Thanks for the great responses, guys!
I think when I was first thinking about this, I was envisioning something similar to the OSI stack (and yes, I know that trying to draw parallels with Virus and modern computer systems is dangerous at best
).
So the analog to the Application and Presentation Layers would be what communicates with biological entities and would therefore be in the language of the computer's design. Also, if a computer has the ability to communicate in more than one language (say, a computer is programmed to work in Galanglic and Gvegh, the Virus that is in that computer will have the ability to communicate in both languages).
As one moves up the stack, it becomes more specific and purely machine oriented until you get to the Physical Layer, where the data transmitted is binary.
As I recall, Virus propagates by copying a compressed version of itself (the "egg") to the target host. There it will try to grow. Once it grows, it will begin to take on attributes of the new host system.
As I type this, I think that I am answering my own question here - I think the ability to replicate itself assumes a kind of "Virus specific" transmission language - which would be based on the Transponder communication as Badbru states.
I guess the extension to this question is, if the Virus replicates by copying a compressed version of itself (keeping in mind these copies can be overwritten or merged), and assuming the replica is complete, would Virus have the ability to communicate in its original language AND the language of the new host?
I suspect so, provided that the new host has sufficient processing capabilities.
The interesting thing about this is that it creates the possibility for Cyms to act as translators in certain situations, mainly when a player-friendly Cym communicates with another Virus, especially if that Virus communicates in another language. Liam points out the ship-to-ship communication discussed in OOTD, and that was in my head as I was thinking about this, too.