The other day I checked on my website and McAfee detected a JS / Downloader Agent Virus. I first attempted to upgrade to the latest version of Wordpress (2.7.1) hoping to resolve the issue. However, somehow the file permissions got messed up as well, and was unable to create or delete anything in my root directory, even though the file permissions were set to 765. This left my website in a state of limbo for a couple days. I contacted tech support at GoDaddy, and they were able to reset my file permissions and resolve the issue.
My next task was then to perform the upgrade and see if the virus issue had been resolved. Unfortunately, the had not. After scanning through my code, I found that somehow a hacker gained access to my WordPress Theme header.php file and appended a bunch of JavaScript. I removed the code from my header file and all is well now. Make sure to keep your virus software definitions up to date, and I’ll keep my eye out for those internet pirates!