Underground biosphere, what can be the possibilities?

[Czcibor]

Good.

Writing time, the renegade AI had to write the virus before it was destroyed by others (i don't want it to guide directly my heroes)

I see here one more idea. What about rogue AI, who do not actually care much about humans... just it kept the virus as way to guarantee not being killed by others.

I don't fully understand that.

You've got a an electronic device, responsible for some minor task, and produced in billions. Just it has got its own software, and inside it there is a virus. The attack comes from within...

Hmm i think they won't be well fed in the sewers neither. I like the regeneration part the best, although i don't know how it could be inserted into a developed lifeform?

In to developed? You'd have to rewrite the source code... I mean DNA... ;)
In DNA there should be additionally added a plan how the organism should look like. In case of any missing part, the nearby cells would turn into stemm cells and start growing that part back.
It would require insane detailed plan. Such system would in theory be somewhat cancer prone, as it would let cells to replicate. (in practice, if you can engineer genes well enough, then presumably cancer is eliminated earlier)

Another important part would be resist infections and drink polluted water. (They can destillate it, but anyway it is a good ability.)

Also reasonable.