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Are there long term effects on muscles and bones of autoimmune hep.?

I was diagnosed with auto hep. about 2 and a half years ago. It's well under control now. It took about 6 months or so to get my bloods right again. A biopsy showed only slight inflammation about 4 months after i presented with incredible joint pain all over. I am now on only 5mg of prednisolone and 75 of azathioprine.

My question is has anyone noticed long term effects of the condition? About 18 months ago i developed a sudden, debilitating pain in my shoulder out of nowhere. I was exercising a lot at the time. Something similar happened last May - headaches, generalised pain - and now again since the start of January when i had been training hard running for over 3 months - headaches, neck pain, back pain, stomach ache.I've been checked out and all seems fine. Could this all be related to a suppressed immune system? Can training hard stress the body, in anyone else's experience?
Are there lifestyle changes I need to make to cope with the disease and to be able to train for long distance running? thanks.
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