As of Thursday, 1,102 sailors on the vessel have active cases of the virus, the San Diego Union Tribune reported. Of the 1,102, one has died and 52 have recovered.
The Navy announced Thursday that the ship's crew of 4,800 is preparing to return to sea after being docked in Guam since the end of March.
More than 4,000 sailors who had been self-isolating in hotels off base while a crew of 700 worked to deep clean the vessel.
About half of those who have tested positive have shown no symptoms. Many of the new positive tests were among sailors who had been self-isolating without symptoms, but were re-tested as they moved back onboard.
"Our mission is to make sure the fighting force in the fleet is ready to go at all times," Capt. Maria Young, commanding officer, U.S. Naval Hospital Guam, said in a statement. "I appreciated the Sailors' patience throughout this whole process, as we worked with one another to maintain the health and readiness of the crew and to get the Roosevelt back to sea. We are happy to help."
Navy officials have also confirmed that a second ship is fighting to contain a coronavirus among its crew. The crew is smaller, but the rate of infection is similar.
On the guided-missile destroyer USS Kidd, due to port in San Diego, Calif., next week, there are 78 active infections among its crew of 330 people, up from 18 last week.
All but 90 sailors on the Kidd have moved off the Kidd and are in quarantine at a San Diego hotel.
The Kidd deployed in early January and stopped briefly in San Diego before setting sail alongside the Roosevelt.
Navy officials believe the outbreak onboard the Roosevelt was caused not by its stop earlier this year in Vietnam -- which continues to have a very low rate of infection -- but by aircraft carrier activity.
Earlier this week the Navy's acting secretary, James McPherson, said the Navy would open a "deeper investigation" into the outbreak and the circumstances that led to the termination of its captain, Brett Crozier, and the subsequent resignation of then-Acting Navy Secretary Thomas B. Modly.
Previously McPherson and Chief of Naval operations Admiral Michael M. Gilday had recommended Crozier be reinstated, but Defense Secretary Mark Esper said he needed more information before making a decision.