In Maternity, there was an epidemic of an unnamed virus among babies. At least two died before they diagnosed it, including Baby Boy Chin-Lupino. But they weren't the POTW (patient of the week.)
Histories - Victoria died because she didn't get rabies shots in time (as in a long time before she ended up at PPTH) so they didn't kill her.
Babies & Bathwater - Naomi died but they saved her baby
Daddy's Boy - Carnell died
The Mistake - Kayla died. Chase's error.
Sex Kills - Laura Neuberger died before she became their patient. Needed to diagnose her so they could transplant her heart.
Euphoria Part 1 - Joe the cop died
Forever - Kara killed her baby then was diagnosed with MALT lymphoma. Refused treatment so she died after the episode ended.
Informed Consent - Ezra Powell died. Cameron euthanized him (although I didn't consider it euthanasia as he was still capable of doing it himself and, as a doctor, he had access to the means.)
Que Sera Sera - George will die of lung cancer after the episode ends
Son of a Coma Guy - Gabe commits suicide before reverting to his vegetative state so he can be an organ donor for his son
House Training - Lupe died of her staph infection because Foreman gave her total body irradiation
97 Seconds - Stark died. Thirteen's error
Wilson's Heart - Amber Volakis from taking amantadine then being in a bus accident
Joy to the World - Natalie dies of eclampsia so Cuddy can adopt her baby (which she gave birth to and abandoned in a tenement)
Simple Explanation - Charlotte dies because she lied about where she had traveled. (It's also the episode when Kutner commits suicide.)
The Tyrant - Chase deliberately falsifies lab report
The Down-Low - Mickey has incurable disease
Help Me - Hannah after a building collapses on her
Unplanned Parenthood - Abbey refuses treatment in order to help her newborn's immune system.
Niles - CDC refuses to allow them to examine the patient who was thought to have small pox
Transplant - Wilson's patient while waiting for donor lungs to be diagnosed & cured
I think that's all. (I'm not doing the clinic patients.)