If it's a genuine copy of Vista, then it probably happened because in removing the virus, you also affected certain files that Windows "checks" to make sure it's genuine, thus making it de-activate itself and tell you to re-activate (usually by contacting Microsoft) incase you really were trying to bypass the genuine notification checks. Just go through the process and it should be fixed. EDIT: Part of the activation process should give you the option to call Microsoft. Do it - it's the easiest method (if using the internet doesn't work).
If you were pirating Vista, then it's probably a sign that Windows knows about it and is trying to get you to buy a genuine copy. Look up tools to remove that notification and force-activate Windows to restore functionality.
EDIT2: Someone can probably explain the whole "Genuine Windows no longer activated" phenomenon better than me (and probably name exactly which files it checks). All I know is that I've seen this happen a few times on genuine copies of Windows and almost every time it has been fixed by going through the steps it lists and contacting Microsoft. Takes about 5 minutes.
