Pinout for Leonardo USB
The USB does not go to pins 0 and 1.  The UART goes to pins 0 and 1 - that is a totally different interface.

The USB is connected to dedicated USB pins on the chip.  If you look at the Leonardo schematic you can see it is pins 3 and 4 on the chip. Note that that is not pins D3 and D4 on the board, but the third and fourth pins anti-clockwise from the "pin 1" dot on the main chip.