I've never really read any of the comics or got into the walking dead until the game came out but I just remembered from "Playing Dead".
They said first episode takes place in the comic where Rick is in a coma, so it basically links with the comic.
So linking with the game's and the comic's story, weather we left her or took her in the RV, she left off and eventually joined "The Governer", and some of you may know, if you read the comic, that she and the others ran out of ammo when the Prison was overrun with walkers and her whereabouts are unknown now, but maybe she'll reappear in season 2, in a later episode.
Considering Robert Kirkman's words, we don't really know what happened.
"I'm not going to say the Woodbury survivors were all killed when their bullets ran out, but it's very unlikely that we'll ever see them again. The prison is dead to me. I've moved on and so have the characters."
We didn't know how Hershel's son died in the comic, but from the game we know now, and maybe we'll know what happened to Lilly's fate from the comic within the game.
Playing Dead Episode 1