The gut is always a good place to start, as it contains 70-80% of the immune system. Also malabsorption will make it difficult to fully utilize nutrients from foods or supplements.
Did any bad bacteria, parasites or yeast show up? You can take probiotics if the good gut flora is low. I'm thinking the malabsorption is probably due to the low good bacteria. Any leaky gut?
Do you know what thyroid tests were run? It's possible to have a normal TSH test while the thyroid antibodies are abnormal, indicating autoimmune thyroiditis. This happened to me.
If she has a history of toxin exposure, and now she's sick, that screams methylation cycle problems to me. This is how I became sick. She should definitely reduce toxin exposure by stopping smoking and avoiding dyes. I agree on toxins possibly causing the weight gain.
It would be good if you could tell us what kind of detoxification program she's on. If you go too fast, and don't take into account her methylation cycle and detox genes, it could make her worse. You can get gene testing through 23andme to see what those are.
I don't know if the anti-viral would be the thing to do or not. I agree on trying to detox first (and work on the gut), before trying an anti-viral. It's possible the other therapies would restore her immune system enough that she wouldn't need it.
Check out the links in my signature, starting with the Methylation Made Easy videos.