Retrovirology Publishes Five Papers on XMRV and Contamination

[Cort]

Amy Dockser Marcus' Blog on the Findings

http://blogs.wsj.com/health/2010/12/20/xmrv-raising-the-issue-of-contamination/

Four papers published today in the journal Retrovirology—and a fifth one commenting on the papers—demonstrated how easy it is for mouse contamination to skew lab experiments involving the virus XMRV.

But they are unlikely to resolve the debate over whether XMRV is linked to diseases like chronic fatigue syndrome or prostate cancer, especially since the authors of the papers disagree on the interpretation of their data.

XMRV has been the topic of much debate since a paper was published last year in Science, linking the virus to chronic fatigue syndrome. The virus was also found in smaller numbers of healthy controls, raising the possibility that the blood supply might be infected. XMRV had previously been linked to prostate cancer. But some other groups have not been able to find XMRV in either CFS or prostate cancer patients or in healthy people.

Greg J. Towers from University College London, a senior author of one of the papers, told the Health Blog that his group’s findings indicate that ”XMRV is not a human pathogen.” Tests used to detect XMRV are also able to detect mouse DNA, and even if a tiny bit of mouse DNA gets in a lab sample, the test can be positive even if the patient is not, he explained. He added that he was not intending to criticize the work of other scientists. ”They published their observations in good faith and we have simply reexamined their findings and made new observations and come to a more likely conclusion.”

But John M. Coffin, a retrovirologist and a co-author of another of today’s Retrovirology papers, told Health Blog that while his group’s study demonstrated that mouse DNA is everywhere in labs, none of today’s published papers ”definitively show that any prior study is wrong.”

Robert A. Smith, a research assistant professor at University of Washington in Seattle who wrote a commentary in Retrovirology summarizing the studies, told Health Blog that the possibility of contamination means that future studies must be done very carefully before conclusions about disease association are made. But he said he is unwilling to state that the reported link between XMRV and CFS or prostate cancer is no longer viable.

The papers focus on various problems associated with a specific kind of test used to detect XMRV but does not examine every method used to detect XMRV. Smith pointed out that some of the previous papers on prostate cancer found XMRV integrated into the patients’ DNA and ”I can’t come up with a mechanism where there would be contamination there.”

Judy Mikovits, who led the team of researchers that published the link between CFS and XMRV in Science last year, said her team was able to culture XMRV from the patients’ blood and show antibody responses indicating they had been exposed to XMRV at some point. ”You will not make an immune response to a lab contaminant,” she told Health Blog.

Dr. Coffin said the debate over XMRV will continue. ”This is not the end of XMRV,” Coffin said, ”but it is a warning we have to be very, very careful.”

Image: iStockphoto

 

[Jemal]

So, how come the British scientists are always making the boldest statements? Somehow it's mostly the British scientists stating contamination is a fact or concluding that the link between ME/CFS and XMRV does not exist. It's like they desparately want to bury XMRV.

 

[Cort]

The papers focus on various problems associated with a specific kind of test used to detect XMRV but does not examine every method used to detect XMRV. Smith pointed out that some of the previous papers on prostate cancer found XMRV integrated into the patients’ DNA and ”I can’t come up with a mechanism where there would be contamination there.”

Very interesting! That indicates an infection....

One of the big questions is where did XMRV come from? Did it come from that 22RV1 cell line and if it did - did it still make its way into humans and THEN become a pathogen? Does that make sense?

What a mystery this all is......Its a head turner all the way around.

But John M. Coffin, a retrovirologist and a co-author of another of today’s Retrovirology papers, told Health Blog that while his group’s study demonstrated that mouse DNA is everywhere in labs, none of today’s published papers ”definitively show that any prior study is wrong.”

There you go - the papers are warnings.....big warnings - but nothing definitive yet....I imagine they will be doing the IAP tests and looking for XMRV integration into human DNA in CFS (???).

 

[kurt]

Ouch....they make the antibody test off of the agent they found. I thought they used a standard antibody test for MLV's though in the original paper??

They used rat and goat antibodies that are cross-reactive with all MLV species (both polytropic and xenotropic). They probably calibrated the antibody study with the strain these new studies say is a mouse contaminant. Then they used that same test on patient samples that were also somehow contaminated. The point is that if contamination explains the PCR results it might also explain antibody results, because the antibody and PCR studies were both calibrated to the same contaminated strain found in the samples. Contamination would throw off more than the PCR results alone.

 

[Cort]

So, how come the British scientists are always making the boldest statements? Somehow it's mostly the British scientists stating contamination is a fact or concluding that the link between ME/CFS and XMRV does not exist. It's like they desparately want to bury XMRV.

On all levels and the US and elsewhere, I think it's true that in Science you generally trust the researchers that are the most cautious and the UK researchers seem more likely to draw conclusions than the US researchers...(Dr. Mikovits is, obviously something of an exception to that rule )

Coffin is always a big key for me; he's very smart and, to me, he's always been balanced and he is here again; he was a co-author of two of the papers and yet here he is very aptly pointing out that while these papers demonstrated that the danger of contamination is higher than previously thought, all these papers except for the Hue paper, were examples of what happened in individual situations....

We don't know if any of those situations occurred at the WPI. The WPI, for instance, ran negative controls and so did Alter/Lo and nothing showed up....

A really basic thing that's missing is handling the controls and patient samples in exactly the same way. That is what happened in Phase II of the BWG study and will continue happening in the next big phase.

 

[Jemal]

Ah well, I can finally go to bed now and sleep peacefully. Thanks to Amy Dockser Marcus

 

[Cort]

You can find the four overviews on the Home Page together plus Amy's blog

http://forums.aboutmecfs.org/content.php?299-Retrovirology-Five-Papers-on-XMRV-and-Contamination

 

[eric_s]

Very interesting! That indicates an infection....

One of the big questions is where did XMRV come from? Did it come from that 22RV1 cell line and if it did - did it still make its way into humans and THEN become a pathogen? Does that make sense?

What a mystery this all is......Its a head turner all the way around.



There you go - the papers are warnings.....big warnings - but nothing definitive yet....I imagine they will be doing the IAP tests and looking for XMRV integration into human DNA in CFS (???).

Well, if the integration into human DNA is proof that the "XMRV is only contamination in any case, no human virus" theory by Hue et al. is wrong, it's sufficient if they could demonstrate integration in prostate cancer to kill the theory. Or am i wrong?
So how could anyone even come to such a conclusion like Hue et al., let alone a journal publish that, if integration has been demonstrated?

 

[LJS]

You can find the four overviews on the Home Page together plus Amy's blog

http://forums.aboutmecfs.org/content.php?299-Retrovirology-Five-Papers-on-XMRV-and-Contamination

The post was publised and open for comments a few minutes ago, now it says "This page will be published on December 21st, 2010 02:05 AM "

 

[CBS]

You can find the four overviews on the Home Page together plus Amy's blog

http://forums.aboutmecfs.org/content.php?299-Retrovirology-Five-Papers-on-XMRV-and-Contamination

Cort,

I suspect that the meaning of these articles will be evolving for sometime but I wanted to say thanks for your work today. A lot patients needed a way to keep this development in perspective and your work (above and beyond simply creating this space) capped off by ADM's article in the WSJ has helped a lot of people get a better night's sleep tonight.

As for Coffin, I have no problem with a cautious thorough approach so long as those working on this issue recognize the real urgency and severity for some patients (those issues will impact each patient's risk/benefit analysis when it comes to comes to potential treatments).

 

[Cort]

The post was publised and open for comments a few minutes ago, now it says "This page will be published on December 21st, 2010 02:05 AM "

I had too many windows on my computer and messed up - it should be up now....Now I have to put Amy's blog back in.....

 

[Bob]

The Hue paper's main argument seems to rest on the Taqman primers not being specific to XMRV...
But, to me, it seems there is a problem using this as your argument...

If the Taqman primers are not specific to the "gag-leader deletion" in XMRV then they could well show up positive for XMRV when testing mice, even if there is no XMRV in mice. I might have missed it in the paper, but the researchers do not appear to have looked for the whole XMRV virus genome in mice, but I think they only looked for the segments with the "gag-leader deletion".

If the Taqman primers are not specific to the "gag-leader deletion" in XMRV then the paper says that they could also detect mouse contaminants when testing human samples. But if mouse contamination is tested for in human studies, then that only leaves XMRV, and not any mouse contamination.

 

[Bob]

Ah well, I can finally go to bed now and sleep peacefully. Thanks to Amy Dockser Marcus

Yes, thank you Amy Dockser Marcus...

What a different picture she paints to some of the other ridiculous "XMRV is dead" articles that have been linked to in this thread.

 

[Bob]

I wonder why the release of these articles was coordinated...
Were they coordinated to cause maximum damage, and to ruin our Christmases, or were they delayed to avoid causing more confusion for the Blood Working Group meeting last week?

Now that these negative studies have been published, will Judy be able to publish her stack of positive studies, for balance?

Judy's study, describing an immune signature in XMRV positive patients, was supposed to be published in December... Has anyone heard any news of that at all?

 

[Cort]

I wonder why the release of these articles was coordinated...
Were they coordinated to cause maximum damage, and to ruin our Christmases, or were they delayed to avoid causing more confusion for the Blood Working Group meeting last week?

Now that these negative studies have been published, will Judy be able to publish her stack of positive studies, for balance?

Judy's study, describing an immune signature in XMRV positive patients, was supposed to be published in December... Has anyone heard any news of that at all?

I have a graduate degree in environmental studies - I used to plough through journals all the time and they do themes all the time. Any time there's a hot topic they'll do a theme on it if they can......... I have no idea about the timing though.....not a particularly appealing one, that's for sure...

A journal will be published next year, I've heard that will feature only XMRV. Perhaps there will be better news there.

 

[Bob]

A journal will be published next year, I've heard that will feature only XMRV. Perhaps there will be better news there.

Do you mean a Retrovirology journal featuring XMRV is to be published next year?
And have you heard if any of Judy's unpublished studies will be published any time soon?

 

[Jim]

Crazy idea - can the WPI hire Coffin as a consultant on any further test verifications? Ego's and $ probably make that unrealistic.

 

[Cort]

Do you mean a Retrovirology journal featuring XMRV is to be published next year?
And have you heard if any of Judy's unpublished studies will be published any time soon?

I just heard that a journal will be publishing the Workshop results and any studies since then. I don't remember which one.

 

[Cort]

There are dozens of reports on the web now. Here's from Science Blog - they have decided...as have some researchers....

Its amazing how fast the UK media has jumped on this - they ignored the Alter study and they are going to town on this one......I don't see much from the US, though....quite a few Science blogs....but other than the WSJ - no major papers yet.

This is what got me about the Hue paper...XMRV's similarity to these other mice retroviruses.

“When we compare viral genomes, we see signs of their history, of how far they have travelled in space or time,” says Dr Stphane Hu, Post Doctoral Researcher at UCL. “We would expect the samples from patients from around the world, collected at different times, to be more diverse than the samples from within a cell line in a lab, where they are grown under standard conditions. During infection and transmission in people, our immune system would push XMRV into new genetic variants.

“Viral infection is a battle between the virus and the host and XMRV does not have the scars of a virus that transmits between people.”

New research shows virus previously linked to chronic fatigue syndrome is a lab contaminant

DECEMBER 20, 2010

A virus previously thought to be associated with chronic fatigue syndrome is not the cause of the disease, a detailed study has shown. The research shows that cell samples used in previous research were contaminated with the virus identified as XMRV and that XMRV is present in the mouse genome.

XMRV was first linked to chronic fatigue syndrome — also known as myalgic encephalomyelitis (ME) — in a study published in October 2009, where blood samples from chronic fatigue syndrome patients were found to have traces of the virus. XMRV had also been identified previously in samples from certain prostate cancer patients.

The new study, published in Retrovirology, identifies the source of XMRV in chronic fatigue syndrome samples as being cells or mouse DNA rather than infection by XMRV. The research does not rule out a virus cause of chronic fatigue syndrome – it is simply not this virus.

The research team developed improved methods to detect XMRV against the genetic noise of other sequences and make recommendations for future study of virus causes of human disease.

“Our conclusion is quite simple: XMRV is not the cause of chronic fatigue syndrome,” says Professor Greg Towers, a Wellcome Trust Senior Research Fellow at University College London (UCL). “All our evidence shows that the sequences from the virus genome in cell culture have contaminated human chronic fatigue syndrome and prostate cancer samples.

“It is vital to understand that we are not saying chronic fatigue syndrome does not have a virus cause — we cannot answer that yet — but we know it is not this virus causing it.”

The team, from University College London, Wellcome Trust Sanger Institute and University of Oxford, showed clearly that the experimental design of previous studies would pick up sequences that resembled XMRV; however, in this improved study, they could prove that the signal was from contamination by a laboratory cell line or mouse DNA. The sequences from the contaminated cell line and chronic fatigue patient samples were extremely similar, contrary to the pattern of evolution expected during the infectious spread of a virus in a human population.

They also showed that the existing methods would indicate that one in fifty human cell lines they examined were infected with XMRV-related viruses: they showed that contamination of human tumour cells with XMRV-related viruses is common and that a principal prostate cancer line used is contaminated.

“When we compare viral genomes, we see signs of their history, of how far they have travelled in space or time,” says Dr Stphane Hu, Post Doctoral Researcher at UCL. “We would expect the samples from patients from around the world, collected at different times, to be more diverse than the samples from within a cell line in a lab, where they are grown under standard conditions. During infection and transmission in people, our immune system would push XMRV into new genetic variants.

“Viral infection is a battle between the virus and the host and XMRV does not have the scars of a virus that transmits between people.”

Together the results demonstrate that XMRV does not cause chronic fatigue syndrome or prostate cancer in these cases. The team’s methods suggest ways to ensure that virus contamination does not confound the search for a cause of disease in future work.

The authors propose that more rigorous methods are used to prevent contamination of cell and DNA samples. They also suggest that consistent and considered standards are needed for identifying viruses and other organisms as cause of a disease.

“Increasingly, we are using DNA-based methods to accelerate our understanding of the role of pathogens in disease,” explains Professor Paul Kellam, Virus Genomics group leader from the Wellcome Trust Sanger Institute. “These will drive our understanding of infection, but we must ensure that we close the circle from identification to association and then causation.

The strongest lesson is that we must fully use robust guidelines and discriminatory methods to ascribe a cause to a disease.”

 

[Bob]

This is what got me about the Hue paper...XMRV's similarity to these other mice retroviruses.

“When we compare viral genomes, we see signs of their history, of how far they have travelled in space or time,” says Dr Stphane Hu, Post Doctoral Researcher at UCL. “We would expect the samples from patients from around the world, collected at different times, to be more diverse than the samples from within a cell line in a lab, where they are grown under standard conditions. During infection and transmission in people, our immune system would push XMRV into new genetic variants.

“Viral infection is a battle between the virus and the host and XMRV does not have the scars of a virus that transmits between people.”

I wonder how the different XMRV strains fit into this theory...
Judy has found a number of XMRV strains now, so I don't know how solidly their theory stands up, if the different strains were taken into account. To my knowledge the different XMRV strains haven't had any info published about them yet.