A pre-restart match at United’s Carrington training ground was cancelled around an hour before kick-off, with the members of the visiting party sent home.
No United players are understood to have come into contact with O’Neill, who will now undergo a period of self-isolation.
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O’Neill had returned negative results in each of Stoke’s previous five rounds of testing. Billy McKinlay, his assistant manager, will now take charge in his absence.