The New York Times reports that at least one sailor aboard the ship tested positive, as Navy officials made preparations for the vessel to deploy.
It further clouds the chances of the ship being able to finally leave Guam.
Navy officials say they have been aggressively screening and testing as crew members return to the Roosevelt after quarantining on Guam over the past month.
A member of the medical department said one sailor undergoing medical screening had failed for four days to report an inability to smell, often a symptom of the virus.
Officials on the ship are repeatedly cleaning and sanitising to prevent another outbreak of the virus that struck in March, which infected about 1100 crew members.