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Certain folders may have to be excluded from antivirus scanning when you use file-level antivirus software in SharePoint

If you didn't know, you are supposed to explicitly exclude certain folders, file types, and processes from being monitored or scanned when using / software on  2003 / 2007 / 2010/ 2013 / 2016 on the wss, foundation, and server editions.  Below are the requirements specifically for 2013 foundation and server but you can also view the requirements for the other versions of SharePoint at https://support.microsoft.com/en-us/kb/952167.  Don't forget that there are also specific requirements for SQL Server, Windows Server, IIS, and other situations as well that require specific exclusions as well.  There is a complete list at http://goo.gl/4IhTkT.
also recommends that customers deploy an antivirus solution based on the SharePoint Portal Server Virus Scanning Application Programming Interface (VS API). The VS API enhances the current core feature set by providing the abilities to optimize and configure the scanning process at multiple

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