I'm curious if anyone knows any stories about a disease that turns people into other species, apart from the pandemic series, the only story I know that has something like this is The Buzzing Death - A history of the Toronto Plague by kspence92 https://www.alternatehistory.com/forum/threads/the-buzzing-death-a-history-of-the-toronto-plague.532105/

It's not Ponies, and it often can get quite .. dark. But Tales from the Blind Pig.
The Complete Archive of stories set in the "Tales from the Blind Pig" Universe. (transform.to)

There is the Taur Virus series which turns people into creatures with traits from different particular species with a centaur like body plan, though the transformation is temporary with the caveat that it can last a really long time and whatever someone is turned into is the same as what any future infections will turn them into.
Taur virus: part 1 by MaLAgua on DeviantArt
Series hub and group:
TaurVirus | DeviantArt

There is a superpower granting mutation disease in the story Super Minion which most notably turned a woman into a giant scorpion and has an escaped shapeshifting bioweapon as the main protagonist albeit in the role of a hired minion and to be fair the researchers that created him had good intentions but were ruthless and didn't realize how intelligent and aware their creation was until he/they escaped. Seems to be inspired by the webserial Worm and could reasonably be set on another entity besieged Earth. Most powers come from people triggering abilities after trauma or dire need during "weird summer" where as the name suggests things take a turn for the weird and you get things like exotic new diseases, superpowered animals, and spooky happenings. Super Minion | Royal Road I highly recommend it.

In many interpretations of the Conversion Bureau the New Foals are seemingly driven near mindlessly to spread their state of being through whatever means necessary and even in other depictions some degree of such behavior tends to be shown.