I think I have a virus on my USB stick. Is formatting enough to get rid of all traces of it or is there some way to make sure all data is completely erased from the drive?

You need to tally erase all data on the USB disk to make sure all traces of the virus is gone.

A program like Active@ KillDisk can make sure any virus or malware in neutralized on the disk, then you can partition (if needed) and re-format it.