The virus/malware likely caused inability to access windows update ( If you are using a genuine copy)
Generally the best idea is to nuke the OS and reinstall fresh (if you do not have clean backups, system restore points do not count)
If you are absolutely sure you got every single bit of the malware removed from the system (just how sure are you?) you could attempt to run the system file checker utility and see if it fixes your issues.
Get to an elevated command prompt (click start, type cmd, press ctrl-shift-enter together or rightclick command prompt and run as admin)
At the elevated command prompt type sfc /scannow
This will check the integrity of all of your protected system files. If it finds any problems it will attempt to replace them with the correct file.