The Passage by Justin Cronin

From the publisher (source: The Internet Book List):
First, the unthinkable: a security breach at a secret U.S. government facility unleashes the mostrous product of a chilling military experiment. Then, the unspeakable: a night of chaos and carnage gives way to sunrise on a nation, and ultimately a world, forever altered. All that remains for the stunned survivors is the long fight ahead and a future ruled by fear-of darkenss of death, of a fate far worse.

As civilization swiftly crumbles into a primal landscape of predators and prey, two people flee in search of sanctuary, FBI agent Brad Wolgast is a good man haunted by what he's done in the line of duty. Six-year-old Amy Harper Bellafonte is a refugee from the doomed scientific project that has triggered the apocalypse. Wolgast is determined to protect her from the horror set loose by her captors, but for Amy, excaping the bloody fallout is only the beginning of a much longer odyssey-spanning miles and decades-toward the time and place where she must finish what should have never begun.

With "The Passage," award-winning author Justin Cronin has written an epic chronicle of human endurance in the face of unprecedented castrophe and unimaginable danger. Its inventive storytelling, masterly prose, and depth of human insight mark it as a crucial and transcental work of modern fiction.

This book is part of the "The Passage" series.
Here are some other books from this series: