Alfresco doesn't do any sort of virus checking of the files that are uploaded in the repository. When you upload documents into the repository, the just get renamed and placed in the content store. If malicious content is uploaded, it's not going to cause any harm to the Alfresco server. The only way it would be harmful is if another user downloads and opens the malicious file. If you need some sort of malware detection when files are being uploaded, you would need to customize.
