WASHINGTON—U.S. military officials are increasingly certain that the coronavirus outbreak last month aboard the aircraft carrier Theodore Roosevelt was sparked by the vessel’s flight operations, rather than a result of the ship’s port visit to Vietnam.

That view comes as officials work to find the cause of an outbreak that forced the aircraft carrier to interrupt a deployment in Asia and divert to port in Guam, where hundreds of crew members, including its former commander, are in quarantine.

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