To ensure your website is secure from viruses and other malicious files, you must install an effective antivirus product. Malicious files could be uploaded via any missing validation on upload file controls or any other Vulnerability.
All antivirus monitor the hard disk and scan files periodically for any changes then alert you about these viruses. This is a good idea to make your website files safe, but what if your website saves the uploaded files into database? The answer is antivirus has no control on these files and you can’t detect you have a malicious files on you website
SharePoint saves contents including files into content database so you need to install SharePoint specific antivirus product that scan the files before saving it into the content database. Microsoft Forefront has such plugin that protect your SharePoint farm against malicious files.