It seems even if Noomi Rapace does return in some capacity, Alien: Covenant is to have a new female lead. According to Deadline, Katherine Waterston (Inherent Vice, Fantastic Beasts and where to Find Them) has been cast in Ridley Scott's Prometheus sequel as a character named Daniels. No other information is provided, but it is mentioned that she'll be playing the lead.
Plot details are also under wraps for now, but it's believed the plot will focus "the crew of the colony ship Covenant, bound for a remote planet, who discover what they believe is an uncharted paradise but is, in fact, a dark, dangerous world, the only inhabitant of which is David (Michael Fassbender), the “synthetic” and survivor of the doomed Prometheus expedition."
Expect casting announcements for some of the other crew members soon, as Scott is apparently gearing up for an early 2016 shoot in Australia.