I have a PC with two HDDs. One to work with (name it “1”) and my old HDD (name it “2”). Both have Windows 98 SE and many common programs installed. While working in “1”, it was infected with a virus by an Email message. I found two suspect files in WINDOWS\SYSTEM and tried unsuccesfully to delete them (they were in use) and remove them from the registry key …WINDOWS\CURRENT VERSION\RUN (they were restored every second). Because I had recently uninstalled my antivirus program in “1” and it wastoo late (1:00am) to consult anyone, I switched off my PC without shuting down. When I rebooted (either in normal or in safe mode), the message “Windows Protection Error” appeared. I rebooted with “2” as master and “1” as slave, updated the virus definitions in “2” and scanned “1” for virus. I found the W32.Elkern@mm virus in many system files (all automatically repaired). I also found the W32.Klez.E@mm virus in several other non-system executables (application programs) and deleted them because they could not repaired. I rescanned “1” and found no virus. But when I tried again to boot from “1” the message reappeared. I tried to reinstall the Windows (with or without deleting win.com first) and restored the registry with one of the previous days backups. In both cases, after the 1st setup reboot, the registry checker inform me that the registry has an error, restores it, restarts and then the message reappears. Drive “A” has no virus anymore (rechecked). The current registry is ratherOK (checked with fc against previous backups). Are there any system files missing (deleted or damaged by the virus)? What can I do to repair my OS avoiding a clean install?