The Frenchman had a super spring. He won the Tour of the Alps ahead of Chris Froome (Sky) and rode as high as third overall in the Giro d'Italia before disaster struck with one day to race.
"I resumed riding yesterday just to get on the bike and think of something else," Pinot told AFP.
"I was riding for fun, to clear my head. The problem with this illness is that I don't know when I can return."
The rides around eastern France in Lure are not enough for Pinot to consider returning in time for the Tour. The Frenchman already won stages in the Tour and placed third overall in 2014 behind winner Vincenzo Nibali.
Without Pinot, France's hopes hinge on Romain Bardet (Ag2r La Mondiale), who finished third in 2017 behind winner Chris Froome and Rigoberto Urán.
Pinot planned on riding both the Giro and Tour this 2018 season, and began the Giro as a favourite with his win in the Tour of the Alps. His consistency, and bonus seconds with several second and third place finishes, put him third overall with one mountain stage to race.
Froome began the last stage as race leader after his solo ride to Jafferau to take the pink jersey from Simon Yates the day beforehand. Pinot began with doubts on how he would make it to Cervinia.
"The Friday was one of the great moments of my career with a legendary stage [to Jafferau]. That evening, I climbed onto the podium. I was confident. I only had to take care of the next day," explained Pinot.
"But on Saturday morning, I knew. From the time I went to bed the previous evening, I was coughing and I only slept three or four hours. In the morning I did not feel well, feverish. I got over the first climb with the top riders, I don't know how. But on the descent, despite the heat, I felt cold."
He slipped from third at 4-17 minutes to 16th at 43-46. Continuing to finish the final flat stage in Rome was not even an option.
That Saturday night, the French WorldTour team had called an ambulance because when Pinot arrived to the hotel he was suffering from dehydration and fever.
Pinot must consider the rest of the season and explained he does not want to jeopardise his chances in the Vuelta a España and World Championship later this year.
The Vuelta a España starts on August 25 and the Worlds comes one month later, September 30.
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