i did not expect the sequences to demonstrate such a high level of variation
My reason for expecting this level of variation includes what I've called my "entropy heuristic". I won't claim this is defensible, only productive as an assumption. It started out from thinking about how researchers could miss long-standing infections, and how diseases with such serious effects could avoid producing a definitive, consistent biochemical signature.
This is not something I have predicted in detail. I'm not trying to do that because I know cognitive impairment gives me an unacceptable chance of errors in details. I've been looking for robust hypotheses which might still be falsifiable. This isn't easy.
What I noticed right away from this new data is that we are very close to overlapping HERV or MLV sequences. Trying to exclude both of these from giving false positives in an assay is very likely to result in 0/0 outcomes. Excluding IAP sequences may compound the problem if active retroviral infections produce similar sequences. The problem may extend to antibodies to proteins resulting from transcription of excluded sequences.
My guess has been that the apparent lack of variation reported in the original Lombardi/Mikovits paper was an artifact not of contamination, but of selection due to the culture test used to validate early PCR testing. Culturing in a cell line characteristic of cancer favored a particular rapidly-replicating strain typical of aggressive prostate cancers. The discovery that PBMCs which were not naturally activated by infection needed to be activated in the laboratory, then allowed to grow in a 'culturing' step prior to PCR, strengthened this conviction. Extensive hypermutation, and the realization that production of enzymes causing this was turned off during mitosis of PBMCs, also fit.
The major discovery of a gamma retrovirus in humans with ME/CFS, defined as an organic disease, was correct. The statement published at that time about a surprising lack of variation was wrong. Failure to publish the need for a 'culturing' step was an honest oversight. At the time of original publication, they hadn't realized everything necessary to make their assay work reliably in practice. There are always such oversights of important details in new research. With publication of subsequent papers blocked, all criticism focused on those understandable missteps in the original publication.
Instead of a vast conspiracy I see a great deal of knee-jerk reaction and predictable administrative response compounding uncertainty and confusion which typically characterizes new discoveries. I can't rule out a half-vast conspiracy.