Does the message appear during the BIOS enumeration phase or after the BIOS POST screen ?
If it is a BIOS-related message, maybe you should check BIOS fan control/temperature settings. It is also a possibility that the temperature sensors on the M/B have become defective. I think there should be a setting in BIOS to remove the (annoying) messages
If it is a Windows-related message, I do not know whether Windows cares about cpu overheating.
Do you think the virus may have written the message to MBR / MFT ?