What’s up with Brandon Aiyuk?

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Of the story lines to emerge from the 49ers’ Week 1 victory over the Lions, Brandon Aiyuk’s apparent disappearance from the offensive game plan was a significant mystery. Head coach Kyle Shanahan shed some light on the 2020 first-round pick’s lack of Week 1 playing time.

Shanahan has insisted Aiyuk wasn’t being punished, and has backed off his claim that the club hit the brakes on the second-year receiver because of a balky hamstring that gave him trouble in training camp.

On Wednesday he gave a clearer explanation for what happened with Aiyuk, and it appears to be a combination of the missed practice time due to the hamstring and free agent signee Trent Sherfield earning his way into the wide receiver rotation.

“Anytime you do have a setback with a hamstring and you have a guy behind you playing as well as Trent’s played, I know Trent wasn’t a first-round draft pick, so that might not be as obvious with the talent level, but he’s been a hell of a football player since he’s been here,” Shanahan told reporters before Wednesday’s practice. “Aiyuk’s been a little inconsistent because he’s been in and out with his injury. And that’s what we felt was the best chance for us last week. Aiyuk’s still got a chance to get that spot up and not rotate as much, Trent just doesn’t make that very easy. So, these three days are important in practice, how we balance out our game plan, how we balance out our routes. And I’m happy with Aiyuk. It’s nothing against Aiyuk. I’m just also happy with Trent too. And I think both of them can continue to get better.”

Sherfield played 27 offensive snaps in Detroit and caught two of his three targets for 23 yards and a touchdown. Aiyuk played 26 snaps and didn’t earn a target.

An injury limiting Aiyuk and opening the door for another player who took advantage of the opportunity makes a lot of sense. How the division of snaps between Aiyuk and Sherfield is now one of the most fascinating things to watch going into Week 2.

While there was plenty of speculation during camp that Sherfield would emerge with the third wide receiver job, he appears to have done enough to warrant more time than the WR3 would normally get. The 49ers’ use of three-receiver sets is relatively limited.Sunday in Detroit they utilized three-plus wide receivers on just 36 percent of their 55 offensive snaps. Only Houston and Atlanta deployed three-plus receivers at a lower rate in the opening week. Combine that with an inconsistent camp from Aiyuk and it’s a recipe for what we saw Sunday.

The question now is what happens to Aiyuk moving forward when he does get back into practice more consistently. It’s far too early to smash the panic button and wonder whether Aiyuk’s career is going the way of Dante Pettis. Shanahan on Wednesday appeared to indicate the second-year pass catcher isn’t in the vaunted ‘doghouse’ that’s been bandied about on the internet since Sunday afternoon. However, it’ll be hard to believe that isn’t the case if Weeks 2 and 3 go by and we’re still searching for Aiyuk’s name in the box score.

If his role does remain relatively small, the only real justification would require Sherfield to emerge as a Pro Bowl caliber talent the way Aiyuk did during his rookie season. The 49ers would have a good problem on their hands if that happens. If it doesn’t, and Aiyuk continues to be an offensive afterthought, there’ll be a lot of hard questions for Shanahan to answer about his receiving corps and what happened to the former No. 25 overall pick.

Don’t smash the panic button just yet, but keep the button nearby just in case.