Sunderland were already without the suspended Tom Flanagan plus injured duo Arbenit Xhemajli and Morgan Feeney leaving Phil Parkinson – who has favoured three centre-backs this season – short of options at the back.
And Willis can now be added as an injury concern, the defender went off 20 minutes into the game with the scoreline goalless at the County Ground.
Youngster Jack Diamond came on as Conor McLaughlin moved into the makeshift central defence, which also included Luke O’Nien on the left-hand-side of the back three.
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Sunderland did sign Dion Sanderson on loan from Wolves on deadline day but not before the midday cut off to be able to play against Swindon.
Parkinson will now be hoping Willis’ ankle injury is not too serious.
Sunderland were unbeaten in League One heading into the game.