Dr. Mario went through various changes throughout it's development cycle. There are 4 known builds of the game, with the earliest one being from 1989. Each build got closer and closer to the final product, but each are different in their own way. These prototypes have been discovered in various places, and as a result, the roms for all the prototypes(except the near-final prototype) have been dumped and are available online for download.
The 1989 version, found at a San Antonio flea market in 2010, is the first known build of Dr. Mario. Right off the bat, you can tell this is very different from the final version. The game is called "Virus" instead of "Dr. Mario", graphics are in a different style than the final, the checkered background is missing, the Viruses have different designs, there's a complete lack of background music, some graphics are missing from the 2 Player Game, and you're helping a nurse take care of a sick dog.
The 1990 build is slightly different from the 1989 build. In this version, the clipboard colors are inverted, "PUSH START" was added to the title screen, blank game options have been added, but most notably, the Viruses are now animated.
Found in an otherwise regular PlayChoice-10 cabinet in 2012, this build is closer to the final version, but still not quite there yet. The Virus logo was redesigned, the dog and nurse no longer exist in favor of having Viruses in the bottom left corner, a checkered background was added in this version, Dr. Mario and the Viruses look similar to how they appear in the final game, and the gameplay is near-identical to the final version.
Dr. Mario prototype
This is the final version but with PlayChoice-10 sprites for Dr. Mario. Otherwise, there is no difference here.