Theory: The Viruses are from Space

Abstract
The viruses from the Dr. Mario series originally came from space.

Arguments

 * Argument 1: In the ending for the first Dr. Mario on the NES, the viruses are beamed up by a spaceship after being defeated by Dr. Mario. Additionally, the NSO Dr. Mario SP description calls it a UFO. And describes the ending as "uncovering the ultimate truth". A UFO also appears in the endings of Dr. Mario Express.


 * Argument 2: In the opening for Dr. Luigi, the virus initially beam down from a spaceship.


 * Argument 3: Word 8 of Dr. Mario World shows us that the virus infestation is present across space, covering multiple planetoids from Super Mario Galaxy and Super Mario Galaxy 2. Additionally, the official Dr. Mario World Twitter shows us that the Red Virus is familiar with that area already.