49ers defense looking to stop big Broncos tight end Julius Thomas (w/video)

SANTA CLARA - A linebacker, safety or cornerback? A combination of defenders? Someone in a 49ers uniform is going to have to cover Denver Broncos all-world tight end Julius Thomas.

The question: Who? Regular inside linebackers NaVorro Bowman and Patrick Willis won’t be available because of injury. Therefore, the job is going to fall upon the likes of linebackers Chris Borland and Michael Wilhoite and safeties Eric Reid and Antoine Bethea, perhaps cornerback Chris Cook.

“When you get a tight end like him, some people think you’re crazy if you don’t put a (defensive back) on him,” 49ers defensive coordinator Vic Fangio said of Thomas. “Then the next guy will think you’re crazy because of the size mismatch if you don’t have a linebacker on him.

“That’s what these good tight ends do. They cause you problems. So, it will be a mix of who’s on him for us.”

Then again, it might not matter who is on Thomas if it’s only one guy. Thomas is playing at the kind of level that causes Fangio and other defensive coordinators to ponder the merits of committing a second defender to the cause.

Thomas, 6-foot-5 and 250 pounds, has nine touchdown receptions through the Broncos’ first five games.

That’s tied with Detroit Lions wide receiver Calvin Johnson (2011) for the most receiving touchdowns through five games in NFL history.

Thomas burst on the scene last season after he caught only one pass in nine games his first two seasons combined. In 2013, he hauled in 65 passes for 788 yards and 12 touchdowns. He has 24 receptions for 277 yards this season.

Bethea said he and his defensive mates are accustomed to matchup nightmares when it comes to tight ends.

“All the tight ends nowadays in this league are big body and it’s tough to get around them. Like last week, Cook had a big body. Week in, week out, we see more of these tight ends with big bodies, wide radius of range of being able to catch the ball.”

In a perfect world the 49ers could devote Borland or Wilhoite to covering Thomas one-on-one, depending upon which side of the field Thomas lines up.

This is far from an ideal situation for the 49ers. Borland will be making his first NFL start, Wilhoite his ninth.

Worse for the 49ers, Broncos quarterback Peyton Manning is adept at exploiting weaknesses, be it one of his receivers left in single coverage or an obvious mismatch in talent level that favors the Broncos.

Also, the Broncos are so deep and talented at wide receiver that the 49ers can’t afford to leave their cornerbacks in man-coverage at all times.

In the end, Fangio said, the best solution might be to treat Thomas as just another player, the Broncos as just another team and Sunday’s game another challenge.

“Ultimately, you got to play your package,” Fangio said. “If you start tinkering here and there to cover up somebody’s perceived deficiencies, that just leads to problems other places, too.

“You got to be able to play.”