It's a possibility I guess, but they'd need to get infected to find out. The cordyceps living in Ellie is a parasite - it may have mutated due to the habitat (i.e. her body/genes), a feature which could possibly transmit to her offspring, but her children probably wouldn't be born infected. They would be born clear of infection, and only by being bitten would they know whether they had the genetic potential to cultivate another mutated strand of the fungus.
...but it involves her partner becoming infected and dying. The devs mentioned at one point that despite her being immune, she still has the full on cordyceps running through her. And she can infect people.
So, assuming the worst: dead lover + Mutant human/fungus hybrids
Assuming the best: humanity is saved by Ellie kill-****ing everyone for immune babies? I don't know. I know the pervs of the board might at least want this.