A man in a wheelchair was found dead in a river in the northern city of Hamburg, according to local firefighters.
Witnesses saw him fall into the water and despite a rescue effort that included divers, a boat and a helicopter, he could not be saved.
A pedestrian also died in Hamburg after he was hit by scaffolding that fell from the seventh floor of a building, police said. He was taken to hospital where he later died.
The storm crossed western and northern Germany today and was bound for the east of the country, German meteorologists said.
Several regions of Germany have issued warnings advising residents to stay home while emergency services clear roads and fix power outages.
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