Hair loss...Help!

My cat (Rogue) is about two years old and she started having some off and on hair loss in the last few months. Here's her story:

When she was still a kitten, she had a really bad case of Giardia. The vet said she probably got it from drinking water out of the toilet. (Keep your lids down!!) She had really horrible diarrhea (I had to put a diaper on her while she was being treated because she couldn't control it at all.) and she lost weight. Well, she never really gained alot of weight afterwards, but she is the runt of the litter and she's always been a small framed cat. Now she's losing hair, but only in the middle of her back (basically in a straight line down her spine). Her skin isn't irritated, there's just not hair there. She has a healthy appetite; eating regularly, not over eating, walking away from her food when she's full. And she doesn't have fleas.
I got a puppy right around the time she started losing hair, but I noticed the hair loss BEFORE the puppy came around...so I don't think it's stress related. BUT it did get alot worse after they had to live together. (The puppy stayed at my boyfriends house for a few months because I lived in an apartment, but now we all live together)

Has anyone else had this problem or recognize it? Any help or advice would be greatly appreciated!!!

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