I never got the impression she was infected, other than the trilobite she "gave birth to".
Also if she got infected, it would have shown up in Prometheus or atleast in "the crossing" prolouge.. Just one drop of the black pathogen made holloway start mutating within one day, so if shaw was infected with say just a quarter or less of this it would surely have started mutating her in the time they took before leaving LV-223 and her going into hypersleep..
My theory is that David infected her in various ways on "paradise" and then started experimenting with her.