SANTA CLARA -- All-Pro defensive tackle Justin Smith was not on the 49ers' field at the beginning of practice Thursday, casting serious doubt whether he will be available Sunday night to face the Seattle Seahawks.
Smith played the first four snaps of the second half against the New England Patriots before leaving the game with a left elbow injury. Coach Jim Harbaugh has been vague while discussing Smith's condition, saying only that Smith will play "if it's humanly possible."
Injured players have spoken privately about receiving warnings from the team about disclosing their injuries to the media. After Sunday's game, Smith said he could not comment on his condition. He underwent an MRI examination on Monday. Late in the exhibition season, the 49ers withheld the extent of outside linebacker Parys Haralson's injury before placing him on injured reserve with a torn triceps.
Smith's situation appeared serious Sunday night, as he could not return to play in the second half. The Patriots scored touchdowns on four consecutive drives without Smith on the field in the third and fourth quarters.
"Obviously, anytime you lose a great player, it's going to have an effect on you," 49ers defensive coordinator Vic Fangio said. "You'd have your head in the sand if you didn't admit that. I think some of the issues we had, plays we could've stopped, didn't have any effect with him being out there."
Fangio said backup defensive lineman Ricky Jean Francois is ready to fill in. Jean Francois ended a Patriots drive late in the game with a sack of Tom Brady.
"He can play both the banging game and got a little bit of athleticism, too," Fangio said. "He's a well-rounded player. He's the one guy in our front who can play all three spots. Nothing will change with him in there."
Safety Dashon Goldson said the entire 49ers defense will have to compensate for the potential loss of Smith.
"We definitely have some guys going to have to step up and carry that load for us," Goldson said.
It appears the Jaguars have passed on Chip Kelly for a second time this month.
After reportedly not getting their head coaching job, Kelly reportedly interviewed for their offensive coordinator position on Monday.
But two days later, Jacksonville announced that Nathaniel Hackett has been retained as offensive coordinator under head coach Doug Marrone.
Kelly told CSNBayArea.com recently he would take his time to determine his next career move.
“I’m not going to close the door on any opportunity, but I have to be very smart in what I do next,” Kelly said two days after his firing. “I don’t have to take anything, but I wouldn’t rule anything out. I need to make sure that I’m in the right situation.
“I don’t know what the future holds. I’ll do my due diligence. I’m not going to coach just to coach.”
The 49ers fired Kelly with three years, $18 million remaining in his contract. The 49ers hired Kelly just two weeks after the Philadelphia Eagles fired him. Kelly went 26-21 with the Eagles after leaving his successful program with the Oregon Ducks after the 2012 season.
The 49ers feel certain they have landed their head coach, according to sources.
And the Atlanta Falcons are reportedly convinced offensive Kyle Shanahan will be entering the head-coaching ranks with the 49ers next season, too.
Atlanta coach Dan Quinn made an announcement to coaches that Shanahan would be the 49ers’ next coach, Mike Silver of the NFL Network reported Wednesday, adding everyone in the room was “super supportive.”
On Wednesday, Quinn was asked at a press conference about Shanahan and the 49ers.
“I know it’s for sure out there, (but it’s) definitely not our story to tell,” Quinn said. “They (the 49ers) will for sure reach out to (general manager) Thomas (Dimitroff) and to the organization and there will be a window for them if they’d like to visit with him for next week. But that’s really where it’s at, and there’s nothing left to do until then."
The Falcons will face the Green Bay Packers on Sunday in the NFC Championship game. The 49ers will have a second interview with Shanahan after the game. Shanahan will also become involved in the process to hire the 49ers’ next general manager.
The 49ers are checking with the NFL to determine what is allowable under the league’s anti-tampering policy, according to a league source. If the Falcons win on Sunday, the 49ers would not be able to officially hire Shanahan until after the Super Bowl on Feb. 5.
According to sources, the 49ers have narrowed their initial search for the next general manager to four candidates: Eliot Wolf and Brian Gutekunst of Green Bay, Minnesota’s George Paton and Terry McDonough of Arizona.
The general manager candidates are expected to meet with Shanahan, but it’s unclear whether Shanahan can interview the candidates if the Falcons advance to the Super Bowl and he is not officially the 49ers’ coach. The 49ers are expected to hold a second round of general manager interviews early next week and could fill the position by the end of next week.