I have an auto-immune disease myself and now.. GHSV1. I have been battling for months and finally got the diagnosis. I am hopeful the antiviral will help, and am including vitamins and an anti anxiety in the mean time.
Though I don’t have advice towards protecting your partner; I can say I think it’s wonderful you two are communicating about it.
Immunosuppressives make you far more open to viruses, (hence my own story of possibly acquiring it - only my previous partner assured me he got tested for everything when he had not in fact anytime recently - and we even had the safe sex talk prior) it is a tricky situation; but the great thing is you two have open communication going into this.
I hope someone with more experience can assist in answering this. Have you considered talking to their specialist? Perhaps they could shed some light.