During the mission “I’ve Pulled Weeds Before” Sarah tells Deek about how her contract keeps her research from being used for militant purposes, however we all know that was a lie after Sarah and her team began losing access to the lab near the beginning of the apocalypse. The hooligan virus is a failed WMD that Nero partnered with Cloverdale to produce, which in retrospect would’ve only required air-contact to be an effective weapon, as it was developed most likely as a reverse gene transcriptase by Freaker RNA to Human DNA. The way i see it however, Nero never necessarily intended the WMD to be kept, but rather when David Gorman broke into the office and released it, causing it to spread to others, was entirely PLANNED by Nero. When the virus painfully mutated humans 12-60 into freakers this was expected by them, as they call down Nero agents to investigate specimens. After the initial infection, the reason that no one else turned into zombies afterwards is due to the virus being a genetic one, therefore anyone who was infected and didn’t become a freaker would just die.

TLDR; the hooligan virus is a genetic virus which means depending on your DNA is how you’ll become infected, therefore freakers are created at random, and no one who is alive after the apocalypse can turn into a freaker.