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I need to know: a system with two HDD, one with operating system and the other with my documents.
Suppose that while connected to the internet a virus is downloaded to the second hdd (i.e. the one with my docs) would it infect the other hard drive(i.e. the one with OS)I know that the anti virus should prevent this from happening but one never knows.

I think while using internet if any virus downloaded into your hard disk which has your documents then your second hard disk will not be infected. But if you transfer any file from infected drive to another then there is possibility of infection. You can prevent your both hard disks by using newly updated anti virus.