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Boot Sector Viruses
Computer viruses are small programs designed to attach themselves to your computer, running without your knowledge and spreading themselves to "infect" other systems. Sometimes malicious, and sometimes just annoying, they are always a concern to the modern computer user. Viruses are discussed in substantial detail here.
The boot code that is stored on the hard disk and executed when the disk is booted up, is a prime target for viruses. The reason is simple: the goal of the virus writer is to get the virus code executed as often as possible, to allow it to spread and cause whatever other mischief it is written to create. What better place to put the virus than in code that is executed every time the PC is run, automatically, and before anything else is in memory?
One of the major classes of viruses, called boot sector infectors, targets the vulnerable boot areas of the hard disk. (The other major groups of viruses attack individual files, or spread using email and other Internet protocols.) Some infect the code in the master boot record while others infect the code in the volume boot sector(s). By infecting this code, the virus assures itself of always being able to load into memory when the machine is booted, as long as you boot from the volume that is infected. There is always code in any disk (hard or floppy) that is formatted, whether or not the system files are present on the disk.
Many people think that when you boot a system from a floppy or hard disk that has no system files--because it was formatted without transferring them--that the system doesn't boot. It's worth pointing out that in truth, it does boot; the boot process just halts very quickly when no operating system files can be found, as described here. In fact, the error message "Non-system disk or disk error - Replace and press any key when ready", is printed by the volume boot code that is read from the volume boot sector on the disk.
The importance of this distinction has to do with the spread of viruses. Since the volume boot code is always executed when the system attempts to boot from a device, a virus can be present on a floppy disk even if you don't format it with the system files on it using "FORMAT /S" or the "SYS" command. As soon as you see the "Non-system disk..." message, the virus could already be in your system memory.