I considered the following choices based on how contagious they were...some are made up.
Ebola
Smallpox
Rabies
N8H0 Flu Virus B
Lyomora
Black death/ Yestis Pestlis (<- hoping I spelt that right...)
Avian Flu Viruses
Tuberculosis
AIDS/HIV
Yellow Fever

Those were my choices and ideas...but I'm not sure...please help me out guys.

4759134
The Black Death is probably the most suiting, since Equestria looks pretty medieval. Along with the fact that it's carried by fleas, and most species in Equestria has fur.

Lymora is a disease that pretty much spreads like black death. But it has nastier symptoms....Bleeding from eyes and mouth. Encephalitis. Internal Bleeding, Lung collapse and other organ collapses.

I made lymora off the top of my head honest...

Genetically (Magically if no humans) engineered and weaponized horse flu