He's infected with a nanomachine-based virus that is slowly turning him into a zombie robot.
Those patches are blobs of nanomachines doing their best to fully convert him, which are only being kept at bay by Sonic burning them away with his super-speed.
However, every moment he's not moving, the nanomachines get right back to converting him, which is why it's spread across his body.
At least, that's the general idea I've gotten based on what info I've learned about this storyline.

The internet has ruined me to a point where I thought that was cum.