>>91981373My understanding is this:
First came the Zero Virus. Dr. Wily created Zero whose defining feature was a virus that he housed within his body that may or may not be working as intended. Sigma encounters Zero in his frenzied feral state, the virus infects him when Sigma defeats him and Zero regains his composure. The Zero virus mutates within Sigma, becoming something new, imprinting with Sigma's consciousness and will.
The Zero virus still exists in maybe trace forms, and the Sigma virus interacts with Zero in unusual ways due to him being the progenitor of it.
As for what the virus physically is, it's mostly just depicted as some kind of digital projection whenever it's tangible.