If you think that you have a virus on your Amiga, then you have to start an antivirus program from a clean scource. That means you have to boot your Amiga from a floppy disk. Virus Help Team have made a floppy disk with VirusZ III that you can download, with the latest version of VT-Schutz, and they are all clean and ready to use, this floppy disk are packed with Disk-Masher (dms), so you have to unpack the archives first.

if you don't have DMS installed on your system, you can download the dms program here, it is not packed, it is an .run file ready to use

DMS v1.11: Disk-Masher v1.11 by SDS Software, Kickstart 1.2 and higher - Download dms.run (40kb)

DMS AmigaDOS commands:
DMS Write file[.DMS], [TO dev:] - (Example for VirusZ: DMS Write vhtdk-vt317.dms TO DF0:)

After unpacking the archive to the floppy disk, it is very important that you write protect the floppy disk, to prevent infection of virus or trojan to the floppy disk. Also turn off the power to your Amiga for 30 seconds, before you boot with the floppy disk.