Manish Pandey sustained a left side strain during a practice session.
Karthik played his last match against Afghanistan at Dhaka in March 5, 2014.
Following the change, the team composition is as follows:
Shami, Umesh Yadav, Bhuvneshwar Kumar, Jasprit Bumrah and Dinesh Karthik.
The defending champions will begin their Champions Trophy campaign again arch rival Pakistan on June 4 in Birmingham following matches against Sri Lanka and South Africa on June 8 and June 11 respectively.
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