Sunday was Samuel's first game since suffering a hamstring injury on October 25 against the New England Patriots.
"He's going to be good," Shanahan said on the Murph & Mac show. "I haven't talked to the guys today, and I haven't seen them in person yet, but I expect him to practice today.
"And he wasn't injured yesterday, but whenever you don't have an offseason, you don't have a training camp -- his first practice since the Super Bowl was, I think, in Week 3 this year. And then he got like two weeks in, and then got hurt, and went out again.
"So the guy's had -- I'm guessing -- but anywhere from like six to 10 practices since the Super Bowl. And then he goes out and plays the way he did on Sunday, and how physical he plays, how much he played, and one of the main reasons we had a chance to win that game.
"It takes the body a little bit of time to recover, and we're in that bind of trying to get him to practice so he can get back in that football shape. But it's tough to do that at this time of the year, especially when you put so much out there on Sunday.
"So, he needed an extra day to get some of that soreness out, and I kind of understand it because he's in shape, but you've got to callus your body, and you've got to play a lot of football. And that's been hard on him because he hasn't been healthy, and its' been that way for a number of our guys."
Shanahan adds that Samuel has the strength to play physically, as he has shown in his first two NFL seasons.
"Deebo's actually got the body and stuff that he can handle it," the coach said. "Deebo's as thick of a guy as I've been around when it comes to a wideout and everything. He's a very dense guy, and that's why when he hits people, it hurts them a lot more than it hurts him."
You can listen to the entire conversation with Shanahan below.
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