Three options come to mind.
A virus that adjusts your mouse sensitivity by like 5% every time you unlock your computer. Just enough that existing muscle memory is off, so you either have to adjust to the change or change it back every time.
A virus that installs and/or sets a similar but not quite right keyboard layout, and swaps to it randomly few boots. For example, setting the keyboard to Canadian Multilingual Standard instead of US English, where its only some of the punctuation keys that are changed.
A virus that randomly pops up a terminal window and outputs suspicious-looking text, and closes itself before the user has time to read it.