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The Gabonese football federation stated that medical officials with the Confederation of African Football had diagnosed Aubameyang and teammates Axel Meye and midfielder Mario Lemina with "cardiac lesions" after returning from positive COVID-19 tests. The federation said CAF "did not want to take any risks.''
The teams played to a 1-1 draw.
Aubameyang tested positive at an airport on arrival in Cameroon last week and was put into isolation. He also missed Gabon's first game, a 1-0 win over Comoros. The Arsenal player had since tested negative for the virus and was out of isolation two days before the Ghana game and was expected to return to the team.
Meye and Lemina had also been in isolation after positive virus tests.
Gabon played against Ghana without two other players because of the virus. Defenders Sidney Obissa and Lloyd Palun tested positive on Wednesday in mandatory testing of the squad 48 hours ahead of its game.
Gabon coach Patrice Neveu also tested positive but returned a negative test ahead of the Group C game and was allowed to take his place on the sidelines.
Information from The Associated Press was used in this reprot.