The right-back was forced off with Atletico drawing 1-1 at the break, as Sime Vrsaljko replaced him at full-back before what proved to be a frantic second period.
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Atletico confirmed soon after his withdrawal that Juanfran’s problem was localised to his right hamstring and is now likely to be touch-and-go for the trip to Leverkusen on February 21 in the Champions League.
He could also miss Saturday’s La Liga match at Sporting Gijon, while Barcelona visit the Vicente Calderon five days after Atletico’s clash in Germany.
Atletico confirmed Juanfran will be sent for further tests and an announcement regarding a return date will be made in due course.