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Pietersen, who suffered the injury while fielding on Friday, would be re-assessed ahead of the third Test at Old Trafford starting on August 1.
"Kevin Pietersen will not take the field for the remainder of the second Test after scans showed a left calf strain," the spokeswoman said.
"He will continue to be monitored and assessed ahead of the third Test."
Pietersen has missed most of England's matches since a knee injury forced his early exit from the tour of New Zealand in March.
The former England captain was sidelined from all cricket until making a superb unbeaten 177 for Surrey in a County Championship match in June.
He was recalled by England for their washed out Twenty20 match against New Zealand at The Oval, his Surrey home ground, on June 27.
South Africa-born Pietersen then played in Ashes-holders' England's 14-run first Test win over Australia at Trent Bridge last week where he made scores of 14 and 64.
Although boasting a Test average of nearly 50, Pietersen managed just seven runs in total across two innings at Lord's.
But Joe Root's superb 178 not out guided England to a commanding 566-run lead at stumps on Saturday.
