The user infects the very nature of the subject's existence. The prefix "onto" has to do with the nature of being or existing, pathogenic has to do with being infectious, and so ontopathogenic has to do with infecting the physical existence of a thing. Unlike common diseases or pathogens that only infect on a biological level, Ontopathogen causes infection on a metaphysical level. Just like pathogens, they can spread to other existences.
The Nothing (The Neverending Story); novel version only
Exsurgent Virus (Eclipse Phase)
When he harnessed the Anti-Life Equation during the Final Crisis, Darkseid (DC Comics) replaced the will of approximately three billion residents of Earth with his own. At the apex of his power through it, Uxas eventually went onto infect alternate realities becoming a multiversal sinkhole.
While fairly weak in its sealed state, The Lord of Terror (Ah! My Goddess) also known as the Ultimate Destruction Program, is revealed to be a transcendent computer virus capable of infecting anything in existence after its unsealed. Including.....
....Gods and Demons.
...Divine and Transcendent beasts/monsters.
...And even the transcendent anti-virus program originally designed to stop and destroy it.
Sir James Jaspers (Marvel Comics) was such an infectious existance that his less powerful Alt. self could warp his entire realities timeline and his more powerful mainstream counterpart could afflict whole multiverses.
Kai (Kung Fu Panda) after stealing the Chi from his victims he infected their existences with Jade cursed forms.
Corruption (Darksiders II) in the form of Absalom the first Nephilim had enough power to reach out and warp, distort and otherwise rot the whole of creation if left unchecked by his lonesome...
from decaying the very landscape of other worlds beyond his reach...
to rending even the most pure and noble minds of heavens considerably pious followers....
until they degenerate into foul obscene lunatics rife with his malicious bane.
The bile, cantankerousness of Gabriel Belmont's vengeful Id, Inner Dracula (Castlevania: Lords of Shadow 2) was so powerful and malignant that not only could it take on a life of its own. But was capable of reaching out warping the very being of anything or anyone unlucky enough to be caught by it.
Anything that is fully consumed by The Nothing (The Neverending Story) is infected and forever transformed into a lie which then enters the human world and begins to cause chaos over time.
Unlike previous iterations of Ganon from the Zelda series, Calamity Ganon (The Legend of Zelda: Breath of the Wild) is more so distinguished as an apocalyptic force of nature whose malicious essence, "malice", permeated the land of Hyrule and a large sum of its sentient, albeit mostly automated, lifeforms.
The Blue Spirit of Ice Naydra (The Legend of Zelda: Breath of the Wild) permeated by malice.