"The epigenetic implications ... are just mind blowing" This is the conversation Cosima is having at the Bubble's dinner.
The key is not in the genome (Ms. S's mother) that is just a red herring.
The real key is ... AMELIA!!!
What does this mean? Well, it could mean that the reason Sarah and Helena are different and are fertile is that something happened in the womb during Amelia's pregnancy that switched off the coded DNA sequence and switched back on their fertility and supercharged their ability to heal that was passed on to Kira.
We have been given at least three hints: 1. Dr. Leekie was doing experiments on manufacturing amniotic fluid 2. The Castor boys sperm could render women infertile (outside influence could turn off fertility) so why can't the opposite be true? 3. Cosima comes right out and says it "The epigentic implications ... are just mind blowing"
However, hold on to your hats--- the reverse is also true: fetomaternal chimerism
Of course this is just a television show but the basic science does exist and shows like this are just exaggerating the science 1000%
But in this vain I am going to predict that Amelie is still alive. I think she survived the stabbing because she has cells from both Sarah and Helena giving her the ability to heal rapidly.