradictory data comes days after the government took legal action to force some schools to stay open, with teachers’ unions arguing that headteachers should be allowed a more flexible approach to remote learning.

Data by teacher survey site Teacher Tapp, showed that only 48 per cent of schools in London were open to all years and classes on Monday, and 10 per cent had closed their premises to all but vulnerable children and those of key workers.

Mary Bousted, the general secretary of the National Education Union, blamed the government for “through the roof” infection rates. “Everything that has come to pass now is the result of an ideological drive to keep schools open, to hell with the consequences,” she said.

A member of the government’s Scientific Advisory Group for Emergencies (Sage) acknowledged the role of schools in driving transmission had “grown in importance” and said they were “clearly implicated in the south eastern resurgence”.

But the member added that if stopping the spread of Covid-19 was the only objective closing schools would be “required”, but preventing other long-term consequences meant keeping them open was “probably essential”.

“We are actively working different school patterns to find an optimum policy,” the person said.

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