Most of the text you see in the game is gibberish, including the text on the big round seal on the game's cover:
The letters used in the icons above the villagers' heads indicating that they have something to say to you are also gibberish.
Almost everything in the game looks like gibberish, but if you look carefully, you'll notice that both the round clock-like indicator used at the end of boss battles, and the Black Scrawl itself, seen here:
...only use four different letters, despite the font having many more than that.
Which four letters are they? Well, test out that font
here and see for yourself. Type in A, T, G, and C (in any order you like, just be sure to use capitals) and you'll see that those letters are the Black Scrawl.
These are the initial letters of adenine, thymine, guanine, and cytosine, the four bases that make up human DNA.
When I figured this out, close to the end of the game, I was thinking, "But why would they go out of their way to make the Black Scrawl correspond to human DNA while people's speech and the rest of the text is meaningless garbage?"
Oh. So
that's what this "disease" is.