SANTA CLARA >> The 49ers’ worst suspicions were confirmed Monday when it was learned Brandon Aiyuk was lost for the season with a serious knee injury.

Coach Kyle Shanahan confirmed during a conference call with local media that Aiyuk had torn both his anterior cruciate and medial collateral ligaments and will be out for the season.

“I talked with him last night, talked to him at his house,” Shanahan said. “He was hurting, just bummed out. Exactly how you’d expect. B.A. is a strong dude, a spiritual guy who thinks everything happens for a reason. He was definitely down last night and I told him how bad I felt for him and we’re all here for him.”

Fox Sports was first to report Aiyuk would be out for the season, with a subsequent NFL Network report revealing the complicating factor of an MCL tear as well.The news was no surprise given Shanahan’s dire prognosis of a torn ACL following a 28-18 loss Sunday to the Kansas City Chiefs.

Aiyuk was injured when hit by defensive backs Trent McDuffie and Chamarri Cooper at the Chiefs 14-yard line late in the first half. He stayed on the field on his back for a time, then with the help of the training staff hobbled off the field. However, he was then placed on a cart, driven to the locker room and could be seen pointing to his right knee.

The injury comes after a contentious offseason holdout for a contract extension in which the former first-round draft pick was nearly traded. He eventually signed a four-year deal worth a maximum of $130 million.

A year after catching 79 passes for 1,342 yards and seven touchdowns and had a miracle catch off the helmet of a defender during the 49ers’ 34-31 comeback win over Detroit in the NFC Championship Game, Aiyuk finishes the season with 25 receptions for 374 yards and no touchdowns.

Aiyuk, 26, had two catches for 23 yards against the Chiefs and one conspicuous drop from quarterback Brock Purdy that could have gone for big yardage. The 49ers were also without wide receiver Deebo Samuel, who reported to work feeling ill Sunday morning and was hospitalized with pneumonia Sunday night.

Jauan Jennings, the 49ers’ No. 3 wideout, was out with a hip injury. The hope is he’ll be ready to face Dallas in Week 8 but it’s not a certainty.

With Aiyuk out and the status of Samuel and Jennings unclear, the 49ers will look to get steady progress from rookies Ricky Pearsall Jr. and Jacob Cowing. Pearsall played 48 snaps — more than expected because of the Aiyuk and Samuel absences — after missing the first six games on the non-football injury list after being shot in the chest during a robbery attempt on Aug. 31.

Also seeing additional time were Chris Conley and Ronnie Bell.

“I was proud of Ricky for him being ready for some spots that we were hoping he wouldn’t have to be ready for,” Shanahan said. “We had to mix a lot of stuff around in the second quarter and halftime and those guys were in spots they didn’t (have) reps at. For the most part, they didn’t make too many mistakes and gave us a chance to get back in the game. Those guys are going to get a lot more reps going forward with B.A. being out and with Jauan and Deebo; not sure if we’ll get them back this week or not.”

Cowing caught two passes for 50 yards, an initial screen pass after Aiyuk went down and then a 41-yard pass downfield.

“I like how he ran on the screen that we got him, I thought he ran it pretty aggressively,” Shanahan said. “He was ready for the curl pump we gave him later in the game. He stepped in and did a good job when he got his opportunities.”

The Aiyuk injury was the latest in series of issues for the 49ers, who have lost defensive tackle Javon Hargrave with a torn triceps for the season and while running back Christian McCaffery, the 2023 NFL Offensive Player of the Year, has yet to play because of Achilles tendinitis in both ankles. There is no timetable as yet for McCaffery’s return.

Talanoa Hufanga, an All-Pro safety in 2022, has played in just one game after recovering from a torn ACL, was felled by a wrist injury, placed on injured reserve and not eligible to return until Week 11. Linebacker Dre Greenlaw remains on the physically unable to perform list rehabbing an Achilles’ tear and his return date has not been determined.

The NFL trade deadline is Nov. 5 if the 49ers want to look outside the organization for help at wide receiver. Recent deals have seen Davante Adams going from the Raiders to the Jets, Amari Cooper from the Browns to the Bills and Marquez Valdes-Scantling signing with New Orleans.

“It makes you look into everything,” Shanahan said. “It has to do with what options are out there and stuff that we can pull off helps us now and doesn’t hurt us for the future. A lot of times, it’s just kind of living in hope. Those answers aren’t always out there.”