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Upamecano returned to training on Tuesday and was named on the bench on Wednesday night, but Rabiot was told to stay at the team hotel.
Deschamps hopes Rabiot and Upamecano will be fit to face Argentina, but says France are taking “necessary precautions” to stop any illness spreading.
“Temperatures have fallen a little [but] you still have air conditioning on all the time,” said Deschamps. “We’ve had a few cases of flu-like symptoms. We are trying to be careful, so it doesn’t spread, and players have made great efforts out on the pitch and, obviously, their immune systems suffer.
“Upamecano felt sick immediately after the match [against England]. It happens when you make such an effort, your body is weakened and you are more prone to be infected by these viruses. We are taking all necessary precautions to make sure it doesn’t spread, but viruses are infectious. We separated Dayot from others, and Adrien as well.”