Thought to share with everyone here. Here's a detailed interview with Neil Druckmann about LGBT stuffs in The Last of Us, and more importantly, how Ellie is designed as homosexual. I'll copy the most important question here, but you should read the full interview as it may helps you understand the game better.
Q. Is Ellie gay?
Druckmann: “Now when I was writing it I was writing it I was writing it with the idea that Ellie is gay, and when the actresses were working they were definitely working with the idea that they’re both attracted to each other. That was the subtext and intention that they were playing with from the opening cinematic when they’re holding each other’s hands for too long, or when Riley bites her on the neck; there’s that chemistry there from the get go that was important for us so that we earned that moment when they kissed each other. So that it wasn’t just out of the blue but also wasn’t so overt that you’re like “Oh of course. Just get on with it.”