The young midfielder is on-loan to the end of the season at the Swiss club, which shares INEOS with United as a club owner.
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However, Lausanne haven't registered Kone for the Europa Conference League.
Lausanne face a playoff against SK Sigma Olomouc over the coming fortnight and have decided to leave Kone out of their registered squad for the remainder of the competition.
Enzo Kana-Biyik, another United loanee at Lausanne, has been included in the Conference League squad.
The 19-year-old forward has made 18 appearances for the Swiss side since joining on loan last summer.