As far as management of anaemia with Telaprevir Riba dose reduction is usually the first line of intervention. Procrit and/or transfusions are not uncommon either. I am not sure why your doctor did not dose reduce since studies show it would not have impaired your chance for SVR.
Rather than recreate your first treatment scenario and the clinical guidelines here is a chart that might give you an idea. It is from the Incivek web site:
http://www.medhelp.org/user_photos/show/320460?personal_page_id=1282072
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***The presence of ANA could be indicative of many conditions***
http://labtestsonline.org/understanding/analytes/ana/tab/test
I'm not sure where the possibility of autoimmune hepatitis came from to the exclusion of other autoimmune conditions - plus, you do state, "The pathology report for the second biopsy did not detect any autoimmune features. "Chronic Hep C with moderate activity ..."
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Switching PIs mid-treatment:
There is little clinical evidence for switching a patient with chronic hepatitis C infection to the other protease inhibitor midway through completion of the original PR-protease inhibitor therapy. In fact I only found one study. This one shows a person switched from Telaprevir to Boceprevir after eight days of being on Telaprevir:
I could only see this much of the article:
"After 8 days of T/P/R, the patient developed a rash over his legs and abdomen (Figure 1). His viral load decreased to 66 International Units/mL"
http://cid.oxfordjournals.org/content/early/2012/12/05/cid.cis960.abstract
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Retreatment with another PI after a failed attempt with one PI:
You treated with Tepaprevir for 10 weeks. Does your Hepatologist think Cross-resistance would not be an issue? I have always understood you could not treat with the other PI if one does not work.
This thread has several links that explains why retreating with the other protease inhibitor (Vic.), is not recommended because the drugs are very similar, so if you develop resistance to one, you will probably have resistance to the other. It has links to outside web sites:
http://www.medhelp.org/posts/Hepatitis-C/victrelis-after-failed-incivek-/show/1785878
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If at all possible I would get a third opinion. Meanwhile I hope others can explain viral resistance with PIs.