Dark Matter season 2 was left with no source material to work with after season 1 adapted the entire standalone novel. So, it's all original material going forward. That being said, the Apple TV continuation of the Blake Crouch sci-fi novel, which still has the author as its showrunner, has managed to compellingly expand the Dark Matter universe beyond my wildest expectations. There was always room for more from this story, but I never imagined it would look like this.
All that being said, it should be noted that although season 1 did add new characters and storylines to the 2016 book, it also brought about 99% of the source material to life as well. There was very little missing in season 1 that Jason Dessen's (Joel Edgerton) literary counterpart didn't also experience, but there was one sequence that was confusingly left out. Season 2 doesn't adapt the scene, either. We do get something that more than makes up for it, though.
FULL SPOILERS for Dark Matter season 2, episode 3, "Everything Beautiful, Everything Terrible."

Dark Matter's return to the Deadly Virus Universe redeems season 1's decision to ignore a great chase scene from the book
In one of Dark Matter season 1's most heart-wrenching moments, Jason ends up in a version of Chicago that has been ravaged by a brutally lethal virus with no cure. In that reality, his son Charlie (Oakes Fegley) and wife Daniela (Jennifer Connelly) had already been infected, and Charlie is already dead, along with that universe's version of Jason. Daniela slips away while Jason stays with her, and then he and Amanda (Alice Braga) head back to the Box to once more try to find Jason's original world. It's a scene that's impressively faithful to the book, but the Apple TV adaptation leaves out the part where Jason and Amanda are forced into a high-octane car chase on their way back to the Box.
It's strongly implied that the SUVs hot on their tail are from an official organization, but the book never actually confirms it. Jason and Amanda just about make it back to the Box, despite being shot at. The Apple TV show never included this sequence, presumably because it would have demanded an explanation that would never come. In book form, it somehow works fine as an unresolved mystery, whereas the show works hard to provide answers along the way.
Thankfully, just as Dark Matter season 2 has also fleshed out the Futuristic Chicago, which also made the jump to live-action in season 1, Blake Crouch and company have done the same thing with the Deadly Virus Chicago. While it's only brief, episode 3, "Everything Beautiful, Everything Terrible," shows Leighton Vance (Dayo Okeniyi) suited up in hazmat gear as he steps out of the Box. He delivers not only a cure to the unnamed virus, but also a vaccine — both sourced from separate realities that have had more luck than this one at stopping the spread. It's a cool piece of worldbuilding, even if it's too late to save that world's Dessens.

Dark Matter season 2 teases an even greater significance to the Deadly Virus Universe
I would be surprised if we've seen the last of this reality. First of all, it's the first time we've ever seen Leighton's father. He's only ever mentioned in the book as the founder of Velocity — where Jason2 developed the Box. This version of Leighton's dad is on life support due to being infected by the virus. Leighton's emotional flashback to his earliest years with his version of his father strongly implies that he's dead, which is why he's so especially interested in this ill iteration surviving. As such, I think it's safe to say we'll see more of these visits as Mr. Vance recovers.
Worryingly, the Deadly Virus Universe may also become a hazard to the multiverse at large, especially if we look at the title of this week's episode: "Everything Beautiful, Everything Terrible." It's a reference to a line from earlier in the episode, talking about how opening up travel between universes comes with huge upsides, as well as terrifying downsides. So, although places like Futuristic Chicago have the potential to share their positive advances with other realities, the Deadly Virus Universe could also spread its most defining feature to countless other worlds via the Box. It would be a macabre (but enthralling) development for Dark Matter season 2 to introduce.
Dark Matter season 2 is streaming now on Apple TV.
