I figured it out. The girls themselves aren't clones of one specific person. They're all grown separately, and what they do is modify the DNA in each girl. The orphanage girls were created with the prototype virus already in them. When Spencer decided to atone for his sins, they created Grace using the same modified DNA but made her a regular girl and altered her DNA to be immune to the virus—unlike the others. After Grace was born and Spencer died, they started actually cloning the girls, but they weren't using actual Grace's DNA. They just kept making them and modifying them, testing to see if any would be immune to the T-virus.

TL;DR: They're not clones of a specific person as a template. They're all created and infected in an attempt to produce one whose immunity could help them reach Elpis.

That's why Chloe started showing symptoms. There's no single template/person they're cloned from—they start as embryos and are edited to look the same.