The impression I got is that Prime thinks Seconde started the pandemic but simply lacks the proof. Also, it looks like only Prime is worried about germs; which makes sense given their paranoia. It's also interesting which world is considered prime! Finally, I don't get the impression that Emily was killed. I got the impression that she was set-up to have had a relapse. They already successfully labeled her as a drugie; so now they are finishing her career.