Is it possible to send real-time notifications to a Android/iOS device (from server) running an HTML5 App? How is it different from native apps? What extra efforts do I need to make for that?
You don't specify your server-side technology stack.
If however you are using Phonegap for the HTML5 App and node.js for the server, you have the option to use:
Both are explained at this post:
http://devgirl.org/2013/07/17/tutorial-implement-push-notifications-in-your-phonegap-application/