Is there a way to scan the entire drive including auto-run and all partitions, including the master boot record (MBR)?
It seems like that cannot be done with ClamAV. See the comments on this site. Definitions are missing for such viruses as well I don't see the patch applied to the clamav I have installed.
In Linux anything is a file. That includes your devices' MBR. All you need to do is simply preform a scan on the associated device driver file.
To find this do the following in your terminal:
mount | grep -e (media|mnt)
This will search your mounted devices for anything
/mnt. Typical distros use
/media/, you should
know your location just by browsing to the root of the device.
Next you should see from the output of mount something like the following:
/dev/sdb1 on /media/sdb1 type ext3 (rw)
/dev/sdb1 is the second device(b), first partition(1)
after the MBR/GUID table. Thus your device file you want to scan
/dev/sdb and you would scan with
sudo clamscan -i /dev/sdb
Make sure you do regular backups with
dd(1) as well
Go to where it is mounted (presumably /media/) and run clamscan like you normally would (-r). (Or you wouldn't have to go where it is if you want to use the -i flag)