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"Vijay Shankar sustained a non-displaced fracture of the left big toe, which will require a minimum of three weeks to heal. The injury rules him out of the ongoing World Cup," said a statement from the Board of Control for Cricket in India.
Shankar was hit on the foot by a yorker from paceman Jasprit Bumrah during a training session in Southampon on June 19 and was not in the team for India's defeat to England at Edgbaston on Sunday.
Shankar played three matches at the tournament in England and Wales, against Pakistan, Afghanistan and the West Indies, but did not bowl in his last two matches.
The 28-year-old Agarwal, a top-order batsman, has played two Tests but is yet to play a one-day international.
Injuries have troubled India throughout their World Cup campaign, with opener Shikhar Dhawan earlier forced out of the tournament with a broken thumb.
Fast bowler Bhuvneshwar Kumar suffered a hamstring strain against Pakistan and has not played since but he is fit and will be available for selection for India's next game, against Bangladesh in Birmingham on Tuesday.
Virat Kohli's India need to win one of their remaining two matches to guarantee a semi-final spot in the 10-team event.
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