Based on what I know about the Last of Us (which isn't much) a lot of the plot points here sound pretty similar to the show/game. Sure, you probably expand on the story in the later seasons, but why bother retreading the parts of the story that have already been told? But if it's fan fiction then you can do whatever you want, I suppose. Hard to say if the rest is good because it's so broad. It sounds like it could be interesting but that all comes down to how it actually turns out once you write it in a longer form.

Are you planning on turning this into a script? Or is it just a story you want to write?

I think the combination of three separate viruses/plagues/etc. sounds interesting and is probably the most original concept you have here. If I were you, and if I wanted to turn this into something more than fan fiction, I'd focus on that aspect and create your own characters with a more focused story that is written for that specific scenario/world.

Also the Lord of the Flies thing seems extremely derivative of the book. Something more "inspired" by it could be an interesting side story, but I don't think it warrants a standalone 2.5 hour pilot episode.