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The Prime Minister has warned teachers not to send home year-round groups or classes unless a student or staff member gets a positive coronavirus test.
Johnson stepped in when he was grilled by MPs on his second appearance before the liaison committee on the government's response to coronavirus, testing capacity and Brexit.
The lack of tests this week created chaos for schools at the start of the fall semester. Teachers, parents, and children are struggling to get tested after showing possible Covid-19 symptoms.
Johnson said the demand for tests had increased and caused the backlog. However, the government intends to hit 500,000 tests a day by the end of October.
Greg Clark, chairman of the science and technology selection committee, who also sits on the liaison committee, said there would be a rolling system of school closings this fall when entire classes were sent home for two weeks because someone had a cough in class.
Johnson said, “That would be wrong and that shouldn't be happening because the reasons for sending such a class or a bubble home would be when someone tests positive.
"If someone tests positive who came in contact with their bladder, the rest of the bladder must self-isolate."
He urged teachers and parents to read advice from Public Health England and NHS Track and Trace.
Clark asked again if students and teachers would be sent home before a test result was received, to which Johnson clarified, "You should go if you test positive."
Johnson faced nearly two hours of questions in a downbeat session that predicted a gloomy outlook on testing, the financial impact of another lockdown, and the death rate from Covid-19.
He said the country currently lacks testing capacity, deviates in any way from pregnancy styles test kits, and that the financial consequences of a second lockdown would be disastrous.
Speaking of the number of deaths likely after the cases surge, he said, “The incidence in the over 80s group is now 12 per 100,000. Just a few days ago it was about half of that. It grows.
“And unfortunately, although the number of cases… is obviously much lower than in the spring, we have to expect that these infections are proportional to the mortality.
"That's the reality."
At Brexit, he accused the EU of failing to act in good faith in efforts to reach a trade deal, particularly over whether food would be sent from the UK to Northern Ireland in the future and whether the EU would authorize imports. This came just hours after Northern Ireland Secretary Brandon Lewis said the opposite: the EU acted in good faith.
Johnson said, "Maybe they'll prove my suspicions wrong."