Only when done by AI.
Here's pictures of a lot of different cases of Virus vs shard of Freedom:
The PvP part will show at least one side a desynchronization error if a new creature is immediately placed on top of those viri. Same happens when you use unupgraded viri and then cancel their ability and replace them.
Shard of Freedom does not seem to enable evasion against Retroviri nor mass CC 9tested with Plagues, too), intended?
Spoiler for Retroviri and Plagues vs Shard of Freedom:
Their Retroviri ignore my Shard of Freedom.
Their Shard of Freedom is useless vs my Retrovirus.