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I am not sure how can you be so sure that actually comus is the root of your problems? I am using comus too, but with tightened security on the server itself and with my OS security I never get hacked, neither get into troubles with any of my sites.
This time I haven't been affected by this comus hack (which I think is not comus hack, just a malware insertion) and my sites are running smoothly.
The only thing I don't like about comus is that its admin interface loads iframe from their website, so if their website has the malware, then technically every site that runs comus has it too.
To get rid of malwares and to actually avoid getting them, just install normal os, like Linux, or buy Mac.
Oh, and just one remark: before doing anything on your own, have host run clamAV on your box/v. acc. and scan for potential infected files, as well as run the rootkit detection tools. Then it's your turn to make your own box clean and more secure.
Good luck!
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