NFL spokesman Brian McCarthy told the Associated Press on Tuesday the investigation began amid the initial allegations and is not expected to be completed before Super Bowl 50 on Feb. 7.
Al Jazeera published a 49-minute documentary, The Dark Side, in December, a good percentage of which zeroes in on Manning. A pharmacist named Charlie Sly said Manning's wife, Ashley, received shipments of HGH in 2011—the same year the former NFL MVP was out of football rehabbing an injured neck.
Manning underwent four neck operations in less than two years, which ultimately led to his exit from Indianapolis and put his career in jeopardy. He returned in 2012 with the Broncos, and on Sunday, he led Denver to its second Super Bowl in his four seasons with the team. His comeback has been considered among the most remarkable in NFL history, as his Broncos stint has allowed him to set nearly every passing record in league history.
From the moment the report became public, Manning has categorically denied all allegations.
"I think I rotated between being angry, furious," Manning told ESPN's Lisa Salters (via ESPN.com's Rob Demovsky and Jeremy Fowler) in mid-December. "Disgusted is really how I feel, sickened by it. I'm trying to understand how someone can make something up about somebody, admit that he made it up and yet somehow it gets published in a story. I don't understand that. Maybe you can explain it or somebody else can.
"It's completely fabricated, complete trash, garbage—there's more adjectives I'd like to be able to use. It really makes me sick."
Manning told the MMQB's Peter King he would "probably" sue Al Jazeera for running the report. There has been no update on a potential lawsuit at this time.
Sly has since recanted his story, saying he purposefully misled reporters after realizing he was being taped without his consent. Speaking with ESPN's Chris Mortensen, Sly said he told Liam Collins a litany of false stories mostly as a test and then continued to do so once he confirmed Collins was working undercover as a reporter.
"I said, 'How did you come up with this story of Peyton and Ashley Manning?,'" Mortensen said on ESPN Radio, per Cork Gaines of Business Insider. "And he said, 'Well, when I was working there [the Guyer Institute] for those three months, somebody said that they used to be patients there.'"
The Al Jazeera report also named Clay Matthews and Julius Peppers of the Green Bay Packers and James Harrison of the Pittsburgh Steelers. Those players have also denied the allegations. It's unclear whether the NFL is looking into all individuals named in the report or just Manning.
Either way, expect the NFL investigation to be a growing storyline during the two-week buildup to Super Bowl 50.
Follow Tyler Conway (@jtylerconway) on Twitter.