It's down to how they're allocated.
First, the airline's REQUEST - So, Virgin *probably* asked for "VA" or "VI" (maybe)
If those are taken, it's then down to Capitalisation, so "Virgin Atlantic" would mean "V.A."
Again, if that's taken, or the same, it's then down to the first and last characters of the name...
So - "Virgin Atlantic Airways" (which was the official name) takes the V from the start, and the S from the end = VS.
Don't believe me? Why do you think BMI (old - "British MidlanD") is BD?!? :-)