My understanding, is that the plug-in only works with its own USB connection. When the plug-in is running, you can't separately send MIDI to the Virus over USB (or DiNs), without going through the plug-in.
This is inaccurate. You have to enable midi in the plugin if it is running, and then it will work. Its on the tab on the right. You will know you are looking at the right page when you see a picture of the Virus panel. "Enable Midi" is in the dropdown. Otherwise just enable midi via the keyboard itself if you want to forgo the plugin altogether.