Journal of General Virology: Review: The Tale of XMRV

[Firestormm]

22 February 2012:

The tale of xenotropic murine leukemia virus-related virus

Abstract: http://vir.sgmjournals.org/content/early/2012/02/20/vir.0.041038-0.abstract

Full paper for free: http://vir.sgmjournals.org/content/early/2012/02/20/vir.0.041038-0.full.pdf?forumid=331851

Abstract:

'In 2006, a new retrovirus was isolated from prostate cancer patient tissue. Named xenotropic murine leukemia virus-related virus (XMRV), this was potentially the third class of retrovirus to be pathogenic in humans.

XMRV made a more dramatic impact on the wider scientific community, and indeed the media, in 2009 when it was reported to be present in a remarkably high proportion of patients with chronic fatigue syndrome as well as a significant, albeit smaller, proportion of healthy controls.

The apparent strong link to disease and the fear of a previously unknown retrovirus circulating in the general population lead to a surge in XMRV research. Subsequent studies failed to find an association of XMRV with disease and, in most cases, failed to find the virus in human samples.

In 2011, the case against XMRV and human disease strengthened, ending with several decisive publications revealing the origin of the virus and demonstrating contamination of samples.

In this review, we outline the passage of research on XMRV and its potential association with disease from its isolation to the present day, where we find ourselves at the end of a turbulent story.'

 

[Esther12]

A few general pieces on XMRV have used this latest controversy as another excuse to kick around CFS patients so I read this with a wary eye, but it wasn't like that at all, and actually seemed down-right sympathetic. Phew.

I'd have been interested to read more about the response of proponents of an association between XMRV and PC, as the latter part of the article focused almost entirely on CFS and XMRV.

 

[FancyMyBlood]

I agree with Esther here, authors seems sympathic as evidenced by their statement that patients were the big losers. It's interesting one of the authors co-authored this paper (http://www.ncbi.nlm.nih.gov/pubmed/21756995) which I believe was a very interesting read also.

 

[Firestormm]

I thought this was a fascinating read and much easier to follow the reasoning from beginning to the present. I think they would have included this more recent paper too had they been able (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030889) but it wouldn't have altered it in anyway.

It lends context and continuity to the whole story doesn't it? When viewed as a piece like this. All right it doesn't dwell on the 'What if's?' but it does lay out how scientific thought has changed (as it progressed and more experiments were completed) from the initial 'excitement' even among scientists to the PC and CFS papers, to where we they are now (pending any future findings).

Thanks for that link FancyMyBlood. I hadn't seen that study before. Groom also seems to have written/contributed to a number of the XMRV-associated papers throughout this thread's paper of which I didn't have instant recall.

 

[Firestormm]

These extracts were worth reposting I thought as there has been confusion about the xenotropic sequences pertaining to XMRV and the polytropic ones pertaining to the findings of Lo et al.

It is often used I think as an argument that what Lombardi et al. really found were polytropic viral sequences when obviously that was not what Lombardi et al. were reporting, and hence not what was subsequently confirmed. I hadn't been as aware of the Tuke et al. importance before now (in respect of Lo et al.'s findings). Hence one reason I kind of like seeing these review articles really as they provide the bigger picture:

'...This reached a peak with news that a second study had detected the presence of MLV-like sequences in 86% of CFS patient PBMCs compared with only 7% of healthy volunteers (Lo et al., 2010). However, the env sequences were more similar to those of modified polytropic MLVs than those of xenotropic viruses, a result that confounded rather than supported previous observations by Lombardi et al. (2009). Additionally, evidence of replicating virus was lacking.

This was accompanied by a report from Switzer et al. (2010), who failed to find XMRV in CFS patients, or other cohorts, using a range of tests. Proponents of an association suggested that the variation in the sequences detected explained why previous studies had failed to detect the virus. But why had Lo et al. (2010) found only polytropic and Lombardi et al. (2009) only xenotropic viruses? It seemed more likely that these could be artefacts.

Both the Urisman et al. (2006) and Lombardi et al. (2009) studies reported very little interisolate sequence variation, which was surprising given the hypothesis that the virus was circulating in a relatively high proportion of the human population. The sequences also bore a very high percentage of sequence identity to common endogenous xenotropic sequences in mice; hence, if XMRV was a zoonotic transmission from mice to humans, very few rounds of replication must have occurred to give such limited sequence diversity.

This would suggest a recent transmission, potentially individual transmission events, which seemed unlikely...'

'...Those believing in an association argued that extremely sensitive detection methods were needed to find the virus, but these detection methods would also increase the likelihood of false positives by detecting contamination. At the end of 2010, things began to unravel further...'

'...The argument for false positives was strengthened by a series of additional studies pointing to contamination of cell lines and commercially available reagents (Erlwein et al., 2011; Sfanos et al., 2011; Tuke et al., 2011; Wolff & Gerritzen, 2011; Yang et al., 2011).

These were supported by phylogenetic analysis of contaminants and patient isolates, refuting the idea that sequence variation seen in longitudinal samples from patients in the Lo et al. (2010) study was the result of virus evolution (Tuke et al., 2011).

Tuke and colleagues isolated contaminating MLV sequences from commercial RT-PCR kits that closely resembled the sequences reported by Lo et al. (2010). They also showed that the claims of Lo et al. (2010) that later isolates from patients had evolved from earlier isolates was incorrect by performing a maximum-likelihood analysis of sequences. A further study showed that two of 14 of the previously sequenced integration sites from PC patients were identical to those reported from deliberately infected cells that were used in the same laboratory (Garson et al., 2011).

This removed the best piece of evidence that XMRV had infected humans. Together, the support for contamination and mounting negative data meant that the case for XMRV in human disease was shaky...'

 

[natasa778]

False negative results from using common PCR reagents

http://www.biomedcentral.com/1756-0500/4/457

The sensitivity of the PCR reaction makes it ideal for use when identifying potentially novel viral infections in human disease. Unfortunately, this same sensitivity also leaves this popular technique open to potential contamination with previously amplified PCR products, or "carry-over" contamination. PCR product carry-over contamination can be prevented with uracil-DNA-glycosylase (UNG), and it is for this reason that it is commonly included in many commercial PCR master-mixes. While testing the sensitivity of PCR assays to detect murine DNA contamination in human tissue samples, we inadvertently discovered that the use of this common PCR reagent may lead to the production of false-negative PCR results.

....
None of the 38 MLV-related publications we examined used internal PCR controls. Given the data presented in this manuscript, we would propose that in cases such as the debate regarding the existence of novel infectious viruses, failure to find a virus is not the equivalent of evidence against its existence. The potential for false negative results needs to be considered and carefully controlled in PCR experiments, just as the potential for false positive results already is.