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NEW YORK. — Medical emergencies are rare, but hardly unprecedented in commercial flights. It’s far less common when they involve the plane’s pilot — and that pilot dies.

That’s what happened on Monday an American Airlines flight between Phoenix and Boston.

Captain Michael Johnston (57), was piloting the plane when he fell ill somewhere en route. The co-pilot landed the jet safely.

Crew members “took extraordinary care of Mike, each other and our customers,” airline CEO Doug Parker said in a statement sent to employees.

“We couldn’t be more proud of the teamwork this crew showed during an extremely difficult time.”

An autopsy and preliminary toxicology tests “showed that the death was the result of natural diseases,” the Onondaga County, New York, medical examiner’s office said — without offering specifics.

Johnston’s wife, BJ, told CNN affiliate KUTV-TV that her husband had a double bypass surgery in 2006. She said she was told he likely died of a heart attack.

“Whatever happened in the cockpit, none of us will know,” passenger Frank Cacciola told CNN affiliate WCVB-TV.

Cacciola was among the 147 passengers and five crew members aboard Flight 550 when it took off around midnight. Their Airbus A320 plane was being operated by US Airways, which is part of American.

After the pilot fell ill, the flight was diverted to Syracuse, New York.

“Medical emergency, captain is incapacitated,” someone in the cockpit told an air traffic controller, according to audio posted to LiveATC.net. “Request handling for runway.”

Those on board knew something was wrong when a woman’s “quivering” voice came over the intercom, alerting them that the pilot was sick, passenger Peter McSwiggin told WCVB. — CNN.