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Shanahan confirmed Aiyuk's season-ending knee injury but noted that he didn't yet have details on any further damage beyond the torn ACL and MCL.
"I talked with him last night, just calling him at his house," Shanahan said. "I haven't seen him today, but he was hurt and just bummed out, exactly how you'd expect. But B.A.'s a strong dude and spiritual guy, and believes everything happens for a reason, so he'll be all right.
"But definitely a little down last night. And I was just telling him how bad I felt for him, and just let him know we're all here for him through this."
Deebo Samuel in the hospital
Shanahan also provided an update on wide receiver Deebo Samuel, who played only a few snaps on Sunday before being sidelined due to an illness. His situation is worse than initially thought, and his status for this weekend's matchup against the Dallas Cowboys remains unclear.
"Deebo Samuel, he had kind of an odd illness, some fluid in his lungs, so technically, pneumonia," Shanahan said. "... He's in the hospital still, and we'll see how he recovers here over these next couple of days."
Shanahan added that Samuel went to the hospital Sunday night after the game.
"It started acting up in the middle of the night, Saturday night, or early Sunday morning, and then it just kind of evolved as the day went," Shanahan explained. "So, once we found out he had the fluid in his lungs and stuff after the game, then I believe they sent him over there. I'm not sure the timeline of it, but I just found out that's where he was on Sunday night when I was at home."
Other game injuries
Regarding other injuries from the game, Shanahan noted that wide receiver Chris Conley is day-to-day with an ankle sprain and tight end George Kittle is day-to-day with a foot sprain.
McCaffrey, Greenlaw, and Moody updates
Shanahan also provided updates on other injured players, including running back Christian McCaffrey.
"Christian is still progressing through his rehab," Shanahan said. "He hasn't had any setbacks, so it's been all good news so far. I'd be surprised to get him back this week, but hopefully, the bye week will go well, and he'll have a much better chance there right after the bye week."
Shanahan added that linebacker Dre Greenlaw's return is still a few weeks later, saying, "Everything's still going fine, but no time soon right now."
As for kicker Jake Moody, the 49ers expect him to return from his high-ankle sprain sometime after the bye week, at the earliest. Shanahan said, "We'll have to wait until then to see how it reacts."
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