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The news comes on the day Germany witnessed its worst spike in cases in more than three months, with 1,445 new infections confirmed, bringing its total to 219,964. The glitch is the result of a scheme to test motorists travelling on motorways in the southern region of Bavaria last month.
Bavaria’s Minister President Markus Soder – a candidate to replace Angela Merkel as Chancellor – described the news as “very, very troublesome”.
Blaming an error at the test centre, he added: “That has to be fixed immediately and mustn’t happen again.
“All structures must be checked immediately.”
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A spokesman for the Bavarian State Office for Health and Food Safety (LGL) said: “People who voluntarily had themselves tested unfortunately had to wait longer for their results.”
However, it was not immediately apparent how many pf the 44,000 had been returning from abroad.
The fact that almost 1,000 people with the illness have not been confirmed as being infected for such a length of time will come as a massive worry to the Germany authorities.
Speaking during today’s press conference, Mr Soder added: “It is now very important that we will inform everyone of their test results in the next hours and days.
“The mistake was due to the implementation, not the strategy.”
CSU leader Mr Soder, who has cancelled his holiday in order to deal with the crisis, has faced sharp criticism from the Bavarian opposition.
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Green parliamentary group leader Ludwig Hartmann described it as a “blatant government failure”.
He added: “This is shocking news for Germany and leaves scratches in the halo of the complacent crisis manager Söder.”
FDP parliamentary group leader Martin Hagen tweeted: “Söder’s pretence to be a corona model student is increasingly falling apart.”
He said the CSU could not blame the “failure of the government” on small coalition partners Mr Hagen added.
The SPD member of the state parliament Markus Rinderspacher said: “This failure requires clarification.”
Speaking yesterday, Mrs Merkel’s Health minister Jens Spahn blamed smaller and larger outbreaks happening in most of the country, in contrast to previous spikes confined to specific neighbourhoods or factories.
He warned: “This obviously – if we don’t all watch out now – can lead to a certain dynamic and the reemergence of the pandemic.”
Mr Spahn also urged people to maintain social distancing and not to go overboard when it came to socialising.
He added: “When there’s alcohol involved, when a festive event turns into a party, it can go very, very quickly.”
(Additional reporting by Monika Pallenberg)
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