Williams suffered a hamstring injury on the first offensive play of the 49ers' Week 17 game against the Chicago Bears, forcing him to miss Week 18's matchup against the Seattle Seahawks.
He is among several players who will not practice on Wednesday, the team's first on-field session of the week. Typically, Williams receives a rest day on the first practice day, but Shanahan confirmed his absence is injury-related.
"No, he's still hurt," Shanahan said. "Hopefully, he'll be better and can get something in tomorrow, but I'm not sure where he'll be at tomorrow yet."
Others sitting out Wednesday include wide receiver Ricky Pearsall (knee, ankle), linebacker Dee Winters (ankle), and defensive end Keion White (groin, hamstring).
Shanahan clarified that Pearsall aggravated his PCL injury during the game against Chicago, not in practice last week, placing him in a similar situation to Williams regarding availability for Sunday.
Tight end George Kittle (ankle), defensive end Yetur Gross-Matos (knee), and linebacker Luke Gifford (quad) are expected to be limited practice participants.
San Francisco also opened the practice window for wide receiver Jacob Cowing, though Shanahan expressed doubt about his chances of playing this weekend.
"We've got him for three weeks, so I'd say there's a chance to get him back in and see what happens over these three weeks," Shanahan said. "But for a guy to not have any practice throughout camp or this regular season, I think it'd be a little unrealistic for this week."
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