Arduino Mega 2560 USB died due to short circuit
If you're arduino still runs but isn't able to be identified at all over USB, you probably fried the microcontroller that handles the UART-USB conversion. 

Easy fix would be to bypass that chip (since it's not working anymore) by using an external UART-USB converter. You could use this TTL-232R-5V cable and plug it directly from your computer to the UART pins of the arduino.