Not much has gone right for the San Francisco 49ers since reaching last season’s Super Bowl. And on Sunday they will come face to face with one of their bigger 2020 regrets — Seahawks defensive back D.J. Reed.

Reed began the season on the 49ers’ roster before they tried to sneak him through waivers and onto injured reserve after he tore a pectoral muscle during an offseason workout.

Instead, the Seahawks claimed him — which meant keeping him on their active roster throughout training camp even though he couldn’t do anything — and waited patiently for Reed to get healthy.

Reed recovered two months into the season and has been a regular in Seattle’s secondary since — starting games at nickel back and left and right cornerback.

And on Wednesday, when he talked to Seattle media via a conference call, 49ers coach Kyle Shanahan mentioned Reed as one of three players who have been keys to the Seahawks’ second-half defensive turnaround (the others being Jamal Adams and Carlos Dunlap).

“He’s playing at a very good level,” Shanahan said of Reed, who played in 31 games for the 49ers in 2018-19, mostly as a reserve defensive back and on special teams. “Made us sick to lose (him).”

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The 49ers waived Reed on Aug. 4. Shanahan said they had no choice due to a spate of injuries he said put them at the limit for players they could put on the Physically Unable to Perform or Non-Football Injury lists.

With both of those lists, players can return after six games. By going on injured reserve during the preseason, Reed would have missed the season. The 49ers gambled that no one would claim Reed because it was unclear when he might return, hoping to stick him on IR and get him back in 2021.

“We had an unprecedented (number of) guys at that time who were on PUP,” Shanahan said. “We couldn’t have more (players) with the roster rules and how many we had to have down, and we didn’t know if he was going to be able to come back during the year from it.

“There were a lot of decisions that went into it. We were hoping we wouldn’t lose him. Obviously, Seattle took him and got a great player because of it. A guy I really like a lot as a person and a player. Something I wish we could have had back.”

Indeed, the 49ers’ loss has been one of Seattle’s biggest gains of the year.

Reed said San Francisco’s decision made him more determined to make it back as quickly as possible. He returned in time for a Nov. 1 game against the 49ers, when he had to play nickel with Ugo Amadi out. Reed had an early interception that helped swing the game Seattle’s way.

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Nickel was the role Seattle coach Pete Carroll thought would be the best fit for Reed, who at just 5 feet 9 doesn’t fit the typical profile of a Seahawks outside cornerback.

But with injuries later knocking out the team’s top three outside corners — Shaquill Griffin, Tre Flowers and Quinton Dunbar — Reed has stepped in to start two games at left cornerback and the past four on the right side.

Flowers is expected to return this week from a hamstring injury.

But Reed figures to be hard to dislodge from a starting spot given how well he has played.

Reed is allowing a passer rating of just 73.9, via Pro Football Reference, the lowest of any of Seattle’s full-time defensive backs.

Pro Football Focus rates Reed 18th of 126 cornerbacks this week, by far the highest of any Seahawk. 

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According to PFF, Reed has allowed just eight completions on 19 targets over the past four games for just 56 yards, and only 14 after the catch.

As he has several times, Carroll on Wednesday credited general manager John Schneider with seeing that Reed might be able to help this season.

“I don’t think this was luck,” Carroll said in response to a question that asked if Seattle had “gotten lucky” with Reed. “I think John knew. John had it. John and his guys that do the evaluations, they knew he was a good enough football player to play nickel, safety or corner. That’s what came right in from the first day we were talking about him. I think the quickness of his transition is what we’re really surprised by, how easy it was for him to learn and to jump in. But our guys thought he was going to be a big factor for us.”

Reed could now be a big factor in how Seattle assesses its cornerback position after the season.

Griffin and Dunbar can each be free agents, with Dunbar’s season already over after he had knee surgery this week. 

Reed remains under contract through the 2021 season, due to make $920,000 next year on the final season of his four-year rookie deal.

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Amadi has played well as the nickel and has two years left on his contract, and Flowers also has one year left on his.

If the team sees Reed as a viable long-term starter at one outside corner spot, Seattle could focus on trying to re-sign only one of Griffin or Dunbar instead of both. Both likely will seek significant long-term deals (though Dunbar’s health will obviously be a factor).

Carroll on Wednesday indicated he thinks Reed could be a full-time starter at one outside corner spot, despite not having the typical Seattle cornerback build.

“D.J. has a chance to be an excellent football player over the long haul, because he has that special element and it makes up for so many other things,” Carroll said. “One of the things I have to do well is be able to adapt to the different makeups of the players and what they bring us and not be shortsighted and closed-minded. Guys can only come in one size and shape and all that. So this is a good opportunity and illustration of that.”