How Philip get infected (my research)

[Peanuckle]

I prefer the theory that

Spoiler below!

She was a TG (hence disabled video feed) and clarence made it appear that she WASN'T once you killed it. After all he can't hurt you, so you'd know what was and wasn't fake

Also: In the Bp there are diagrams, the description reads for one of a human body "Theres a red circle around the spine (or was it head?) possible infection point"

additionally there are the xrays which show a weird anomaly in the spine of human.

I dunno, Clarence has a lot of power over your perceptions.

Spoiler below!

He completely shuts off your senses at one point, and hides a door too. My guess is that he made you interpret Amabel's hug as an attack and fooled your body into dying, placebo-style.