I've finally got to play Prototype and i have to say it is an excellent game. Unlike many games of the same style it's gameplay doesnt get repetive fast like in Assassins Creed. And story ain't that bad. In fact i think it's story got a lot of inspiration from Biomega manga by Tsutomu Nihei and some Alex abilities might in fact be inspired by Abara manga also by Tsutomu Nihei.
In Biomega's story a governement corporation goes rogue and releases a dangerous funguae onto Earth where it starts to grow in living organism and turns them into various kinds of zombies and there is basically one guy, an artificial human to try to stop the end of the evil plans. To do this, the other industrial corporation which made him gives him an order to find Ion Greene a little girl (sounds familiar? in Prototype one of your main enemies is a girl named Elizabeth Greene) who seems to be immune to the fungus but turns out to be the second creature created by the evil corporation but who has only ability to neutralise the growing fungus. (in Prototype Elizabeth itself the evil virus turning people into monsters [but in Biomega there is another girl, Ions sister with an odd name Reload who is the origin of the fungus, but she only appears in flashbacks from 500 years past]). In middle of Biomega all humans but few are turned into the monsters and soon after Earth is destroyed and humanity becomes almost extinct. Quite similar in Prototype but the outbreak is only in Manhattan.
As i said some Alex powers are inspired from Abara like (possibly) bone armor, razor fingers and sword hand. In Abara main character can grow anything out of his own bone like armor and swords and spine whip.