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Running back Michael Turner #33 of the Atlanta Falcons runs the ball as he is hit by inside linebacker Patrick Willis #52 of the San Francisco 49ers in the first quarter in the NFC Championship game at the Georgia Dome on January 20, 2013 in Atlanta, Georgia. Photo by Kevin C. Cox/Getty Images.
Running back Michael Turner #33 of the Atlanta Falcons runs the ball as he is hit by inside linebacker Patrick Willis #52 of the San Francisco 49ers in the first quarter in the NFC Championship game at the Georgia Dome on January 20, 2013 in Atlanta, Georgia. Photo by Kevin C. Cox/Getty Images.

At the beginning of the season, I mentioned injuries as one thing that could possibly derail the 49ers’ season. The bug has already bit Jim Harbaugh’s team, and with a tough stretch of games over the next few weeks, their backs could be up against the wall. With a date in St. Louis tonight on Thursday Night Football and at home against the Texans on Sunday Night Football, the Niners are staring at 1-4 squarely in the face. Without Vernon Davis, the offense had no teeth on Sunday against the Colts. Additionally, Thursday will be the first time the 49ers will be without Aldon Smith and Patrick Willis on the defensive side of the ball.

I have no problem calling Vernon Davis the second-best all around tight end in football. Rob Gronkowski is an elite blocker, and we’ve all seen what he can do in the passing game, so if he’s healthy, he’s the best. But, Davis is still a phenomenal blocker in an offense that emphasizes the run. The Niners were ramming the ball down the Colts’ throat in the first quarter, running the ball at will with Frank Gore. They abandoned run after the quarter, and being without Davis might’ve had something to do with it. In the 49ers’ 21 personnel, with two backs and one tight end, they could probably run the ball against anyone. But, that’s when Davis is healthy. With Gore running behind a dominant offensive line, as well as Davis, fullback Bruce Miller, and elite blocker Anquan Boldin, it’s incredibly difficult to stop San Francisco when they want to run. However, that hasn’t really been the case this season. Teams are stacking men in the box, forcing Colin Kaepernick to beat them with his arm.

Without Vernon Davis though, Kaepernick struggled to find any open receivers against the Colts. In addition to being a game-changing blocker, Davis is the 49ers most dynamic receiving weapon without Michael Crabtree. Davis can beat linebackers, safeties, and cornerbacks, which is something that’s foreign to the other receivers. Anquan Boldin is still a capable receiver, but he cannot separate from some of the better cornerbacks in the league. Likewise, over the last few weeks, Marlon Moore and Kyle Williams have seen snaps at wide receiver. They haven’t fared much better, failing to use their speed to gain separation. Kaepernick just didn’t have anyone to throw to against the Colts. It’s a bit concerning, because he hasn’t looked poised in the pocket, dropping his head after only one or two reads.

However, you have to believe if Kaepernick has Crabtree and Davis, he’d be appreciably better than what he’s currently doing. With Davis looking likely to suit up tonight, Kap should be a good bet to bounce back with a performance closer to Week 1, instead of the six turnovers he produced in Weeks 2 and 3. However, with Frank Gore looking good last week, and only receiving 13 total touches, look for that to change. The 49ers are reeling on defense; they want to control the ball on offense to limit the opportunities St. Louis’ up-tempo offense gets. Trent Baalke has been stockpiling draft picks, which means he could role the dice on a guy like Kenny Britt before the trade deadline. Counting on Michael Crabtree to be full strength when he returns this season is not a great idea.

The troubling injuries really are on the defensive side of the ball. Obviously, Aldon Smith is out indefinitely and will be until he takes care of his issues. It likely will be around a month or so, and I won’t debate whether that’s long enough to fully recover. We just don’t have all the information to make that decision. Patrick Willis’ groin is troublesome. There’s next to no chance he’ll suit up tonight, and probably is a game-time decision for next Sunday’s game against the Texans. There are few details on the nature of the injury, but with these types of injuries, you can never be too careful. One wrong foot and Willis could aggravate the injury and be out longer than two weeks.

It doesn’t matter how well their replacements play, when you lose two players such as Willis and Smith, your defense is going to take a hit. Michael Wilhoite is an undrafted free agent taking over at inside linebacker for now, but if anything, this puts more pressure on NaVorro Bowman to step up while his partner in crime is sidelined. Likewise, Justin Smith, Ray McDonald, and Ahmad Brooks, the other starters in the once vaunted front seven, have to up their play as well. Dan Skuta and rookie Corey Lemonier will be playing outside linebacker in Smith’s role. Since being picked in the third round of the 2013 draft, the coaching staff has been raving about his ability to rush the quarterback. Look for Lemonier to play in the nickel package, on clear pass rushing downs. However, with two new pieces getting acclimated to the front, there will clearly be growing pains.

Another troublesome injury is that of Ian Williams. He’s out for the year with an ankle injury sustained on a low block by J.R. Sweezy in the loss against Seattle. Glenn Dorsey is currently manning the nose tackle spot, but if Sunday’s loss was any indication, the Niners may have some difficulty stopping the run. Two divisional opponents, the Cardinals and Rams, don’t look to be huge threats in the running game. But, obviously the Seahawks, and San Francisco’s Week 5 opponent, Houston, pride themselves on having a sound running game.

If the 49ers can’t stop the run, they’ll struggle to stop anyone with their secondary currently playing poorly. That places even more on Colin Kaepernick and the offense to solve their issues and start scoring some points. You can’t question Greg Roman and his offensive creativity, but until he starts putting Kap and company in situations to succeed, he will continue to see some criticism. However, if the Niners don’t start moving the ball, they’ll start facing some real questions. Like do they have the offensive weapons to succeed? Stay tuned.