I've been looking for an yaoi omegaverse that I read months ago. I don't know the name or author, but the story is about the first omega and first alpha ever documented and no one knows what's heat or rut is. I don't remember much, but I think they were locked in the sport storage room at their (high) school and the omega is about to go into heat.

I've been searching like crazy, I hope someone can help me please!!! ( 人ゝω・）

Megumi to Tsugumi is the only omegaverse that comes to mind. Let me clarify, by no means are the MC and ML the first omega/alpha in the world, but what leads me to mention this title is (1) the alpha/seme doesn't realize the uke is an omega until (2) they are locked in a gym storage room together. Perhaps it's this one?

The equipment room trope is not unusual for high school omegaverse. Omae no Koi wa Ore no Mono and Kiraide Isasete are 2 but they aren't the first ever alpha/omega. Hatsujou Virus and Omega Syndrome are about the start of the alphas/omegas but they aren't set in high school. Do you remember anything about the characters?

Kamisama Nanka Shinjinai Bokura no Eden

There is a manhwa titled "The Last Omegaverse". Not too sure about one that is about the first Omega and Alpha.

I think I found the one that you are looking for:

https://www.mangaupdates.com/series/x0oms0v/kamisama-nanka-shinjinai-bokura-no-eden