However, why does your own DNA need to be used. We know clonejacks are a thing. Why can't non-identical DNA be used and just have the body sculpted to look like your old one? (which is what I thought was done anyway)
The cloning article states the way Cromeux Inc. handles their clone manufacturing. I wouldn't go so far and limit it to "only they do it that way" since it is a rather convincing argument why they need customer DNA, although it is, of course, possible that there are solutions so far in the future we can't think but only dream of.
Their clones come without an immune system as a necessity of the process. It is generated on the basis of the customers stem cells, a process which should* be necessary, since the new grown brain is a 1:1 copy of the old one, which means that they have the same surface cell epitopes fitting to the old immune system. The alternative seems ditching the idea of any sort of immune system, which would suck
and provide a nice idea for rp or the usual "we gots nanites!" approach which will, of course, fix the whole problem.
I'd prefer the 'pre-infection clone works" approach, since it gives plenty of creative opportunities to deal with the situation in any of the two (Cure, no cure) ways. Although the idea of a severe psychological addiction is interesting, since it is not too far fetched, that someone will get a relapse once he's in a new, clean body.
*I'm neither a physician nor a full blown biologist, so maybe there's someone around with a more profound understanding of the matter at hand ( immune system <-> cell surface epitopes <-> autoimmune reaction )