For me, I'm going with this theory. Anersadora crew member brings Alien on board Sevestapol station via her tummy. Chestburster grows into the Alien. Alien captures a few people, eggmorphs them, one of those gives birth to the Queen. She grows up, lays the eggs we all know and love, and is never once seen in the game.
And I like to think that the queen was there, and that they didn't show her as to save that big reveal for Cameron's Aliens film. Meaning, lets say Isolation was a movie, for arguments sake, it could be watched right after Scott's film and before Cameron's.
That's how I like to look at it anyway.