ESPN reporter Tim McManus first reported the news, saying Pederson, 52, told the team on Sunday night after a second positive test.
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Pederson is asymptomatic and is feeling fine.
He will continue to lead the Eagles from home virtually like he did during the offseason and NFL Draft. RB Coach Duce Staley will be in charge of the Eagles' on-site operations at the Novacare Complex until Pederson returns.
One other staff member who had been in close contact with Pederson was sent home. A source tells Action News that the staffer has not tested positive for COVID-19.
Eagles coach Doug Pederson tests positive for COVID-19
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Pederson, who is believed to have contracted COVID-19 outside of the team's training facility, needs to quarantine and have multiple negative tests before returning to work.
The Eagles said in a statement that Pederson is currently in self-quarantine and in communication with the team's medical staff.
"I feel extremely safe.. but we can't control everything," said Pederson on Tuesday responding to a COVID-19 outbreak involving the Miami Marlins.
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Pederson becomes the second NFL head coach known to have contracted coronavirus, but he is the first one to do it in season.
In March, New Orleans Saints coach Sean Payton revealed that he had tested positive.
Earlier this week, right tackle Lane Johnson was placed on the "reserve/COVID-19" list after testing positive for the virus.
ESPN contributed to this report.