PHOENIX — Zack Wheeler’s latest setback in his rehab from Tommy John surgery likely will end his already fleeting hopes of returning to the Mets this season.

Wheeler will be shut down for a few weeks, Mets assistant general manager John Ricco said on Wednesday, after Dr. James Andrews diagnosed the pitcher with a strained flexor tendon, which had been causing lingering elbow soreness. The tendon also was repaired during surgery in March of 2015.

An MRI exam showed no new ligament damage was found, sparing Wheeler the worst-case scenario. But the shutdown -- which will allow the righthander to receive a platelet rich plasma injection — leaves Wheeler with perhaps too narrow a window for a comeback.

“I’m not going to jump to that [conclusion] at this point,” Ricco said, “but the clock is ticking.”

Manager Terry Collins sounded a more sobering tone.

“You’ve got to certainly prepare for yourself for the fact that he might be one of those guys that just for some reason doesn’t bounce back like you hope,” he said.

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The Mets had targeted a second half return for Wheeler, the hard-throwing 26-year-old who hasn’t pitched since going 11-11 with a 3.54 ERA in 2014. But Wheeler made slow progress in his throwing program and endured setbacks such as elbow discomfort and nerve irritation.

Though minor, when taken together, the roadblocks may keep Wheeler off a big-league mound until 2017.

“We started out the year very confident that he would — at some time we thought in July — be back,” Collins said. “As the summer proceeded on where he just never felt comfortable . . . especially in the last month where every time it seemed like he got on the mound all of a sudden there was discomfort, we realized that this might not come, this might not be what we thought was going to happen.”

With that, Wheeler joins the ranks of those who have had to endure complications from Tommy John surgery, a group that includes Mets lefthander Steven Matz.

The Long Island native lost the first two years of his professional career to various setbacks after surgery. Though he was drafted out of Ward Melville in 2009, he did not make his pro debut for the Mets until 2012.

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“Yeah, it’s really tough,” Matz said. “All you want to do is come back and compete. It’s a little different scenario because he made it to the big leagues so I imagine it would be even tougher for him. For me, it was like you can come back, but you make it to the big leagues? That’s all in your mind as well. But for him, he knows what he can do at the major league level so I imagine it’s frustrating for him.”

When Wheeler joined the Mets for a series in Miami recently, he spoke with Matz about his challenging rehab.

“I’ve been on that rocky road, I feel for him,” said Matz, who has shown enough mental toughness to pitch through a painful bone spur in his elbow this season. “I know how it is when everybody’s saying ‘it’s just in your head, it’s in your head’ when my elbow’s still hurting. Nope. My head’s telling me my arm hurts. It’s frustrating to see people coming back in 12 months and you’re just not turning the corner.”

The most agonizing jolt that came with every setback was the thought that a second surgery might be needed.

“The last thing you want to do is hear it didn’t work,” Matz said of surgery. “So, it’s always a big fear.”

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Though Wheeler has been spared from that fate, his road remains pockmarked. If a return to the big leagues isn’t in the cards, Ricco said the Mets still may get Wheeler game-ready through action in the instructional league.

But even then, Wheeler will have lost two full seasons to surgery.

“It was very discouraging to hear today that he’s got to be shut down,” Collins said. “I just hope that with the rest and recuperation he can come back in the future and be effective.”