This is exactly what it said in the paper:
"Using the Whittemore Peterson Institute’s (WPI) national tissue repository, which contains samples from well-characterized cohorts of CFS, we isolated nucleic acids from PBMCs and assayed the samples for XMRV gag sequences by nested PCR (5, 6). Of the 101 CFS samples analyzed, 68 (67%) contained XMRV gag sequence. Detection of XMRV was confirmed in 7 of 11 WPI CFS samples at the Cleveland Clinic by PCR-amplifying and sequencing segments of XMRV env (352 nt) and gag (736 nt) in CFS PBMC DNA (Fig. 1A) (6). In contrast, XMRV gag sequences were detected in 8 of 218 (3.7%) PBMC DNA specimens from healthy individuals. Of the 11 healthy control DNA samples analyzed by PCR for both env and gag, only one sample was positive for gag and none for env (Fig. 1B)."
I am not an expert in virology, but to me that means 68/101 patients tested were positive by PCR WPI ran the set. It appears they also sent 11 samples to the cleveland clinic who then detected 7/11 positives by PCR as well. There appear to have been 218 controls tested for the WPI batch, 8 of which were PCR positive. 1/11 were positive in the 11 samples the cleveland clinic tested.
We have all inferred from non published data that Dr. Mikovitz went back and tested the same samples using culture, antibody, and PCR. After this expanded set of testing 98 of the original 101 patients showing CFS symptoms tested positive *in one way or another* using those methods. In fact I think that in the slide deck that was used for the pro-health video, it shows the breakdown.
I have not seen any data that says they went back and tested the controls using antibody or culture and if the number of positive controls increased or stayed the same. One could speculate that if the number of positives in the CFS symptom cohort went up when they used expanded testing, so would the number of positives in the control batch. But we don't know...
But what if some of the aditional 31 patients that brought the "post paper" positive count to 98/101 were *only* antibody positive? This situation is conceivable if the person cleared the infection and developed immunity. And as mentioned above, since we don't know if they went back and tested controls with antibodies and culture, we don't know A) if there are more true positives that weren't picked up by PCR (culture positive) or B) that there weren't a significant amount of antibody carriers that presumably don't have the virus anymore but are immune.
Also, its not clear to me what it would mean if you were culture positive and antibody positive, but not PCR positive. I guess I would presume that, at least at the time that sample was drawn, you had the virus but it was dormant and not replicating (at least not in the blood). Were people with that results sick? Or would the dormacy mean a remission?