I would not plug a mouse into a keyboard port.
Since it did work, then it follows something must have changed or something broke.
Do you have any devices plugged into the USB ports, especially something recently? Have you checked the motherboard connections for the midboard USB connections? Do you know if Windows installed a driver update? Do all the ports behave the same? Could either your mouse or Keyboard be causing the problem or one of their drivers?
If you have not done so, you might use Device Manager to remove all instances of the USB drivers and let windows reinstall. Or you might check the ASUS site for a chipset driver update. Have you checked for a bios update for your board. This would not seem necessary since they were already working, but another change might cause a problem.
Since the USB works during boot, it would make sense the USB controller is still working, at least at
some level. You might try loading a live version of Linux and see if the system works normally with it.
If you can't get into safe mode, that might seem to indicate the failure of a primary driver, device or service. Perhaps booting into the WinRE would allow for you to try a startup repair or a System File Check.
I have not heard of a virus that would keep the USB ports from running, but you might look for an anti-virus that can be booted to check. Microsoft just came out with a beta of MSE called
System Sweeper.