well lets think about this logically for half a second, how could clutch mates pass these viruses and diseases, if they don't exist in the box in the first place? They have to be exposed to something to get something. I guess rotting eggs could make some bad stuff grow, but the clutch being together isn't your problem.
personally I separate them, just because it's easier for me and how i've always done it. I see no reason why you can't keep them together until their first shed, many people, if not most people do it that way.
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