The Education Policy Institute said the high rate of pupils out of school across England is a continuing concern with higher absence linked to greater learning loss.
The latest snapshot figures released by the Department for Education estimate that 1,179 pupils in state-funded Leeds schools were absent because of Covid-19 on December 16 – 2.4 per cent of all those in schools which responded to the survey.
Of them, 900 were off because of a confirmed or suspected case of the virus.
A further 196 pupils were absent due to attendance restrictions in their school, 20 pupils were required to remain at home or isolate in line with government guidance, and 63 were isolating for other reasons.
Including absences for non Covid-related reasons, 89.3 per cent of Leeds pupils were attending class that day, though the DfE warned that just 39 per cent of schools responded.
This was down from 89.8 per cent on December 9.
Across England, 3.7 per cent of pupils were absent for coronavirus-related reasons on December 16 – the most since the start of the school year in September.
Natalie Perera, chief executive of the EPI think tank, said: “Our research has shown an association between pupil absence and higher learning losses, so the high rate of pupils out of school continues to be a concern.
She added that staff shortages are likely to persist for some time due to the high level of infection in the general population.
On December 16,three per cent of teachers and school leaders were off because of Covid-19 in England – also the most since term began.
In Leeds, 2.2 per cent of teachers were off – up from 1.7 per cent a week previously, and also the highest proportion yet.
Geoff Barton, general secretary of the Association of School and College Leaders, said: “The challenges posed by having so many staff absent will continue to put schools and colleges under severe pressure.
“The costs of bringing in the supply staff needed to maintain learning is crippling for schools and colleges and the Government needs to step in to help, as well as providing more support on ventilation.”
More recent national figures suggest the picture got worse over Christmas, with 3.9 per cent of pupils and 8.6 per cent of teachers absent for reasons connected to coronavirus on January 6.
A DfE spokeswoman said: “School staff are working tirelessly to ensure classrooms are safe, and it is thanks to their efforts that 99.9 per cent of schools are open once again and millions of pupils have returned to face-to-face learning after the Christmas break.
“We are supporting schools through encouraging former teachers to come back to classrooms and extending the Covid workforce fund for schools that are facing the greatest staffing and funding pressures.”
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