chinense Using ghost peppers with spots

I have 2 earth boxes full of thriving ghost peppers that I grew from last years seeds. About 1/2 of the peppers have spots that eventually rot. I think it's caused by tobacco mosaic virus. Obviously I can't share or sell these peppers but is there any reason I can't use the damaged peppers in cooked recipes? I have at least 15 pounds of peppers in this crop alone and would hate to waste them.

I had that problem with a ghost pepper plant last year. I used mine before they started to get moldy if they weren't too bad. Freeze some while they are still good for later use.