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The forward, who is asymptomatic, has left the national team squad and will not feature for Les Bleus in their forthcoming Nations League fixture with Croatia in Paris on Tuesday, a match in which he was expected to form a forward trident along with Wissam Ben Yedder and Anthony Martial.
He featured in Saturday's 1-0 win over Sweden and scored the winning goal in that clash after breaking through a couple of challenges in the box before finishing from an acute angle.
He will not, however, take part in the rematch of the 2018 World Cup final, a match in which he memorably found the net.
"Kylian Mbappe will not participate in France versus Croatia on Tuesday evening at 20:45CET at the Stade de France," a statement from the French FA has confirmed. "The result of his Covid-19 test carried out by UEFA on Monday morning was found to be positive. He was placed away from the group after receiving the results, at the end of training, before going back to his own home in the evening.
"Like the entire delegation, Kylian Mbappe had undergone a test prior to the games of the international break. The result was negative, like the one last Wednesday, at the request of UEFA, before Sweden against France."
It also throws into doubt his immediate participation when PSG finally start their Ligue 1 campaign. Thomas Tuchel's side are slated to play Lens on Thursday followed by Le Classique against fierce rivals Marseille on Sunday.
Additionally, they will then face Metz next Wednesday and have a trip to Nice slated for September 20.
PSG could be severely shorthanded for their forthcoming fixtures as they are suffering from a cluster of coronavirus infections.
Several stars returned from holiday having tested positive for the virus, with Neymar, Marquinhos, Keylor Navas, Angel Di Maria, Mauro Icardi and Leandro Paredes all currently laying low.