I like this idea alot

Maybe you can sorta let the virus loose to its target, wait a couple hours, and see what it comes back with?

It might come back with:
- what you want
- something else if you didn't enter the prompt right
- nothing for various reasons
- a counterattack (ouch)

or accidentally destroy what you were trying to get. Make it a gamble

Viral transfer would be a nice way to make viruses more realistic.

They could transfer themselves to other servers owned by that company, and sometimes even external companies. This would leave a 'File Transferred' log, so that you could track copies of it. This could be great for a new mission type like 'Remove a virus from our network'.