The paper says that possible "reasons for differences in the detection of XMRV in both prostate cancer and CFS" in the different studies "could include the following":
1. Contamination: "Contamination cannot, however, account for all positive findings of XMRV in humans, which are based on multiple lines of evidence from different laboratories . . . Furthermore, the nucleotide sequences of XMRV are similar but not identical to any known strain of MLV, which limits the likelihood of contamination from mouse sources."
2. Geographical Differences: "Geographical differences in the distribution of XMRV are likely to account for some, but not all, of the differences in findings."
3. Sequence Variation: "Sequence variations in XMRV, or XMRV-like viruses, could explain why some studies fail to detect XMRV. While XMRV strains that have been reported to date are more than 99% identical, the existence of divergent or related viruses is possible and these could easily be missed by many of the methods, in particular PCR, used to search for XMRV."
4. Clinical Criteria: "In CFS studies, clinical criteria for patient selection varied (Oxford, CDC or Canadian criteria) between the different studies, which might have contributed to the different findings of XMRV."
5. Absence of Standardized Detection Methods and Positive Control Samples: "The absence of standardized, highly sensitive methods of detection coupled with a lack of widely available, positive control human samples is likely to contribute to the different results obtained between studies."
[Nothing new, but nice to see it spelled out, just the same. Could add this "reason" to the CFS studies: 6. Determination to NOT find XMRV.]