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Most of the viruses leave a code in every .php file.
You have to clean all the .php files or put a back up.
But they where able to inject code in your pages.
So there must be a leak somewhere.
And that can be done in a lot of software.
So you have to check als installed scripts.
Maybe you can see where they got in in your log file.
This can be solved in 1 hour. But it also can takes days before you find out where they get in. Look what software could be vunerable and search the forums of that software. Most of the time other people suffer the same problems and questions pop up on forums.
When it is fixed you have to send your page to google again. The blacklisted your domain. I had that once and they got me of the blacklist a few hours after i send in my site to get of the blacklist.
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