Washington CNN  — 

The USS Theodore Roosevelt has returned to sea after spending weeks in port in Guam following a major coronavirus outbreak on board in March.

The aircraft carrier left Guam Wednesday and entered the Philippine Sea to conduct carrier qualifications, the Navy announced.

More than 1,000 of the ship’s nearly 4,900-member crew tested positive for Covid-19 following the outbreak. After evacuating some 4,000 sailors from the ship to Guam, the Navy had been returning sailors following a period of quarantine and isolation in the hopes of getting the aircraft carrier to sea as soon as possible.

“After cleaning the entire ship from bow to stern, the appropriate number of crewmembers to operate the ship underway have returned from quarantine after passing rigorous return-to-work criteria,” the Navy said in a news release.

Navy Surgeon General Rear Adm. Bruce Gillingham previously told CNN in an exclusive interview he is “very confident” the Roosevelt is “medically ready” despite the fact a number of sailors tested positive for the virus after returning to the ship.

Before returning to sea, the Roosevelt had been carrying out some preliminary in-port exercises to test the operational readiness of key systems on board. Even though more than 600 hundred sailors are still in isolation, the ship is be able to go to sea as it has enough healthy crew members to run essential functions on board.

Gillingham’s medical assessment follows 14 sailors testing positive for the virus over the last week, after initially having been thought to have recovered and being allowed to return to the ship.

The sailors had reported atypical body aches to the ship’s medical team which caused them to be tested again. But it’s believed they are not infectious, Gillingham said.

“Individuals may have persistent symptoms for quite a while, but given the information that we have to date, they’re unlikely to be infectious at that point,” he said.

The US Centers for Disease Control and Prevention estimates people are unlikely to be infectious 10 days after symptoms emerge, but the Navy is keeping sailors who tested positive in isolation for at least 14 days as an extra precaution to minimize the chances of infection once they are at sea.

Gillingham emphasized that the sailors who recently tested positive self-reported the symptoms, which led to them being tested again. The ship has instituted strict social distancing measures ranging from one-way passageways and stairwells to extended meal hours so sailors can eat in smaller groups.

Inquiry in progress

The outbreak aboard the aircraft carrier triggered a chain of events that led to the firing of the ship’s commanding officer, and the resignation of the acting Navy secretary.

Last month the Navy announced that it was launching a broader inquiry into the circumstances surrounding the outbreak, effectively delaying its initial recommendation that the ship’s commanding officer be reinstated.

The announcement came days after Secretary of Defense Mark Esper declined to immediately endorse the Navy’s original investigation into the issue, which included a recommendation to reinstate Capt. Brett Crozier.

US officials told CNN that senior Navy officials had recommended that Crozier be reinstated but Esper was not prepared to immediately endorse that recommendation and the wider inquiry was launched the following week.

Crozier was fired for what then-acting Navy Secretary Thomas Modly said was poor judgment for too widely disseminating a warning among Navy officials about the spread of the virus aboard his vessel, a warning that eventually made its way into the press.

While Modly publicly accused Crozier of sending his letter of warning to 20 to 30 people, the email to which the letter was attached shows that Crozier sent it to 10 people including his direct superior, according to a copy of the email obtained by The Washington Post.

“I believe if there is ever a time to ask for help it is now regardless of the impact on my career,” Crozier wrote in his email, the contents of which a US official directly familiar with the message confirmed to CNN.

Modly resigned days later over his handling of the incident, actions which included a $240,000 trip to Guam where he slammed Crozier and admonished sailors for giving Crozier a rousing send off in public remarks to the crew.

This headline and story have been updated to reflect the USS Theodore Roosevelt has returned to sea.

CNN’s Paul LeBlanc contributed to this report.