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The cull was ordered after a mutated version of the coronavirus was found to have spread among the country's mink herd. It later emerged the government did not have legislation in place for the order.
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The strain found in the minks is the same one found in humans, an agriculture official said, and a breeder at one farm also tested positive. Some 2,500 minks have reportedly been culled already.
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The government announces a number of restrictions on parts of northern Denmark, the area hit hardest by the infections. Danish officials recently ordered the killing of up to 17 million minks.
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The country said it discovered a virus mutation that can spread to humans. Danish officials are concerned it could impact the body's ability to form antibodies.