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In the past, I've used WSUS 3 in disconnected mode by exporting updates from a server on the public internet and importing them to a server on a private totally disconnected network. Sophos has been used in the same way to provide anti-virus capabilities.

We're looking at a new Windows Server 2012 based network, but it isn't clear how to bring virus definitions for Endpoint Protection across to the offline network.

Are there any existing instructions available that I haven't been able to google up?

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There are download links for System Center offline definitions in Step 6 of this Technet article:

http://technet.microsoft.com/en-us/library/ff823818.aspx

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The virus definitions are here so it is a valid answer, but after standing the WSUS server up I found the SCEP virus definitions in the WSUS catalog. –  Simon Gill Oct 18 '13 at 14:03

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