Microsoft Security Essentials and the Windows Intune Endpoint Protection client do share the same engine and signatures. However, the WIEP agent allows policys to be set via the Windows Intune Admin Console which gives an admin greater control of their
Anti-malware configuration. That said, you can deploy a policy that will allow you to use Microsoft Security Essentials on your machines if you choose to instead of installing the WIEP agent.
Also, Microsoft Security Essentials is only licensed for up to 10 machines at a small business so that must be taken into consideration when deploying at a small business of more than 10 machines.
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