Kruis, 28, has won 25 England caps and played for the British and Irish Lions in the first test against New Zealand last year.
“He’s not going to tour,” McCall told BT Sport.
“He’s going to have surgery at the end of the season.”
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England captain Dylan Hartley, centre Jonathan Joseph, winger Anthony Watson and forwards Courtney Lawes and Nathan Hughes have also been ruled out of the three tests against the Springboks in June.
(Reporting by Ed Osmond, editing by Pritha Sarkar)
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