Friday, January 6, 2012

VP62 in the Lombardi 2009 study

In all positive cases, the XMRV gag and env sequences were more than 99% similar to those previously reported for prostate tumor–associated strains of XMRV (VP62, VP35, and VP42) (fig. S1)
Sequences of full-length XMRV genomes from two CFS patients and a partial genome from a third patient were generated (table S1). CFS XMRV strains 1106 and 1178 each differed by 6 nt from the reference prostate cancer strain XMRV VP62 (EF185282), and with the exception of 1 nt, the variant nucleotides mapped to different locations within the XMRV genome, suggesting independent infections. In comparison, prostate cancer– derived XMRV strains VP35 and VP42 differed from VP62 by 13 and 10 nt, respectively. Thus, the complete XMRV genomes in these CFS patients were >99% identical in sequence to those detected in patients with prostate cancer. To exclude the possibility that we were detecting a murine leukemia virus (MLV) laboratory contaminant, we determined the phylogenetic relationship among endogenous (non-ecotropic) MLV sequences, XMRV sequences, and sequences from CFS patients 1104, 1106, and 1178 (fig. S2). XMRV sequences from the CFS patients clustered with the XMRV sequences from prostate cancer cases and formed a branch distinct from non-ecotropic MLVs common in inbred mouse strains.
On this base, over 100 scientists in over 30 studies went on a wild goose chase, in order to burn up millions of USD – money that could have been well spent doing proper biomedical research into ME/CFS. But the worst will be the conspiracy crackpots who will cling on to this study as if would bring them salvation.

What's great in the Lombardi 2009 paper, after this paragraph, with differences being as low as 6 to 13 nt (!), how they can come to the following conclusion is beyond me:
Thus, the virus detected in the CFS patients’ blood samples is unlikely to be a contaminant.
And oh, this makes it look even more like the prostate cancer samples were contaminated while in storage.

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