The Last of Us finale explains how Ellie is immune to the Cordyceps infection

gamesradar.com:

Warning, we’re getting into serious spoiler territory for The Last of Us finale in this article. If you haven’t seen episode 9 yet, bookmark this page for later.

One of the major threads through this season of The Last of Us has been Ellie’s immunity to the Cordyceps infection. Now, the finale may have just explained why exactly the infection does not harm her.

In the final episode’s brutal cold open, we see Ellie’s mom Anna (played by none other than Ashley Johnson) running to a safe house. She finally makes it inside, but the infected runner isn’t far behind, and she’s bitten just before she gives birth to Ellie. Realizing she has seconds, she quickly cuts the umbilical cord – despite her later protestations to Marlene that she was bitten after she did this.

Ellie was attached to her for about a minute before she cut the cord, but given how fast the infection acts, it seems likely she would have still got some in her bloodstream. While not explicitly explained, it’s very possible this very unique circumstance could have given her some immunity to Cordyceps. 

During the final stages of pregnancy, antibodies are transferred from mother to baby via the umbilical cord. If Anna’s body was fighting the Cordyceps infection as soon as she was bitten, some of these may have been transferred to Ellie in the brief moments they remained connected.

This is seemingly later confirmed by Marlene when she tells Joel that Ellie is being prepped for surgery. "Our doctor, he thinks that the Cordyceps within Ellie has grown with her since birth," she tells him. "It produces a kind of chemical messenger so that normal Cordyceps think that she’s Cordyceps, which is why she’s immune. He’s going to remove it from her, multiply the cells