rocknbil - 5:09 pm on Mar 1, 2012 (gmt 0)

Are you sure the virus was actually on your server, and not insecure scripts modified to add malicious Javascript? Since you're posting in the PHP forum, I'm guessing this is the case. Generally files are modified to add a malicious bit of Javascript code that **leads** to a compromised server, which is what kicks off AVG warnings. So though it appears it's "on your site," it's just the code on your site leading to a compromised site.

This would have nothing to do with virus scans, it would have more to do with how you code and how you secure your scripts.