ZDNet has a story about a piece of of malware(virus, spyware, etc.) which infects Windows below the operating level, which caused some PC’s to stop working during or right after Automatic Updates in February.
This type of malware is called a ‘rootkit’, because it is a ‘kit’ of programs that infects Windows at the ‘root’ of the software.
If you looked at the listing of all of your files and folders, you would notice that all of the folders appear to start downward from the Desktop and branch out from there; kind of like an upside down tree. (This is why the listing is called a “folder tree.”)
The very top is called the “root,” like the root of a tree; If you have access to the root of any computer, you can do anything you want, even reprogram the whole computer.