I have installed ClamAV to scan for viruses. It has 2 commands for scanning: these are clamscan and clamdscan. I use clamdscan because it is faster.
However, clamdscan cannot scan within home directories, or any directory it does not have permissions for, even when running as root. clamscan does not have this problem.
Try using setfacl to set extended attributes on the homedirs to give root read access.