If the motherboard is infected, then that means that it's in the BIOS itself and it not a worm, but a RootKit, one which installs itself to the BIOS.
The RootKit writes itself to the empty spaces in the BIOS code and depending on if it's an older type RootKit or a newer type RootKit, the older type (v1) will just infect the BIOS where as the newer types will infect the BIOS and the MBR (v2) the the last type of which I am aware of will also load itself to memory (v3).
Those are the developmental stages of each new variety of BIOS RootKit which Loads before the Operating system itself can even load, making it extremely difficult to detect and even to remove.
Video Cards can become infected very easily too once the motherboard BIOS becomes infected and even the firmware of Hard Drives can become infected. Anything which uses a Firmware/BIOS can be infected these days if it is networked and not secured.
When a Motherboard does become infected, the easiest way to remove the infection from the system and any other infections from your hard drives is to pull the drives and set them to one side making sure to label which drive as to which drive is which. the drives can be connected to another system as Secondary drives and fully scanned with several choice pieces of software, then visually looked over with Windows Explorer so as to remove the majority of infections.
The Motherboard itself you should be able to remove the BIOS chip from it's socket, then use the CLR CMOS jumper to clear out anything that might remain behind. You should be able to order a New BIOS chip from the Motherboard Manufacturer or possibly some other company.
If the BIOS Chip is soldered on the Board, then chances are, you're SOL and you'll need to order a new motherboard.
Once you reconnect your drives and boot up the system, you'll still need to run a few scans so as to clear out any registry entries which could not be accessed while the drives were connected externally and maybe catch a few strays that may have been missed in the mean time.