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I always encourage administrators to implement a layered antivirus solution which includes gateway, information store, and desktop scanning. It sounds like you are doing gateway and information store scans. I would hope that you also include an antivirus product at the desktop.
I feel that your question might best be answered by Symantec tech support. However, my experience with antivirus software is that each product is Exchange version specific. So as long as you have the correct version of the antivirus for Exchange 5.5, 2000 or 2003, respectively, you can run two different antivirus products on two different servers even within the same organization.
The only problem I can foresee is additional complexity when administrating different versions. You must be careful to administer each server with the product-specific administrator tool and avoid the temptation to administer all of your servers with the same antivirus management tool, as many of them include "enterprise" management capabilities.
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