"How does Ridley Scott's Prometheus fit into universe of the Alien films?
Quite simply: it has the Alien aliens in it. The catch, though, is that you might not recognise them – at least, not at first.
Remember how the alien took on canine qualities after gestating in a dog? You may even suppose that the first film's alien was so recognisably humanoid because it had grown in a human. The same applies here: generation by generation, the creature mutates. As Prometheus begins, the xenomorph is not too recognisable. Sure, it has that alien DNA that Scott and Fassbender teasingly referred to, but it's missing... well, it's missing human DNA. Or dog DNA.
All you have to do is imagine how it might look if it were to mix DNA with another alien species... and I think we're starting to work it all out."
Also, this quote from bleedingcool way back in February suggests a never before seen version of the alien is in Prometheus. But these sources could all be full of shit. obviously the source who told Corporal Hicks that they seen the 'Giger designed Alien' was telling fibs as scott has blatantly confirmed that the original alien will not be in Prometheus at all.