"We're going to put him on IR today," Shanahan said. "I think we had to by one, so if we didn't, he'll be on it tomorrow. So, we're going to shut him down."
"You'd always like to avoid surgery," he continued. "The risk is, the longer you wait to see if you end up needing it, even though it's not a huge injury, it's a huge recovery. I don't want to say it that way. They're all pretty big injuries, but the shoulder injuries take a while to recover so once we decide we're going to go in that direction, the sooner, the better."
Shanahan did not want to get into specifics about the injury itself.
"It's not my expertise," he said. "I'll mess it up. Something with his labrum."
Brown injured the shoulder during a practice on Thanksgiving Day. While he came back and played two weeks ago against the Chicago Bears, Shanahan says the injury didn't get worse but simply did not go away.
Guard Zane Beadles will start in his place for the second-straight week. This past Sunday against the Houston Texans, Beadles allowed a sack, and six quarterback hurries in place of Brown, according to Pro Football Focus.
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"I have a lot of confidence going into games with Zane because the game's not too big for him," Shanahan said. "If we sit there and put him on an island all game, just like any person, they'll struggle. But Zane, we know what we're going to get from him. He'll play as hard as he can. Nothing's too big for him. If he gets beat, he won't shut down. He'll come back the next play and go just as hard. So I have a lot of confidence going into the games with Zane."
Brown, who is in his third season with the 49ers, was selected by the team in the seventh round of the 2015 NFL Draft. He has played in 31 games with the 49ers and started all but three of those appearances. All three were during his rookie season.
Brown has missed three games this season, which includes two of the last three, due to injury.
"I think Trent has a chance to be very dominant at his position and I think he made huge strides this year," Shanahan said. "By no means is he fully there. I think he had a much better year this year than just watching him on tape his previous two years, especially last year because I know he played the most last year.
"But Trent tries to battle through it, came back for a game for us for Chicago, helped us win that game, and then Trent's a very important part of this place and our future. When you're talking about a five- to six-month injury, that's something we want to get going as fast as possible so I fully support this decision."
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