I think that is it, I think I slept awkward then jarred it or trapped a nerve when I was startled awake.Maybe you just slept awkwardly? I do that all the time and sometimes it can be pretty painful. One time I went to sleep resting on my arm, and when I woke up, I couldn't turn my wrist without my whole arm "burning up" (that's what it felt like), and it took a couple of days before it got any better. Of course if it's muscle pain it could easily just be the flu.
One things for sure it's certainly not the muscular ache that comes with flu, it's far too painful for that.