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Baker, the Somerset quick who was expected to lead England's attack in the Caribbean, experienced discomfort while bowling in a warm-up fixture and was subsequently sent for an MRI scan that revealed bone stress in his lumbar spine. He will now return to his county for rehabilitation work.
Yorkshire right-armer Cliff, who picked up four wickets at 23.25 on England's tour of Sri Lanka in December, will come in as Baker's replacement. England started their campaign by bowling out Bangladesh for 97 in St Kitts on Sunday.
Baker's addition was approved by the ICC technical committee and is available for England before their game against Canada.