Plaquenil is hydrochloroquinine. I am assuming that the Methotrexate was suggested because of your previous reaction to the Prednisone. If corticosteroids cannot be used for treatment, the natural next step would be immunosuppressants such as Methotrexate. It is normal for the treatment to use both quinines and corticosteroids or immunosuppressants. It is also not unusual for doctors to prescribe both hydrocholoquinine and quinacrine with Methotrexate.
Methotrexate was first used as a cancer treatment. Please know that the dosage used for Lupus is substantially lower than the dosage used for cancer. However, one of the most frequent side-effects are still the nausea (which, also, is not as severe as the nausea in cancer treatment). This nausea can last for 24-48 hours, but most people say that this is worth it because their general overall symptoms are greatly reduced.
I agree with your interpretation of your doctor's notes, but please do discuss this at your next appointment. Keep us advised and I wish you the best.
Peace and Blessings
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