I was thinking something like this:
Each organism has some sort of ID code (or shell code, semantics) that it uses for most battle related problems. Ie: who does my venom effect and who does it work additively with? Anything that works with conspec immunity would use this instead of ancient species lines.
Organisms may change their codes at anytime they wish. Codes can range from, say, 1, 32000, and only the bot in question may modify or examine its code, or 0 which treats the bot as not conspec with anything at all.
Any intercellular DNA of any kind must match up with the code of the bot it finds in order to be injected in. This would include HGT or viruses. Bots with a code of 0 never intake DNA.
Once inside, viruses have all the same options that regular bots have, and may change attempt to change the ID code, or whatever it wishes.