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The USS Theodore Roosevelt will return to sea later this week, nearly two months after the ship was sidelined in Guam with a rapidly growing coronavirus outbreak, U.S. officials said as the crew finished final preparations to depart.

In an interview from the aircraft carrier, Navy Capt. Carlos Sardiello said Monday the ship will sail with a scaled-back crew of about 3,000, leaving about 1,800 sailors on shore who are still in quarantine. Those include up to 14 sailors who recently tested positive again, just days after getting cleared to return to the carrier. The puzzling COVID-19 reappearance in the sailors adds to the difficulty in getting the ship's crew healthy again, and fuels questions about the quality of the testing and just how long sailors may remain infected or contagious.

FILE - Capt. Carlos Sardiello, who was then the commanding officer of the aircraft carrier USS Theodore Roosevelt, addresses sailors in this Oct. 15, 2019, photo provided by the U.S. Navy.

Sardiello would not discuss timelines or planned operations. But other U.S. officials said the ship is expected to leave in the next few days, and if all goes well it will conduct naval operations in the Pacific region for some period of time before heading home to San Diego. The officials spoke on the condition of anonymity to discuss military operations. 

Asked about the possibility the ship will be able to conduct missions after its two-month layoff in Guam, Sardiello expressed confidence. 

"Do I have a crystal ball? I do not. But I think we have set the conditions for a high probability of success, and we're going to go to sea and do our mission," he said.

The Roosevelt has been at the center of a widening controversy that led to the firing of the ship's previous captain, the resignation of the Navy secretary and an expanded investigation into what triggered the outbreak and how well top naval commanders handled it. More than 1,000 sailors on the ship have tested positive over the past two months, and the entire crew has had to cycle through quarantine on shore before being allowed to reboard.

COVID precautions

Preparing to go back to sea has been an intense process, requiring sailors to go through mandated preparations and training to ensure all the systems are working and that troops are ready despite the added requirements of masks, constant cleaning, social distancing and other virus-related restrictions.

FILE - Lt. Cmdr. Jennifer Knapp with 3rd Medical Battalion, 3rd Marine Logistics Group, briefs U.S. Navy sailors assigned to the aircraft carrier USS Theodore Roosevelt on coronavirus disease quarantine procedures at Naval Base Guam, April 8, 2020.

Sardiello said they were able to get special black neck gaiters for the flight deck crew, because wearing regular masks wouldn't be safe. And they've set up one-way corridors, spaced out berthing for the crew members, and are keeping mess halls open longer so fewer sailors are there at any one time.

Once at sea, the crew will conduct carrier qualifications for the flight-deck crew, including fighter jet take-offs and landings. After about two weeks, the carrier plans to return to Guam to pick up healthy sailors who have finished quarantine and then return to sea.

The virus resurgence was a surprise wrinkle.

"We're at the time where expect the unexpected and deal with it. There's no good news. There's no bad news. It's COVID and we don't understand it completely," Sardiello said. "We're executing according to plan to return to sea and fighting through the virus is a part of that."

Reappearance of virus 

As of Monday, 14 sailors had tested positive for a second time, and 30 others who came in contact with them were sent ashore for quarantine. All 14 had previously tested positive for the virus and had gone through at least two weeks of isolation. Before they were allowed to go back to the ship, all had to test negative twice in a row, with the tests separated by at least a day or two.

The sudden reappearance of the virus reflects a broader puzzle for health and science experts. It may suggest that the test wasn't given properly or that the virus wasn't in the nasal passages but was still elsewhere. There also are questions about whether the virus level can sometimes be too low for detection.

FILE - Sailors on the aircraft carrier USS Theodore Roosevelt, who have tested negative twice for COVID-19, are asymptomatic and completed their quarantine, prepare to board the clean ship, May 1, 2020. (AFP/US Navy/Nathan Carpenter/Handout)

Air Traffic Controller 1st Class Daniel Wright said a few sailors who work for him were among those who tested positive again.

"They were obviously discouraged at first," Wright said in an interview from the Roosevelt, adding that one sailor had just returned to the ship, had unpacked and was eager to get back to work. "The nice thing is that the majority of them have little to no symptoms at all and are just waiting for that final check in the box with a clean bill of health so they could join the rest of the crew."

Wright said that while things were difficult in the early days of the outbreak, morale is better now as sailors look forward to getting back to sea, wrapping up their deployment and heading home.

"Half the crew would, I'm sure, be happy to just sail straight home to San Diego once we're ready," he said. But he added that this is some sailors' first deployment and some sailors' last, so "to be able to finish something that they started back in January — it's a good milestone for all of us to shoot for."

Fired captain

After the outbreak was discovered and the ship docked in Guam, more than 4,000 crew members went ashore for testing and quarantine, while about 800 remained on the ship to protect and run the high-tech systems, including the nuclear reactors that run the vessel.

In recent weeks, sailors were methodically brought back on board, while the others who had remained went ashore for quarantine.

Sardiello, a former Roosevelt captain, was abruptly sent back to the ship in early April to take command after Capt. Brett Crozier was fired for urging his commanders to take faster action to stem the virus outbreak onboard. 

After a preliminary review last month, Adm. Mike Gilday, the Navy's top officer, recommended that Crozier be reinstated as ship captain. But the Navy decided to conduct the broader investigation.

That review, which effectively delays a decision on Crozier's reinstatement, is supposed to be done by the end of the month.