The Sunderland defender has been forced to withdraw from Nigel Worthington's squad because of a foot injury.
Manchester City youngster Ryan McGivern has been drafted in to replace McCartney.
Worthington admitted it was a blow to lose McCartney for the trip to Prague and remains hopeful there are no more injuries to contend with ahead of next Wednesday's clash.
"It's a blow but it's part and parcel of football," Worthington told the News Letter.
"The good thing is there are no more fixtures between now and Wednesday, so that should be the end of our injury problems."