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This is wholly unrelated to clamav. ClamAV is used on a Virtualmin system for scanning email, and nothing else--it would not catch the problem you've described. (Though, I've been rolling out the 0.93 version for all platforms over the past week or so...it'll reach our platform soon, though you haven't told us what platform that is.)
You have one or more php scripts on your system that have one or more security vulnerabilities. You need to make sure you are running the latest versions of all of your PHP scripts--most PHP apps in the wild have pretty horrible security records (there are a few exceptions with stellar records, of course, but most are pretty dodgy), so you must keep them up to date, or you will run into problems like you describe. And, of course, cleaning it up is a temporary solution--you need to fix the root cause of the problem, which is probably an insecure PHP script installed on your system.
Again, clamav has nothing to do with finding and preventing this kind of problem. This is not a "virus" in the traditional sense, and would not be detected by clamav, even if you did choose to scan your system with clamav periodically. The vast majority (like 99.99%) or viruses in the wild are Windows-only viruses, and so it would make no sense to scan a Linux box with clamav--it is only for detecting viruses in emails as they arrive on the server.
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