"K'Waun had a knee sprain, did not return," head coach Kyle Shanahan said after the game. "We'll have to get that looked at tonight. Find out tomorrow."
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Tests show that Williams indeed suffered a knee sprain and will head to injured reserve, forcing the defender to miss at least three games.
Williams is in his seventh NFL season. He spent his first two seasons with the Cleveland Browns, did not play in 2016, and then signed with the 49ers the next year.
Williams, one of the best slot corners in the NFL, has recorded nine tackles and two passes defensed through three games this season.