I'd like to say I knew the answer about antivirals and gut flora for certain but I really don't. What I do know is my gut settled down once I introduced a probiotic and I don't think there are many people have taken as much valacyclovir as I have. The suspicion I have is prolonged use of antivirals carries the risk that eventually the gut flora can become collateral damage in a long war.
I have tried very basic probiotics and they didn't help and I have taken yoghurt for years and that didn't make a difference. The probiotic I have found very effective is a capsule which contains-
Hopefully I have read the tiny print correctly but forgive any spelling mistakes. Of course, I have no idea which one of the strains fixed up my tender tummy but hopefully the combination is the right thing to have. The only way I discovered this (rather expensive) brew was to ask the chemist if she had a better product behind the counter than the usual ones available in the store.
Good luck with the Avonex. It can be rather a shock initially. I found it worked best when used in conjunction with Valtrex. (see my old posts under Avonex and Valtrex in the regime section). If you don't want Valtrex then the note I put under the Resevesterol post may be of interest.