The 30-times stage winner has not raced since the Milan-San Remo one-day race on March 18 with his absence initially attributed to pain in his right ankle, due to overuse.
But now Team Dimension Data have announced the Manxman has also been suffering “unexplained fatigue” and analysis of a recent blood sample diagnosed the virus leaving him with an uncertain timescale for his recovery.
Team Dimension Data doctor Jarrad van Zuydam said: “Mark has been experiencing some unexplained fatigue during training.
“Unfortunately, there is no effective specific treatment against the virus but rest will be required to aid his recovery.
“It is difficult to give an accurate estimate of when we can expect him back at full fitness but we are hopeful of a significant improvement of his symptoms over the next two weeks.”
Cavendish last year won a first Olympic medal at the third attempt, with silver in the omnium, after combining objectives on the track and on the road.
With the Tour once again Cavendish’s primary objective for the year, he will have a gradual return to action and his race programme will be altered.
The Tour begins in Dusseldorf on July 1, with Cavendish bidding to move closer to Eddy Merckx’s record of 34 stage wins.
Cavendish’s wife Peta wrote on Twitter: “Just the year that keeps on giving of injuries and illness…”
Van Zuydam added: “His training load and symptoms will be monitored very carefully and he will make a gradual, step-wise return to full training and racing.”
The team statement added: “(We) are in full support of the Manxman and his ability to bounce back from this unfortunate setback.”