The way my GM ran it when two of his PCs were turned, and the way I'm running...
Basically, all the bits of metal in your, and all the bioware too (since it isn't fully natural, it just cons your body into thinking so) is "liquified" and pushed out through any and all available holes. Very painful, very messy, and very, very nerve-racking to watch. If the meta succesfully lives through the transaction (Meaning he didn't roll a 1 or somesuch), they come out very feral, and slowly gain intelligence.
So, say Runner A and Runner B are fighting Wendigo A. Wendigo A manages to kill off Runner B after he inflicts some damage, but is regenerated. One less peon to worry about. Instead of doing the usual demeted thing, Wendigo A decides to eat now (Especially since he figures out Runner A is packing EX Ex). He chows down after a short melee scuffle and drains Runner A's Essence (What little there is, thanks to cyberware) to 0. He decided ahead of time to infect him, so Runner A now becomes HMHVV-In-Progress A and succesfully accepts the virus and doesn't decide to rip chunks of himself apart/blow his head off.
Now he runs off in incredible pain as his body regenerates all the 'ware out of him, finds a place to hide (Perferably dark, since sunlight is bad) and squeeze all that stuff out of himself. During this time, he is of the same mind as a beast. Up until, say, Essence hours (After you roll your wonderful 2D6 to see your new Essence), you are feral and running entirely on subconscious thought. You are now in "Fight or Flight" mode until that time elapses. Once it does, you are now fully sentient and won't just kill because you have no other option.
At least, that's my take on it.