The gold virus scan subroutine that you download in the first room when loaded into memory automaticly detects and removes infection when you download an infected subroutine from an archive bin. Hitting "Tab" on the subroutine in the subroutine screen tells you what it does at each optimization level.

If you didn't have the virus scan subroutine you wouldn't know a subroutine was infected until you downloaded it and it started spreading infection to other programs in your memory. A green fungus type effect is shown on infected subroutines in the subroutine screen, since none of your subroutines are infected the disinfect procedure doesn't do anything.