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Chris Borland, Michael Wilhoite in the spotlight with Patrick Willis, NaVorro Bowman injuries

The 49ers face big question marks at inside linebacker with Patrick Willis likely out for the year and NaVorro Bowman still a question mark. Fortunately, the team has a pair of guys that are stepping up their game.

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The San Francisco 49ers faced more bad news Tuesday as word got out that Patrick Willis will reportedly have season-ending toe surgery. This news comes on the same day Ed Werder reported NaVorro Bowman is still dealing with some knee pain in his recovery. Jim Harbaugh was on KNBR Tuesday morning, and he said Bowman's doctors want him to get another MRI:

"Talking to our doctors yesterday, they want to get another MRI, and see exactly where he's at before that takes place," Harbaugh said.

"It's been 9 ½ months, so as they see fit and what is prudent to get that MRI and make a good check of where he is and then proceed"

Harbaugh is trying to make these seem like something run of the mill, but an MRI combined with pain in the knee is something we can't overlook. socalisteph put together some thoughts on the injuries over on Twitter. Here is the Bowman specific tweet.

The 49ers have to decide by next Monday whether or not to return Bowman to practice. Jim Harbaugh said the team would consider it this week, but pain and an MRI likely mean a final decision won't be made for at least a couple days. Moving him to practice does not necessarily mean he has to be a full participant. Rather, it is about getting the 21-day window started for determining if he can be activated to the 53-man roster. That means the 49ers have a few weeks to really figure this out.

Barring something really bad in the MRI, I suspect the 49ers activate the 21-day window, and take it day-to-day from there. Maybe Bowman gets back, maybe he ends up on injured reserve with Willis. We can't say anything for certain.

What this does mean is Chris Borland and Michael Wilhoite will be firmly in the spotlight. Wilhoite has been in the starting lineup since Week 1, while Borland moved into the lineup during the Week 6 win at St. Louis. Borland struggled the following week against Denver, but the last two weeks he has been an absolute beast. He has 35 tackles over those two games, but more importantly he is making impact plays, with big stops each week.

Tackles can be an overrated stat, but various accompanying metrics support his strong performances. According to Pro Football Focus, he accumulated a +5.9 overall grade this past week, with 7 stops, 1 quarterback hurry, and the fumble recovery. They gave him a +1.7 grade in coverage, which is especially huge. He allowed 7 catches in 9 targets, but only for a total of 41 yards and had three stops in coverage. Coverage was my biggest concern with him, and he showed some great work. Among linebackers with at least 25 percent of total snaps, Borland leads the NFL in run stop percentage, is 5th in tackling efficiency and is No. 24 of 51 in pass rush productivity.

Borland and Wilhoite have been starting next to each other the last three and a half games, and all indications are that they will be next to each other for the foreseeable future. Best case scenario with Bowman seems to be a few weeks from getting back on the field in game action. Worst case scenario is Borland and Wilhoite are starting the rest of the season.

Either way, the 49ers prepared for this with the addition of Borland, and the development of Wilhoite. It is far from an ideal situation, and it is a downgrade. And yet, as we've seen the last two weeks, these guys can do some great things together. And the good news is they will have Bowman and Willis there to help them learn and grow. Willis is still the guy breaking down the team at midfield before kickoff because he is a leader of this team. Willis and Bowman have a wealth of knowledge to share, and that will only help Borland and Wilhoite to improve as the season moves along.