From what I remember on a recent thread over on the BT forums, viruses (virii?) were only a tiny part of the attack. Considering that cores were replaced from scratch, loaded on non-infected systems, and brought online...only to still fail, it's not a virus causing the Blackout.
Unlike the Blakist Whiteout, the Blackout appears to be a fundamental flaw or change in hyperspace itself. The medium is the problem this time, not the machinery that delivers through said medium.