We believe that an Admin account was compromised. After ensuring all of the Admin local machines were clean and clear of infection, the Admins changed their passwords and it was then that we set to work to clean the site.
Useful information for the Admins on A.org
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The infected file was in the admincp folder on the server and had edited the index.php file with some encrypted script. Once we had identified the infection and cleared it, we were able to fix the index.php file and the site has remained stable from then until now.
If this attack happens to you at some point, this information should help you.