This is amazing!. Well done! =)
EXCELLENT work, to say the least.
A bit ambiguous about them being in a relationship BEFORE this happened- it might have been more effective if the retrovirus just made them act on previously-restrained desires rather than make previously-expressed feelings more 'explicit'-, but I can't fault the subsequent exploration of their feelings after the mutation.
After all, what is NOT to find cool about the scale of the bond they develop here; not only do we have John and Elizabeth establishing a psychic link as they're mutating, but Elizabeth's feelings actually 'survive' even when her mutation's practically completed itself and turned her all the way into a QUEEN!
Hope you're planning on writing more stories; if this is an indication of what you're capable of, I have a feeling any other plots you come up with are going to be VERY enjoyable...
Nice story. Very well written and in-character. Good work.