When the San Francisco 49ers brought Deebo Samuel back on a one-year deal this summer, it felt like a reunion that made sense for both sides. 

The front office needed help after Ricky Pearsall’s knee problems came back in training camp, and Samuel got a chance to return to the offense, where he became one of the NFL’s most unique weapons. 

General manager John Lynch said on KNBR Thursday that Samuel likely won’t be available Sunday against the Las Vegas Raiders, which would be his third straight missed game since hurting his hamstring against Seattle in Week 5.

Samuel went down late in the third quarter of that game, losing a fumble on the play and staying on the turf before being ruled out. Kyle Shanahan said the next day that he expected his receiver to miss at least a couple of weeks.

With a loss to Atlanta followed by the bye, the 49ers had hoped Week 9 would be the comeback date.

Samuel still hasn’t returned to practice this week, though, and Shanahan said he would be surprised if Samuel played Sunday, even while noting that the receiver is making progress.

Few players in the league affect a game plan the way Samuel does. Shanahan has spent years building plays around him, lining him up in the slot, out wide, and in the backfield, and handing him the ball on jet sweeps, screens, and designed runs that make defenses unsure how to defend him.

Since entering the league in 2019, Samuel ranks first among receivers with at least 100 catches in yards after the catch per reception, averaging 8.7.

His 2021 All-Pro season, when he totaled 1,770 yards from scrimmage and 14 touchdowns, is still the best example of how much Shanahan can do when he has a player who blurs the line between receiver and running back.

That versatility matters even more right now, because Mike Evans is also expected to miss Sunday’s game with Achilles tendinitis.

Without Evans, the 49ers lose their big-bodied target on the outside. Without Samuel, they also lose the player who turns quick, simple throws into big gains.

Expect Shanahan to lean even harder on Christian McCaffrey, who returned to practice on a limited basis Thursday, and George Kittle to create the kind of after-the-catch plays Samuel usually provides.

Jacob Cowing is the closest match on the roster to Samuel’s quickness and could see more motion and manufactured touches, while Brandin Cooks, Jordan Watkins, KhaDarel Hodge, and Demarcus Robinson handle the rest of the receiver snaps.

The 49ers are still expected to handle Las Vegas, but their offense is noticeably less creative without Samuel.

Getting him back healthy for the second half of the season could matter just as much as any move the team makes before the trade deadline.