Fighting a virus I picked up somewhere

[wavic]

If the partitions are mounted there is no difference if a partition is on a separate drive. If you have network devices mounted they will be affected too. One must put defenses wherever it's possible. The router, the OS's network, the OS. You may try to create an encrypted disk image and put your important stuff there. Or just use external hdd and plug it in the usb only when you need to use it. It could be complicated sometimes.