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The new Borg queen in S2, the one that took residence in the mind of Jurati, is from an alternate universe/timeline. She came from the timeline where Seven was president of Earth.
The old original Borg queen that we see in S3 was assumed dead from the virus that killed all the Borg. But in reality she had been in hiding.
So there are 2 factions of Borg now, each with their own queen?
Yes, ut the Jurati Borg are apparently permanently engaged in guarding the wormhole to another realm where a giant elder god resides, or something. They've been relegated to the status of a cosmic bung cork.
Well the original Borg are now presumably all dead now, since the queen was defeated and the cube destroyed at the end of S3. The Borg led by the new Queen/Jurati are no longer evil and they are doing their own thing.
Where did the virus come from? Voyager?
Yes.