USS stands for “United States Ship.” This prefix was used since day one. During World War II, the United States had a very workable ship naming system. Battleships were named for states, cruisers for cities, destroyers for distinguished individuals, aircraft carriers for battles and submarines were named for fish.
Since then, some time after the war, some Admiral had an epiphany, realizing that “fish don’t vote.” As battleships are obsolescent, we reserve state names for our most powerful warships and ballistic missile submarines. (The Ohio Class, the Virginia Class...) Fast-attack submarines are now named for cities.