Whether or not the retrovirus XMRV is a human pathogen has been debated since the virus was first described in 2006. The answer is now clear: the results of Blood XMRV Scientific Research Group, along with a partial retraction of the 2009 Science paper describing identification of the retrovirus in patients with chronic fatigue syndrome (CFS) show that detection of XMRV in patient samples is a result of contamination.
The Blood XMRV group obtained new blood samples from 15 individuals previously shown to be positive for XMRV (Lombardi et al., 2009) or MLV (Lo et al., 2010) ; 14 of these were from CFS patients. Fifteen blood samples were also obtained from healthy donors. The samples were coded and sent to 9 laboratories for analysis. These laboratories (Abbott Molecular, Abbott Diagnostics, CDC, FDA/Lo, FDA/Hewlett, Gen-Probe, NCI/DRP, and WPI) conducted validated assays for viral nucleic acid, viral replication, or viral antibodies. Positive control samples were also included that were ‘spiked’ with XMRV, in the form of cell culture fluids from the cell line 22Rv1. Each laboratory was at liberty to choose which assays to carry out.
Two laboratories reported evidence of XMRV in the coded samples. Only WPI identified positive specimens by PCR: two from negative controls, and one from a CFS patient. The FDA/Lo laboratory did not detect any positives by PCR, using the same nested assay that they had previously reported in their published study. The samples tested included 5 specimens that were positive in the Lo et al. study.
Lombardi and colleagues have previously concluded that viral culture is the most sensitive method for detecting XMRV; however the FDA/Hewlett laboratory failed to culture virus from CFS samples. This laboratory did culture virus from positive control specimens, demonstrating the sensitivity of their methods. The FDA/Ruscetti laboratory recovered virus from 3/15 CFS samples but also from 6/15 negative control specimens. WPI did not carry out viral culture assays due to contamination of their cell lines with mycoplasma.
Four laboratories tested the samples for the presence of antibodies that react with XMRV proteins. Only WPI and NCI/Ruscetti detected reactive antibodies, both in CFS specimens and negative controls. There was no statistically significant difference in the rates of positivity between the positive and negative controls, nor in the identity of the positive samples between the two laboratories.
These results demonstrate that XMRV or antibodies to the virus are not present in clinical specimens. Detection of XMRV nucleic acid by WPI is likely a consequence of contamination. The positive serology reported by WPI and NCI/Ruscetti laboratories remained unexplained, but are most likely the result of the presence of cross-reactive epitopes. The authors of the study conclude that ‘routine blood screening for XMRV/P-MLV is not warranted at this time’.
One of the authors on Lombardi et al., Robert Silverman, decided to reexamine some of the DNA preparations from CFS patients that were originally used to detect XMRV DNA by PCR. He found that all the positive specimens from CFS patients were contaminated with XMRV plasmid DNA. Therefore the authors of the original study have retracted Figure 1 (single-round PCR detection of XMRV in CFS PBMC DNA); table S1, XMRV sequences, and figure S2, phylogenetic analysis of XMRV sequences.
A puzzling aspect of Silverman’s results is that XMRV plasmid DNA was detected only in samples from CFS patients, not healthy controls. This pattern would not be expected if the specimens were properly blinded, that is, coded so that the investigators did not know which were controls and which were from CFS patients. The authors offer no explanation of these findings.
The paper reporting contamination of samples with XMRV is entitled ‘Partial Retraction‘. It’s not clear to me why the entire paper has not been retracted. After removing the PCR and nucleic acid sequencing results, there is no evidence indicating the presence of XMRV in the patient samples. The remaining experiments show detection of a retrovirus by cell culture experiments, and the presence of viral proteins or antibodies to the virus in clinical specimens. None of these findings prove that what is being studied is XMRV. The title of the original paper ‘Detection of an infectious retrovirus’, XMRV, in blood cells of patients with chronic fatigue syndrome‘, is unsupported.
In an accompanying article on the XMRV story entitled ‘False Positive‘, Judy Mikovits of WPI notes that “Anyone who says this is a lab contaminant has drawn the wrong conclusion and has done a disservice to the public”. She goes on to imply that a gammaretrovirus is likely involved in CFS. On the contrary, pursuing the CFS-gammaretrovirus hypothesis is a disservice to those with CFS, and detracts from efforts to solve the disease. There are no data to support such an association, and to suggest that a lab contaminant, XMRV, has pointed the way to a bona fide etiologic agent seems implausible.
XMRV does not cause CFS. The virus arose in mice between 1993-96, and its detection in patient samples is clearly a result of contamination. Reaching these conclusions has required a long and often contentious journey that has highlighted the best and worst aspects of scientific research. There are many lessons to be learned from XMRV, but an important one is that science progresses not from the work of a single investigator, but from the collective efforts of many laboratories. XMRV reminds us to trust science, not scientists.
But it was sent to the WPI in 2007:
‘Silverman was happy to collaborate and sent WPI a clone of the virus, known as VP62.’
http://www.sciencemag.org/content/333/6050/1694.full
Now there have been numerous comments over the past months categorically stating that WPI never had VP62 in their labs, but it is stated here that they did.
And if they did…
That I linked to ERV is relevant as I am a patient not a scientist and ERV does a far more impressive job of explaining these latest results than can be found on most pseudo-scientist/CFS/ME Forums – IMHO.
And she was a guest of Prof Racaniello’s recently.
It’s really pretty ironic when you think about it.
Mikovits repeatedly aludes to the notion that publications are being blocked. However, when the most prestigious science magazine in the world gives her an opportunity to publish some data that could actually help her case, she is unwilling to share her data.
She apparently like to keep things unpublished.
That’s not about this data though. Mikovits presented this all in public on Friday. Really you are not making sense.
Silverman is agreeing he made a mistake. I don’t think you need to bash him when he has gone out of his way to say the VP62 issue was his. Wow he has shown souch integrity and you want to take that away from him.
– Hanson has reported that her PCR results are due to contamination
– Only two members of the BWG feel sorry for themselves
– Those patients were selected by WPI/Lo themselves
– Spiked controls showed the integrity of the PBMC samples was not comprimised
– The odds of accidentally selecting this many positives are inifintely small regardless of the extent of pedigreeing
– Yes, the tubes that were spiked with 22Rv1
– Controls all screened by all labs that claimed they knew how to find it.
– Lo’s assay did detect positives. For instance, check Figure 2Â of the Lo paper
– “Lo’s patients not determined to be negative”. What the heck do you mean? They were “known positives”, not only through Lo’s lab, but also tthrough Ruscetti’s lab (virus isolation AND immune response)
– Nowhere in the paper (of which Mikovits is co-author) it is suggested that WPI wanted to delay publication because of their contamination. Also, if the WPI had finished their culture and we had to wait for another half year, we would now have discussions about the vast conspiracy because of the delay in publication.
– The fact that you use VP62 as a control, does not mean that you have a “VP62 assay”. Fact is that Mikovits was talking about this more than a year ago and still she and Ruscetti were able to predict positives worse than my newly developed dart board XMRV assay(c).
That is about this data.
Presenting some pictures in public and submitting all relevant data relating to an experiment to ScienceMag are two different things. You do realize that?
Silvereman is not agreeing he made a mistake to the extent you are asserting. He specifically states that he believes the contamination did come from an outside lab. Seeing how he got his samples from WPI, it means that he thinks it’s not unlikely that the WPI lab contaminated his samples.
Finally, please don’t put words in my mouth. I have the greatest respect for Silverman who, unlike some other not-that-good scientists, was willing to take a critical look at his own data and was willing to admit that his data was wrong. So yes, I agree he is of the highest integrity.Â
Again, this does not mean that he admits that his lab was the source of the contamination, something that you apparently and erronously deducted from his statements.
How do you know how much VP62 was in the samples? Â
The WPI and NCI virus was wrongly called XMRV, they are HGRVs. Â Detection of a clone is hardly going to inform a lab whether their assay is capable of breaking CpG island bonds. Â Is this still over your head. Â Silverman has been extremely brave and admitted his error. Â Why are you attacking his integrity after he made such a gesture? Â
That has nothing to do with the data discussed here. Â
Mikovts gave a lecture. Â There was a whole host of scientists present in that audience. Â I think you will find it very difficult to suggest she stood their saying nothing. Â
Silverman is agreeing he made the error. Â He has not stated the VP62 contamination came from anywhere else. Â Again, will you stop trying to harm this person. Â Silverman does not deserve your outbursts.
The magazine journalist you are quoting from is incorrect. Â VP62 was never in the WPI of NCI lab. Â
The blogger called ERV is still not a specialist in HGRVs or GRVs. Â She is trained in lentiviruses, and is yet to graduate. Â I’m not going to take her word on an area she is not involved in any more than I would Bugs Bunny.
Again, what data? Â It is not the data presented on HGRVs not containing VP62. Â
Coffin and Pathak are not forthcoming regarding their RT-PCR assay used in Paprotka. Â Luckily people could have some chance to replicate as there is a video recording.
“Trust science, not scientists.”
Sounds like good advice. So in this case let’s trust the science that says CFS is a functional somatic syndrome, the science that says it’s a condition in which one can find a large percentage of personality disorders. The science that reports a strong association between CFS and childhood/sexual abuse. The science of the PACE trial and other studies that show that the only treatments considered safe, effective, and evidence-based, are Cognitive Behavioral Therapy and Graed Exercise Therapy. The science that shows that performing various tests, especially the ones that would show otherwise, is not helpful. The science that has disproved any and all associations with several pathogens.
The CDC’s Empiric Criteria. Or…the UK’s Oxford Criteria.
You are correct; we should trust in this science. Every time a pathogen tested for in CFS has been tested for, it has inevitably and invariably been debunked. I have to wonder why virologists are even bothering with this to begin with.
Actually it rests on several studies over the last 2 years that can’t find the virus or viruses. Moreover the number of samples is not that important in this study since it is done to test if the labs can find the virus with their own methods. Even 3 samples should be enough to do that. If a lab can’t detect a virus with their own methods in 15 samples, or find it in negative samples, that should be good enough evidence that they never had the means to detect this virus.
That’s not about HGRVs not being VP62.
What are you people reading? Vincent never asked for retraction. But pointed out that after the partial retraction the conclusions and the title of that paper becomes meaningless. And He once said in a previous TWIV that he believed papers should be retracted only in the case of something like fraud. What I don’t understand is that why are you people attacking Vincent and friends? Don’t you people understand that he is on your side? He’s been covering this story since the beginning and just because the science didn’t agree with your point of view doesn’t mean that he hates you now!
VP62 is not the virus found by the WPI or NCI. Â Silverman made a mistake and has been honest when discovering this mistake. Â As VP62 does not exist in the wild there is little point in suggesting that assays that have only provided proof of analytical sensitivity to that clone would detect an integrated virus that is not VP62. Â
The WPI and NCI, who were the only labs with diagnostically validated assays in the BWG, and they were not given the opportunity to use their assays. Â Trizol was not used on the PBMCs, which would degrade the virus. Â The NCI performed no PCR and the WPI were stopped from completing their culture panel. Â Controls and were not all screened by all labs and the 22Rv1 was in the same lab as the collection tubes. Â Patients were also all taking drugs that will result in a false negative. Â No lab with a diagnostically validated assay checked the Lo samples before blinding. Â
The study also only contained 9 CFS patients approved by the WPI/NCI.Â
Busch is not as happy as you are suggesting. Â He knowns he couldn’t have made more of a mess.
“How do you know how many VP62 was in the samples”
That is EXACTLY my point, we don’t. We only know that Silverman’s assays was sensitive enough, or else he wouldn’t have detected itI have the highest respect for Silverman. Her presented a exciting new results but remained critical towards his own finding. That is the sign of a good scientist.
Why are you lying about the extent of Silverman admitting his error? And why are you essentially repeating the same (erronous) argument as Pet101? Is that some kind of “coincidence” too?
Now, to make this perfectly clear: While Silverman admitted his samples were contaminated, he has also stated that he thinks the contamination was from an external source.Â
That is a scientific position that can be tested experimentally. Judy Mikovits’ “efforts” in resolving this have not been conclusive, unfortunately. When will she release all the necessay information? Why is she keeping this a secret to other scientists when millions of lives are at stake?
Anyone who disagree’s with Judy or has questioned the xmrv involvement in CFS will be considered an enemy…Â I love that a lawyer feels he is more intelligent than a man who wrote the book in virology…
In fact most patients post like they are all experts in viruses….
I never thought this condition was psychiatic based, but these posts are changing my mind….they are full of delusions of grandeur, paranoid thinking, and rationalization….
quote – A puzzling aspect of Silverman’s results is that XMRV plasmid DNA was detected only in samples from CFS patients, not healthy controls. This pattern would not be expected if the specimens were properly blinded, that is, coded so that the investigators did not know which were controls and which were from CFS patients. The authors offer no explanation of these findings – end quote
This also puzzles me…a little tampering going on???Â
You  and your pet are now resolving to trolling? That quote from Bruce Alberts and the Retraction Watch article have everyting to do with the VP62 plasmid contamination and the fact that WPI will not share their data regaring their own VP62 plasmid contamination experiments.Rather amusingly, the article reports that they are waiting for Mikovits’ reaction. She’s probably too busy.
Hanson has done no such thing. My god that’s a desperate remark to make.
The WPI could not have selected Lo’s patients, neither did the NCI.
Spiked samples with imaginary VP62 is not integrated wild virus. Preservatives are essential to the assays or virus degrades.
No the tubes used for patients and lab controls.
Check the Lo paper and BWG. Lo’s staff went with the assay that has never worked.
No one with a validated assay checked the Lo patients before blinding.
You conspiracy ideas really let you down. The WPI were not allowed to complete culture.
Who do you mean by You regarding VP62. Neitherthe WPI or NCI haveused it.
Agreed. Silverman is an outstanding scientist. He agreed to making an error. Unfortunately not the one you are lying about. Anyway, in case you still didn’t get the message: Silverman is a great scientist.
And wow, a lecture! Of course, now I understand. Why would anybody submit their data to Science when you can present it at a lecture? In a lecture you can choose to say what you want, whereas in a paper, you must provide all the data. Therefore lectures are so much more thrustworthy than papers. I’ve even heard they are doing away with the peer review system and  will start basing science on lectures by Wakefield and Mikovits.
Obviously Mikovits wasn’t up to the task of sharing all of her data to a whole greater host of scientists than were just present at the lecture and which only saw the data that Mikovits chose to show. In case you are wondering, this still makes Silverman a great scientist.
Mary there is no conspiracy. Â Only positive samples were sent to Silverman to fully sequence.Â
Silverman has set the record straight after discovering his error. Â They are HGRVs.Â
Silverman would also state he never sent the WPI or NCI VP62. Â Why are you prepared to lie?
Are you saying Mikovits destroyed the data that she refused to show to Science?Â
I don’t think that is true, to be honest.
RRM, trolling yes…, you have tried hard in the past to teach these socks the science involved..I think they understand you and the science….they just refuse to admit it…so instead, they change socks again!
If you don’t know how much VP62 was in Silvermans samples, then how can you possibly state “Â but outside of Silverman I know of noone that has shown they were able to detect VP62 plasmid at the necessary sensitivity for these trace contaminations.” Â LOL Â What sensitivity?
What is the significance of CpG islands?
Silverman has never made any comment but that he had contamination. Â You have provided no source for your lies.
All the data is in the public domain. Â Are you living in a fantasy ?
Mary if you have no training in the field how would you possible know what the data shows.
All the data pertaining to Lombardi is in public. Â Silverman has admitted his error and again you are challenging his honesty. Â
The editors is not referring to VP62 as he would have had no knowledge of that mistake until Silverman had presented his data. Â
Now you are defaming scientists for kicks. Â Outrageous behaviour. Â Then you are suggesting that people who present at conferences don’t wish to share data. Â What is the matter with you.
I will repost the new data for others. Â
http://1.bp.blogspot.com/-pCSELs4zkeM/TnzsYR_SI9I/AAAAAAAAAEI/JpeGZc6kkyQ/s1600/Slide08.jpg
http://3.bp.blogspot.com/-LE3KbJjEN2g/TnzsXvAzL0I/AAAAAAAAAEE/Otc07jeQbFs/s1600/Slide07.jpg
All the data pertaining to Lombardi is in public. Â Silverman has admitted his error and again you are challenging his honesty. Â
The editors is not referring to VP62 as he would have had no knowledge of that mistake until Silverman had presented his data. Â
Now you are defaming scientists for kicks. Â Outrageous behaviour. Â Then you are suggesting that people who present at conferences don’t wish to share data. Â What is the matter with you.
I will repost the new data for others. Â
http://1.bp.blogspot.com/-pCSELs4zkeM/TnzsYR_SI9I/AAAAAAAAAEI/JpeGZc6kkyQ/s1600/Slide08.jpg
http://3.bp.blogspot.com/-LE3KbJjEN2g/TnzsXvAzL0I/AAAAAAAAAEE/Otc07jeQbFs/s1600/Slide07.jpg
You are also questioning the ethics and integrity of Frank Ruscetti. Â All data is in the public domain. Â What is your problem.
You are also questioning the ethics and integrity of Frank Ruscetti. Â All data is in the public domain. Â What is your problem.
Nice to see I made you LOL too.
However, it is very possible to state what I have stated. I don’t know how much VP62 there was in Silverman’s samples (he didn’t use a quantative assay BTW), but there was enough of it for his assay to pick up.
Without showing that she could detect VP62 plasmid in Silverman’s samples (of course in a blinded setting), there is no way to evaluate if Mikovits’ assays are in fact sensitive enough to detect the contamination in her own samples (if it is there).
I fail to see how this can be so hard to understand.
People with ME are delighted at the death of the VP-62
clone and that VP-62 was not in any way related to the gammaretroviruses
detected by Dr Ruscetti and Dr mikovits
and others in the blood of people with ME.
 The VP-62 clone is
dead, but other XMRVs and PMLV’s are very much alive and replicating in the
human population. People with ME also feel vindicated regarding their
 comments that
relying on analytical sensitivity of PCR assays based around VP-62 was terrible
science. This was portrayed as harrasment by the scientists so criticised when
 in reality
patients were just targeting the inadeqacy of their science.
Â
People with ME are
delighted at the death of the VP-62Â clone and that VP-62 was not in any
way
related to the gammaretroviruses detected by Dr Ruscetti and Dr
mikovits  and others in the blood of people with ME.Â
The VP-62 clone is dead, but other XMRVs and PMLV’s are very much alive
and replicating in the human population. People with ME also feel
vindicated regarding their comments that relying on analytical
sensitivity of PCR assays based around VP-62 was terrible science. This was
portrayed as harrasment by the scientists so criticised when in
realityÂ
patients were just
targeting the inadeqacy of their science.
“Trizol was not used on the PBMCs, which would degrade the virus.”
If that was true (and actually anybody who knows anything about retrovirology would say it isn’t) why did the “spiked” controls come back positive? Some labs seemed to have done PCR from genomic DNA. Even if the cells were destroyed they should have detected the integrated provirus in the DNA if the cells are infected with the virus (and no drug can remove that provirus). Retroviruses can’t just hang out in the cells without integrating.
 “The NCI performed no PCR”
Not true, read the supplementary methods again.
I know, right?
People who have never worked in a lab or have never even done any PCR are questioning the methods in these papers. Amazing! And not only that but they also hold on to the strange conclusions of some people and keep repeating them in every discussion. I thought this type of stuff was only happening in topics like politics or sports (everybody believing they are the experts).
What are you questioning about HGRVs now? Â IF you don’t have the relevant experience why do you imagine your comments are correct. Â
We know for certain that there was no contamination in the samples when they left the WPI and NCI. Â The viruses found are those confirmed by Lo et al. Â
If you do not know the sensitivity you cannot possible state “but outside of Silverman I know of noone that has shown they were able to detect VP62 plasmid at the necessary sensitivity for these trace contaminations.”  The
WPI did not perform testing, an independent lab did. Â I fail to see why you are confused about this. Â
http://1.bp.blogspot.com/-pCSELs4zkeM/TnzsYR_SI9I/AAAAAAAAAEI/JpeGZc6kkyQ/s1600/Slide08.jpg
No Drosha they would not. Â As no Trizol was used in the BWG with PBMCs. Â You could quote the section of the paper if they did, but here they did not use Trizol. Â Without this preservative the virus would degrade. Â How did you ever conclude that degrade would translate as hang out. Â
The virus found in people with ME is not VP62. Â VP62 has never been isolated from a single source. Â Why would you imagine that assays diagnostically validated to a virus that is not VP62 would detect an imaginary clone they were not designed to detect. Â
The NCI/Ruscetti only performed serology and culture. Â What is confusing you about this? Â This is the labs who conducted the PCR testing. NCI/Ruscetti is not included.Â
Considering that I’ve been working in the retrovirus field in the last 5 years, I’d say I do have the relevant experience!
The negative results weren’t only negative for XMRV, some of them tested the “HGRV” theory as well. The fact that XMRV turned out to be false connection doesn’t mean that “HGRV” theory is correct, you can’t make that conclusion. One PNAS paper doesn’t prove anything, but the fact that others can’t confirm it says a lot.
Which retrovirus? Â Have you any experience with gammaretroviruses? Â
There is no testing described for HGRV’s in the paper except the WPI and NCI/Ruscetti labs. Â
Silverman has already spoken very plainly about this. Â He gave the viruses the wrong name. Â The Lombardi team found HGRVs, as did Lo and Alter. Â Â Are you agreeing that Lo found the same?
Why is the name of the independent lab being held a top level secret? If it is kept secret, other scientists cannot verify that this was indeed an independent experiment. Therfore, by definition, not all the relevant data concerning this experiment has been made publicly available.
 And I understood from a source that WPI did perform testing, and that after WPI’s test, another lab “confirmed” their findings. Oh well, another reason for not presenting your evidence to a peer reviewed journal, I guess…
that’s more like it. Yes, some people should not forget what science is really about. A clone does not validate an assay for finding integrated virus.
Who is the independent lab? That is “data” and relevant too, you know.
Do you understand that VP62 is irrelevant to finding of the WPI and NCI and why none of their work has been retracted. Â HGRVs are infected people with ME. Â Coffin will soon support this as he is aware of the data also. Â
Silverman gave the virus the wrong name. All of this is in the public domain and not hard to understand if you have had the relevant training.
How squished up can writing here get?
smaller
A lab has every right to remain anonymous, their data is in the public domain. Â Your ignorance of the peer review process is evident.Â
So now you have a secret source. Â Is it really worth the bother of stating that your comments will have to remain opinion.
This is shear ignorance of the peer review process.
That is why they should have opted for peer review. You see, if you opt for peer review, you can disclose your data to the peer reviewer. That way, these independent peers can scrutinize your data and check if it is really an independent lab. If they don’t trust this or Mikovits refuses to name the lab, they can advise to reject the paper or ask for an additional experiment at an independent lab by thier choise.
Of course, when you choose not to opt for peer review and reveal your study results at conferences, there is no way other scientists in the field can check whether the lab is truly independent or ask for additional experiments to verify the validity of the data.  So, what remains in  the public domain, is the fact that Mikovits refused to submit her data to Science.I don’t have a secret source. Where have I said that? I just stated that I have this information from a source. There’s nothing secret about this and I stand corrected regarding this. When you assert that there is in fact less data to support Mikovits’ assertions,  I trust you completely in the matter.