If you are not using VC (Virus is stand-alone) then the knobs' MIDI data goes out the MIDI out port. When you are using VC the knob data is hijacked by VC and turned into plugin automation. But, not all hope is lost. The Virus has something that's called remote mode, which turnes the Virus surface into a MIDI controller. In this case the knobs' MIDI data comes in from the Virus MIDI in port, while USB is connected. You set up remote templates in VC under the [pathc/utility]->[remote] tabs. You put the Virus in remote mode by pressing shift+config on the physical surface.
When the Virus is connected to your computer using USB but VC is not loaded, the Virus becomes a soundcard, which means that you get "Virus synth" ports that let you communicate with the synth internal hardware, and "Virus MIDI" ports that let you use the physical in/out ports at the back of the Virus.
The data is transmitted also via USB in case you use the USB connection solely for Midi I/O (which is possible).
Best wishes,
Jörg Hüttner
Thank you both for the clear answers 
