While I realize this is probably old...

 Black Plague

Yersinia pestis: MILF. Was very popular back in her day (the Black Plague. ) and still
looks quite youthful. Dresses in gothloli fashion. Acts playful and innocent, but thought
to be a demon and opposed by the crazy man next door who dresses as a plague doctor.

 Ebola

Ebola: Shy, pale girl who blushes a bit too intensely. As in, she bleeds from her cheeks when embarassed. Ebola kills by damaging blood vessels after all. She doesn't appear to have a home to go to and is very secretive about it (Ebola has no currently identified natural reservoir.) Most of the route is about trying to make her get over her shyness, but once she does open up, an ebola pandemic sweeps over the world. Totally unrelated to her, of course.

 Influenza

Influenza: Cheerful loli prankster. Smarter than she seems.
She is a playful, disguise and prank-loving virus, so colorful would be a must. And not with a happy broad smile type of girl, maybe just a knowing, prepared grin. Like she knows a thousand jokes and is preparing to put them in play. Maybe full of gadgets too.

 Rabies

Rabies: Typical yandere, but doesn't keep her regular facade around the protagonist, think Gasai Yuno. Has a pet bat (or dog? Bats are more closely associated with rabies though, I suppose. ) As the protagonist interacts more with her, he begins to lose his higher reasoning and becomes more like her. If he notices this and tries to leave her, she strangles him to death in a bad end (rabies victims usually die of respiratory failures. ) If he keeps on, however, they become an insane couple utterly devoted to each other. Rabies should totally have bat wings and/or inumimi (dog ears).

 Tuberculosis

lots of latent cases, but an active infection can kill you. Also, I believe long-term infections like a longstanding tuberculosis deal can make your hair go white from the stress, so maybe tuberculosis could be the
cool-looking white-haired girl.

 White Blood cell

White Cell/Medicine: Normal happy cell turned overprotective by the effects of medicine/vaccine. Since this two ideas had the same role, I decided to fuse them, since it works just fine.

-She at the beginning really wants to be on the good side of the protagonist, so she starts getting friendly with the virus girls. And she really is enjoying herself. But, her nature isn't meant to be like that. After some event (Maybe she disappears for a while or something, we can plan the excuse later), she becomes more serious. Almost near the end, rumors of her hunting down viruses start spreading, maybe even a scene showing it (Not in every route, of course, just if the writer wants it). But she doesn't really want to do that, she has a huge internal conflict. In the end, we could make her repent, or suicide, maybe let the virus girl escape or whatever.
-Vaccine or medication characterized as a nurse. Her character and purpose would justify a tsundere, as she'd be angry at you for hanging out with the girls that would most likely kill you. This would make her the overprotective onee-san girl that slowly develops feelings for the protagonist.

 Spoiler