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Johnson confirmed that educational settings would remain open during the lockdown - which will last from November 5 to December 2 at the least - despite statistical evidence showing that transmission of the virus is high in schools.
The PM said that he would not let the virus 'damage our children's futures even more than it has already'.
However, before that announcement was made, the National Education Union's Joint General Secretary Kevin Courtney asserted that the Office for National Statistics data shows that schools are 'an engine for virus transmission'.
Mr Courtney said that the NEU's analysis of the data showed that virus levels are nine times higher in primary schools and 50 times higher amongst secondary school pupils from the start of term.
Speaking before the Prime Minister, but after the news of the second lockdown was leaked to the press, Courtney explained: "It would be self-defeating for the Government to impose a national lockdown, whilst ignoring the role of schools as a major contributor to the spread of the virus.
"The Government should include all schools in proposals for an immediate national lockdown."
The ONS said on Friday that young adults and older teenagers 'continue to have the highest positivity rates, while rates appear to be steeply increasing among secondary school children.'
Despite the calls from the NEU, which represents the majority of teachers and education workers in the UK, Johnson confirmed that the schools would remain open.
He said: "My priority - our priority - remains keeping people in education.
"So childcare, early years settings, schools, colleges and universities will all remain open.
"Our senior clinicians still advise that school is the best place for children to be.
"We cannot let this virus damage our children's futures even more than it has already and I urge parents to continue taking their children to school.
"I'm extremely grateful to teachers across the country for their dedication in enabling schools to remain open."
The NEU said that 85,000 teachers and support staff have backed their #CloseThe Schools call, which trended on Twitter shortly after the announcement.
They did say that children of key workers and vulnerable pupils should still attend school, but that not closing them to other children would result in the lockdown lasting for longer.
Figures show that more than half of England's secondary schools sent at least one pupil home as a result of the virus last week.
However, some scientists say that the role of children in transmitting the virus is not yet fully understood.
The National Head Teachers' Association (NAHT) said that it is 'right to prioritise keeping pupils in schools'.
However, they also called for more support for pupils and staff that are forced to self-isolate due to the virus.
The Deputy General Secretary of NAHT, Nick Brook, said: "Children learn best when in school.
"At a time when we should be talking about how best to support pupils to catch-up lost learning, we are instead faced with the challenge of ensuring that they do not fall even further behind.
"Government now need to accept that reliance upon a summer series of exams in 2021 is a wholly inadequate solution.
"We must be confident that the continued disruption to education this year does not result in the award of grades that do not fairly reflect students true ability.
"Future opportunities and life-chances of 16 and 18 year olds must not be limited as a result of government dithering."
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