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XMRV articles in Retrovirology

Thursday 23 December 2010

RetrovirologyThe journal Retrovirology has published five papers on problematic XMRV research results:

 

ImageViewpoints    Image
Contamination of clinical specimens with MLV-encoding nucleic acids: implications for XMRV and other candidate human retroviruses
Robert A Smith
Retrovirology 2010, 7:112 (20 December 2010)
[Abstract] [Provisional PDF]

Efforts to assess the prevalence of xenotropic murine leukemia virus-related virus (XMRV) in patients with prostate cancer and chronic fatigue syndrome have relied heavily on PCR-based testing of clinical samples and have yielded widely divergent findings. This week in Retrovirology, reports from four independent research groups illustrate the extreme care needed to exclude DNA or RNA contamination in PCR analyses of XMRV. In addition, phylogenetic evidence suggesting that previously-published XMRV sequences originated from a commonly-used prostate carcinoma cell line (22Rv1) is presented. These findings raise important questions regarding the provenance of XMRV and its potential connection to human disease.

 

ImageResearch    Image
Disease-associated XMRV sequences are consistent with laboratory contamination
Stephane Hue, Eleanor R Gray, Astrid Gall, Aris Katzourakis, Choon Ping Tan, Charlotte J Houldcroft, Stuart McLaren, Deenan Pillay, Andrew Futreal, Jeremy A Garson, Oliver G Pybus, Paul Kellam, Greg J Towers
Retrovirology 2010, 7:111 (20 December 2010)
[Abstract] [Provisional PDF] [1 comment]

We demonstrate that Taqman PCR primers previously described as XMRV-specific can amplify common murine endogenous viral sequences from mouse suggesting that mouse DNA can contaminate patient samples and confound specific XMRV detection. To consider the provenance of XMRV we sequenced XMRV from the cell line 22Rv1, which is infected with an MLV-X that is indistinguishable from patient derived XMRV. Bayesian phylogenies clearly show that XMRV sequences reportedly derived from unlinked patients form a monophyletic clade with interspersed 22Rv1 clones (posterior probability >0.99). The cell line-derived sequences are ancestral to the patient-derived sequences (posterior probability >0.99). Furthermore, pol sequences apparently amplified from PC patient material (VP29 and VP184) are recombinants of XMRV and Moloney MLV (MoMLV) a virus with an envelope that lacks tropism for human cells. Considering the diversity of XMRV we show that the mean pairwise genetic distance among env and pol 22Rv1-derived sequences exceeds that of patient-associated sequences (Wilcoxon rank sum test: p=0.005 and p<0.001 for pol and env, respectively). Thus XMRV sequences acquire diversity in a cell line but not in patient samples. These observations are difficult to reconcile with the hypothesis that published XMRV sequences are related by a process of infectious transmission.

 

ImageShort report    Image
An endogenous murine leukemia viral genome contaminant in a commercial RT-PCR Kit is amplified using standard primers for XMRV
Eiji Sato, Rika A Furuta, Takayuki Miyazawa
Retrovirology 2010, 7:110 (20 December 2010)
[Abstract] [Provisional PDF]

We found that the enzyme mixtures of the one-step RT-PCR kit from Invitrogen were contaminated with RNA derived from PmERV. The nucleotide sequence of a partial gag region of the contaminant amplified by RT-PCR was nearly identical (99.4 % identity) to a PmERV on chromosome 7 and highly similar (97.4 to 97.8 %) to recently identified MLV-like viruses derived from CFS patients. We also determined the nucleotide sequence of a partial env region of the contaminant and found that it was almost identical (99.6 %) to the PmERV.

 

ImageResearch    Image
Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences 
Brendan Oakes, Albert K Tai, Oya Cingoz, Madeleine H Henefield, Susan Levine, John M Coffin, Brigitte T Huber
Retrovirology 2010, 7:109 (20 December 2010)
[Abstract] [Provisional PDF]

DNA from the peripheral blood of 112 CFS patients and 36 healthy controls was tested for XMRV with two different PCR assays. A TaqMan qPCR assay specific for XMRV pol sequences was able to detect viral DNA from 2 XMRV-infected cells (~ 10-12 pg DNA) in up to 5 mug of human genomic DNA, but yielded negative results in the test of 600 ng genomic DNA from 100,000 peripheral blood cells of all samples tested.

 

ImageResearch    Image
Mouse DNA contamination in human tissue tested for XMRV
Mark J Robinson, Otto W Erlwein, Steve Kaye, Jonathan Weber, Oya Cingoz, Anup Patel, Marjorie M Walker, Wun-Jae Kim, Mongkol Uiprasertkul, John M Coffin, Myra O McClure
Retrovirology 2010, 7:108 (20 December 2010)
[Abstract] [Provisional PDF]

These results show that contamination with mouse DNA is widespread and detectable by the highly sensitive IAP assay, but not always with less sensitive assays, such as murine mtDNA PCR. This study highlights the ubiquitous presence of mouse DNA in laboratory specimens and offers a means of rigorous validation for future studies of murine retroviruses in human disease.

 

All of the above articles appeared on the home page of the Retrovirology website.

 


 

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