The captain of a nuclear aircraft carrier with more than 100 sailors infected with the coronavirus pleaded Monday with U.S. Navy officials for resources to allow isolation of his entire crew and avoid possible deaths in a situation he described as quickly deteriorating.

The unusual plea from Capt. Brett Crozier, a Santa Rosa native, came in a letter obtained exclusively by The Chronicle and confirmed by a senior officer on board the aircraft carrier Theodore Roosevelt, which has been docked in Guam following a COVID-19 outbreak among the crew of more than 4,000 less than a week ago.

“This will require a political solution but it is the right thing to do,” Crozier wrote. “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.”

In the four-page letter to senior military officials, Crozier said only a small contingent of infected sailors have been off-boarded. Most of the crew remain aboard the ship, where following official guidelines for 14-day quarantines and social distancing is impossible.

“Due to a warship’s inherent limitations of space, we are not doing this,” Crozier wrote. “The spread of the disease is ongoing and accelerating.”

He asked for “compliant quarantine rooms” on shore in Guam for his entire crew “as soon as possible.”

“Removing the majority of personnel from a deployed U.S. nuclear aircraft carrier and isolating them for two weeks may seem like an extraordinary measure. … This is a necessary risk,” Crozier wrote. “Keeping over 4,000 young men and women on board the TR is an unnecessary risk and breaks faith with those Sailors entrusted to our care.”

The Navy did not respond to The Chronicle’s requests for comment Monday, but on Tuesday morning as the news spread, the Acting Navy Secretary Thomas Modly spoke to CNN.

“I heard about the letter from Capt. Crozier (Tuesday) morning, I know that our command organization has been aware of this for about 24 hours and we have been working actually the last seven days to move those sailors off the ship and get them into accommodations in Guam. The problem is that Guam doesn’t have enough beds right now and we’re having to talk to the government there to see if we can get some hotel space, create tent-type facilities,” Modly said.

“We don’t disagree with the (captain) on that ship and we’re doing it in a very methodical way because it’s not the same as a cruise ship, that ship has armaments on it, it has aircraft on it, we have to be able to fight fires if there are fires on board the ship, we have to run a nuclear power plant, so there’s a lot of things that we have to do on that ship that make it a little bit different and unique but we’re managing it and we’re working through it,” he said.

“We’re very engaged in this, we’re very concerned about it and we’re taking all the appropriate steps,” Modly said.

So far, none of the infected sailors has shown serious symptoms, but the number of those who have tested positive has jumped exponentially since the Navy reported infections in three crew members on March 24, the first time COVID-19 infections had been detected on a naval vessel at sea.

Asked Tuesday what should be done about the Roosevelt, President Trump said he would “let the military make that decision.”

Retired Admiral James Stavridis, former NATO Supreme Allied Commander Europe, told The Chronicle Tuesday in an e-mail that “we should expect more such incidents because warships are a perfect breeding ground for coronations.”

“Unfortunately, naval vessels are ideal breeding grounds for the spread of viruses because it is impossible to do social distancing on one” because of the tight quarters on board, Stavridis said.

The ship’s problems will “compound,” Stavridis said, because you can’t tie the vessel up “and send everyone ashore. It is full of weapons, billions of dollars of equipment, fire hazards, and nuclear reactors.”

Mark Cancian, a Marine colonel who served for 37 years before retiring, said that “the Navy has got to figure out how to do this right or else they can’t deploy the rest of the fleet.

“This is like the test case,” said Cancian, a senior adviser with the Center for Strategic and International Studies think tank in Washington, D.C.

Stavridis advised the “entire U.S. Navy” to “test, test, test,” and immediately isolate those infected off of ships.

Scrubbing the Theodore Roosevelt of the virus will not be complicated, but “time-consuming,” he said. He estimated cleaning would take five to 10 days with a crew of 350 people.

Senior military officials said last week that the entire crew of more than 4,000 will be tested. The carrier’s home port is San Diego.

At the time, Modly expressed confidence that they identified all the sailors who had been in contact with the trio of infected sailors and they had been quarantined.

“This is an example of how we are able to keep our ships deployed at seas and underway, even with active COVID-19 cases,” Modly said.

But by the time the ship reached port in Guam on Friday, the number of cases had grown to 25, and soon after to 36, according to reports.

Chief of Naval Operations, Adm. Mike Gilday responded to the increasing numbers late last week by saying the Navy was taking “this threat very seriously” and working to isolate positive cases to halt the spread. He promised to increase the rate of testing and to isolate infected sailors. He stressed that the top two priorities were caring for their sailors and maintaining “mission readiness.”

“We are confident that our aggressive response will keep U.S.S. Theodore Roosevelt able to respond to any crisis in the region,” Gilday said.

But by Monday, a senior officer on board the massive aircraft carrier, who wished to remain anonymous because they are not authorized to speak to the media, said between 150 and 200 sailors had tested positive. None had been hospitalized — yet, the source said. The Chronicle agreed to withhold the officer’s name based on its anonymous sources policy.

In his letter to top Navy command, Crozier said if it was operating in wartime, the ship would cope and continue operations and battle the illness as best it could.

“However, we are not at war, and therefore cannot allow a single Sailor to perish as a result of this pandemic unnecessarily,” Crozier wrote. “Decisive action is required now in order to comply with CDC and (Navy) guidance and prevent tragic outcomes.”

Lawrence Korb, a former assistant secretary of defense in the Reagan Administration, said that “it is very unusual” for a ship captain — someone who is typically on a career track to become an admiral — to write such a letter.

“It shows that this is a person who is putting the welfare of his sailors ahead of his career,” said Korb, a retired Navy captain who is now a senior fellow at the left-leaning Center for American Progress think tank.

Gilday told reporters last week it was unclear if sailors became infected following the ship’s previous port of call in early March to Da Nang, Vietnam. Gilday said they debated whether to go on with the Vietnam visit, but at the time there were only 16 coronavirus cases in northern Vietnam and the port was in the central part of the country.

Sailors were screened prior to returning on board. The first three sailors tested positive 15 days after leaving Vietnam, officials said.

The virus has been hard to contain on board ever since. Federal and military guidelines recommend individual quarantine, including no use of common areas.

“Due to the close quarters required on a warship and the current number of positive cases, every single Sailor, regardless of rank, on board the TR must be considered ‘close contact,’” Crozier wrote.

The tight quarters on the carrier are “most conducive to spread,” he wrote, including large amounts of sailors in a confined space, shared sleeping quarters, restrooms, workspaces and computers, a common mess hall, meals cooked by exposed personnel, and movement constraints requiring communal contact with ladders and hatches.

He called the current strategy followed so far — of moving a small infected group onto the pier, increasing cleaning and attempts at social distancing ineffective.

“The current strategy will only slow the spread,” he wrote. “The current plan in execution on TR will not achieve virus eradication on any timeline.”

The captain compared the situation to the Diamond Princess cruise ship, citing a study that focused on what could have happened to that cruise ship had no isolation been done. A total of 712 passengers eventually tested positive for COVID-19 from that cruise departing from Japan; however, the study found if there had been no early isolation close to 80% of passengers and crew would have been infected. And had the cruise line immediately evacuated the ship after the first positive tests, the study found only 76 people would have tested positive.

Crozier said the Theodore Roosevelt could fare even worse, as a warship is not designed to provide such individual isolation like guest cabins.

“TR’s best-case results, given the current environment, are likely to be much worse,” he wrote.

As for the senior military officials’ promising tests for all crew aboard the carrier last week, Crozier said it is not a solution.

“Testing has no direct influence on the spread of the COVID-19 virus. It merely confirms the presence of the virus,” he wrote.

Of the first 33 Roosevelt sailors testing positive, seven, or 21%, originally tested negative. After testing negative, those seven sailors presented symptoms within 1 to 3 days after their initial negative test, Crozier said.

The testing should be utilized, the captain wrote, after a proper 14-day quarantine to ensure no infected sailors return on board a clean ship.

Only one of the pier-side accommodations meet Navy guidelines, he wrote, adding that two sailors tested positive after sleeping in a gym with cots.

If the Navy focuses on being battle ready, it will lead to “losses to the virus,” Crozier said. The second option, the captain recommended: “Achieve a COVID-free TR.” Methodically clean the ship, while isolating the crew in port with a massive amount of individualized lodging equipment.

As part of his plan, 10% of the crew would stay on board to run the reactor plant, sanitize the ship, ensure security and provide contingency response for emergencies.

“As war is not imminent,” Crozier wrote, “we recommend pursuing the peace time end state.”

(By San Francisco Chronicle)