There was a mass crash with 200 metres to go, in the midst of the mass sprint. Fernandez suffered cuts and concussion and was taken to hospital.
Such a head injury requires the patient to remain 24 hours in hospital for observation, the team said on its website.
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In Thursday's stage, Fernandez' teammate Ruben Perez Moreno lost the overall lead to HTC-Columbia's young Australian Leigh Howard, on bonus seconds. The sprint was won by Robert Wagner of Skil-Shimano, with Howard finishing second.
Fernandez, 28, most recently finished second in the Tour de Picardie. He has been with the Basque team since 2004.
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