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As 93 of the nearly 5,000 sailors assigned to the USS Theodore Roosevelt, now docked in Guam, have tested positive for the coronavirus, the Navy is removing nearly 3,000 sailors aboard the U.S. aircraft carrier by Friday.

Acting Navy Secretary Thomas Modly made it clear that while several thousand will leave the ship, other sailors will remain on board in order to continue to protect the ship and run critical systems.

He also said the situation “won’t be resolved in the next couple of days.”

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Navy officials said almost 1,273 sailors have been tested and, as of Wednesday, 593 of those tests came back negative. Officials are awaiting more results and more testing.

Testing of the crew has "accelerated," Modly said, adding that only 200 sailors could be tested each day.

The acting secretary said the aircraft carrier is the only known deployed warship with COVID-19 cases on board.

Of the 93 sailors who tested positive, 86 of the sailors exhibited symptoms for the virus while seven others didn't, Modly said.

As of Tuesday morning, the Navy said that a total of 334 personnel had tested positive for the virus, including 243 sailors. Of the 334, 19 have been hospitalized and 15 have recovered. None have died.

Modly told Fox News’ Jennifer Griffin: “We don’t have any forensics if that would indicate that that was what caused or brought the virus onto the ship. As I mentioned, when the crew came back onto the ship, we tested certain members that we thought might have an issue. And none of those tests came back positive."

"As I said before, we also had members flying on and off the ship from the air wing. So we are not really sure where it could have come from. Someone could have brought [it] from San Diego when the ship actually deployed. We just don’t know. Once the virus gets on a ship like that, it’s going to spread. And it’s hard to tell where it actually started.”

The carrier, like other Navy ships, is vulnerable to infectious disease spread given its close quarters. The ship is more than 1,000 feet long. Sailors are spread out across a labyrinth of decks linked by steep ladder-like stairs and narrow corridors. Enlisted sailors and officers have separate living areas, but most share rooms with multiple people, work in close quarters with other sailors, routinely grab their food from crowded buffet lines and eat at tables joined end to end.

Navy officials said they struggle to quarantine crew members in the face of an outbreak.

Navy Capt. Brett Crozier, the carrier’s commander, raised warnings this week in a memo to his leaders. He said the ship was facing a growing outbreak of the coronavirus and he asked permission to isolate the bulk of his crew members onshore, an extraordinary move to take a carrier out of duty to save lives.

Crozier said the spread of the disease was accelerating and that removing all but 10 percent of the crew would be a “necessary risk” to stop the spread of the virus.

“We are not at war. Sailors do not need to die. If we do not act now, we are failing to properly take care of our most trusted asset: our sailors,” Crozier said.

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Defense Secretary Mark Esper had said just the day before that he did not think the Navy ship would need to be evacuated.

Fox News’ Griffin questioned Modly: “When we asked about this last week, you said that you had no evidence that it was the port visit to Vietnam. Have you changed your assessment in light of the exponentially rising numbers? And was it the letter from the Captain that caused you to start to take -- move faster to remove people from the ship? And is the Captain going to be punished for having raised this in -- in very stark terms?”

Navy leaders were quick to praise the captain for bringing the dire nature of the matter to their attention. They brushed away suggestions that he could be punished because the issue became public so quickly.

"This is exactly what we want our commanding officers and medical professionals to do," Modly said.

"We're not looking to shoot the messenger," he added.

The letter from Crozier to top Navy brass was first obtained by the San Francisco Chronicle.