Trust science, not scientists

27 September 2011

XMRVWhether 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.

  • Pet101

    Yes as Ruscetti and WPI never screened lo samples in the working group.

  • Pet101

    That assay never detected the positives. Not much of a reader are you.

  • Anonymous

    The VP62 plasmid was never in the WPI or NCI.  The findings of HGRVs is not related to Silverman giving the viruses the wrong name.

    The section you are quoting is Silvermans work which was contaminated with the plasmid in his lab, it is not about the Lombardi findings. That was the single round PCR.

  • RRM

    However, if Mikovits’ tests don’t fucntion, she wouldn’t have found the spiked clone.

    Although it is indeed a clone not found in nature, succesfully detecting it shows that you’ve maintained the integrity of the sample. 

    Now, even if all of the free virus was destroyed during the test, then still the virus integrated into the sample (which has shown to keep its integrity), should have been amplified.

    Oh, and Mikovist has confirmed that she had VP62 in her lab.

  • kipper7

    Not PCR, Gobmeister, serology. Silverman didn’t perform serological assays so the the XMRV-VP62-infected cell-lines — hey, let me repeat that! — the  XMRV-VP62-infected cell-lines were in the WPI / Ruscetti labs.

  • kipper7

    Not PCR, Gobmeister, serology. Silverman didn’t perform serological assays so the the XMRV-VP62-infected cell-lines — hey, let me repeat that! — the  XMRV-VP62-infected cell-lines were in the WPI / Ruscetti labs.

  • RRM

    I didn’t. You only proved that you’re not even able to read blog comments. ;-)

    Oh, and source or it didn’t happen.

    Oh, and VP62 was in the WPI lab according to Mikovits.

  • RRM

    I didn’t. You only proved that you’re not even able to read blog comments. ;-)

    Oh, and source or it didn’t happen.

    Oh, and VP62 was in the WPI lab according to Mikovits.

  • kipper7

    What is your experience with PCR, Darkow?

  • RRM

    He did check the Lo samples BE-for-E the BWG study, though.

  • RRM

    But Cohen did what you requested: he stated his sources. 

    Now it’s really up to Mikovits (or Silverman) to correct this if it is indeed untrue, as you seem to incorrectly think.

    I am not questioning their integrity. They were honest enough to tell Cohen what happened. It’s a pity you  aren’t honest enough to admit this.

  • Anonymous

    The VP62 plasmid has never been in her lab, she will never have said that. They used VP35 as per Urismans design.

  • Anonymous

    The VP62 plasmid was not in the WPI or NCI labs.  How much clearer does it get.

  • Anonymous

    The WPI and Ruscetti did not

  • Anonymous

    Then Laurie you should know that the science shows human gammaretroviruses were found in Lombardi and Lo.  Silverman only named the virus incorrectly due to VP62 plasmid contamination, which has never been in the WPI and NCI labs.  

  • Anonymous
  • Anonymous

    Not fisher price like yourself. 

  • Anonymous

    Cohen is wrong.  The VP62 plasmid was not in the WPI or NCI.

  • RRM

    No, it is not a fact. In fact, it is a fact that VP62 was sent to WPI by Silverman.

    Mikovits admits this
    Silverman admits this

    Why can’t you?

  • Anonymous

    Incorrect RRM.  The VP62 plasmid was never in the labs (WPI and NCI).  

    Mikovtis will not have said this.

    What is your problem.  I will take the word of scientists. Cohen is not a scientist.

  • RRM

    It certainly was in WPI’s lab. 

    At least, if you believe, as I do, that Mikovits isn’t lying.

  • scooter

    Figure 1 from Silverman’s lab led to the negative studies that focused on single round PCR.  WPI has consistently said culturing and serology are better methods.  Alter and Lo, and WPI with further sequencing found more MLV related retroviruses some variations of which are found in currently healthy people.  Most of the BWG participants have not claimed to have a test which worked on anything except a clone spiked sample. Labs in Belgium and Spain which used the WPI temperatures etc have found the viruses.  The virochip pointed to XMRV in ME patients out of all known viruses.  Some patients have been helped by ARVs.  Science is learning more about retroviruses, ME immune responses, contamination of materials and vaccines with retroviruses from this research.  Many of the HMLV (x-related or p) positive patients also are positive for lyme.   Science would allow research to continue.  WPI should have the money to sequence what they’ve found.  And WPI is in the best position to do small treatment trials which will lead to more answers.  Some scientists say don’t look there.  

  • RRM

    They used VP35 for the study. That doesn’t mean VP62 wasn’t in their lab. It was.

    Even Mikovits confirms this.

  • Anonymous

    The VP62 plasmid was not in the WPI or NCI labs. This is a fact.

    RRM as you now have admitted that they used VP35 in Lombardi. Why is it that the negative papers have not used that and why look for VP62 strain, which does not exist in nature.

  • RRM

    Cohen is a reporter and reporters actually have quite an incentive to properly show their sources.

    That is why Cohen’s admission is very reliable and your personal “vouch” for it not being true is  not. Please support your assertions with a proper source, i.e. a Mikovits quote. Or admit that you are wrong about this.

  • Anonymous

    I’m afraid you are still incorrect.  The VP62 plasmid has never been in the WPI or NCI labs.

  • RRM

    I bet you don’t even know how many full length sequences Silverman submitted.

    Many of those WPI partial sequences are 100% identical to the contaminant VP62. Such bad luck for Mikovits….

  • Anonymous

    How many HTLV full length sequences are in the GenBank since that was discovered by Frank Ruscetti?  Once you have the answer, you won’t make such remarks.

  • Anonymous

    The VP62 plasmid was certainly not in the WPI or NCI labs.  It’s not going to happen post experiments because you keep saying it was.  Not even if you say it really hard.  

  • Guest

    @Darkow
    Wrong Again,

    Problem #1 is Silverman sent the WPI VP62 plasmids in 2007 (before they ‘found’ XMRV in patient samples.
    Silvermans lab found VP62 plasmid in their samples. Which means the positives Silvermans lab reported in 2009 were all because of plasmid contamination. The positive results were NOT the result of real infection.
    He unquestionably found VP62 plasmid in the samples he got from the WPI… and only in the CFS patient samples.

  • RRM

    Small correction: Silverman sent VP62 to WPI in March of 2008.

  • RRM

    Yes, it has, and this has now been confirmed by several sources.

  • RRM

    It is a fact that you are delusional, as several sources, Including Judy “we had VP62 in our lab” Mikovits, have now confirmed this fact.

    “I have now admitted this”. Yes, of course, I’ve never stated otherwise. It’s in the paper. It’s no problem to use VP62 though, as it is ~100% identical to VP35 in the targeted region of Lombardi et al.’s primers (and which is just as unlikely to exist in nature  as VP62 BTW).

  • RRM

    It’s clear that you don’t have a source for this delusion, while Mikovits herself has admitted that VP62 was in her lab.

  • Pet101

    the VP62 plasmid wasn’t there in those labs. You only hoped it had been.

  • Pet101

    That’s not true. The vp62 plasmid hasn’t been in the WPI or NCI. Silverman was found with it in his samples and evidence proves it wasn’t in WPI or NCI when it left to go to Silverman. They discovered human gamma retroviruses. Lo and Alter found those too.

  • Pet101

    You are always wrong

  • Pet101

    Lo and Lombardi yes

  • Pet101

    Made up quote. No source

  • Pet101

    So wrong it’s untrue. The VP62 plasmid was never in the WPI or NCI. Its a falsehood to say anything else.

  • Pet101

    Please then RRM, who is no scientist, quote where it says NCI/Ruscetti and WPI touch the Lo samples in the BWG. You know you can’t because they didn’t.

  • RRM

    Here you go. “Dart board” testing of the Lo samples by WPI and Ruscetti in the BWG group, after they had found all of them to be positive in 2010.

  • RRM

    No, I’m just with Judy on this, who has confirmed that VP62 was indeed sent to her.

  • Anonymous

    The VP62 plasmid has never been in the WPI or NCI/Ruscetti labs.  You cannot change that.

  • Anonymous

    There is no source and no one has confirmed  as the VP62 plasmid has never been in the WPI or NCI labs.  VP62 contamination was only found in the Silverman samples.  The WPI, NCI, NIH and FDA all detected human gammaretroviruses.    

    What is the diversity of the px region of HTLV?
    What is the diversity of all isolates of HTLV?

  • Anonymous

    That is the results, not the pre-screening, which the NCI and WPI did not do.  

  • Anonymous

    You have no source for the VP62 plasmid.  It was never in the WPI or NCI labs.

  • Anonymous

    Incorrect information you have there.  The VP62 plasmid was never in the WPI or NCI labs.  Silverman is the only lab that had this plasmid.  Your story by the way, doesn’t match the other story that is being bandied about.  Have a look at the dates.  

    Silverman never sent the WPI or NCI the VP62 plasmid.

  • Anonymous

    No Trizol was used by the organisers of the blood working group with the PBMCs.  This will have degraded the virus present in those samples and defeated the WPIs assay.  

  • window

    Two quick examples, and then a partial defence of ‘science':

    re personality disorders:

    This is the biggest study to make claims of a link between CFS and personality disorders: http://content.karger.com/ProdukteDB/produkte.asp?Doi=319312

    It was promoted with a press release titled ‘Is Chronic Fatigue Syndrome a personality disorder?’, and got a lot of coverage.

    http://www.rehacare.com/cipp/md_rehacare/custom/pub/content,oid,27211/lang,2/ticket,g_u_e_s_t/mcat_id,7772/local_lang,2/~/Is_Chronic_Fatigue_Syndrome_A_Personality_Disorder.html

    If you read the paper, you can see that the answer is ‘no’.

    Those with CFS are more likely to fulfil the criteria for a personality disorder than the healthy population, but not more likely that the control group with health problems.  The paper acknowledged that previous studies comparing CFS and MS had also found the same levels of personality and psychiatric disorders.

    When personality disorders are diagnosed according to the individuals ability to fit in with society, it’s inevitable that those with chronic health problems will be more likely to fulfil the criteria, and when you look at the PDQ4 questionnaire used, this point is particularly clear.

    re PACE and CBT/GET – That the researchers started their study claiming that an SF36-PF score of 85 indicated recovery and a score of 65 indicated severe and disabling fatigue, yet by their press conference were claiming that patients with an SF36 PF score of just 60 should be considered back to normal, reveals rather more about the efficacy of the treatment they were promoting, and their honesty, than they might realise.

    We should not just trust scientific consensus, nor the abstracts of papers, and certainly not the claims researchers make in the press releases – particularly with CFS, but science does give us the tools and information needed to pick apart false claims.  With CFS, we’ve seen a lot of bad science, where the prejudices of researchers have been imposed upon data that does not support their conclusions, and not nearly enough interest from sceptics keen to pick apart the misleading claims made about patients, but the scientific process has still provided us with some meaningful data, and allowed us to see how misleading the claims made by some ‘experts’ are.

    So long as there is so little interest in criticising poorly done papers which increase to the stigma and burden faced by patients, there’s going to be an ongoing culture of distrust between patients and the medical community.  I had some hope that this might be starting to change, partially thanks to the XMRV story, but I’m not sure that it ever will.  Trusting ‘experts’ and authorities helps simplify life, and I’m not sure how interested many are in engaging with the complexities and uncertainty of a condition like CFS, and pushing to hold those who have treated patients poorly to account.