Trust science, not scientists

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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.

344 thoughts on “Trust science, not scientists”

  1. Anonymous

    AGain, you are questioning the integrity of 3 highly respected scientists.  Robert Silverman, Frank Rusectti and Judy Mikovits.  VP62 was never in the WPI or Ruscetti labs.  What is you issue with this fact?  

    The journalist (not scientists) is incorrect.

  2. RRM

    “Not a validated assay shown to work on a pedigreed positive. 
    Absence of evidence of the VP62 plasmid by some secret lab is not evidence of absence.”

  3. RRM

    Until you come with evidence, I and I hope every other rational person, will take the word of the Science investigative journalist over your “vouch”.

    If asserting what I did is “questioning the integrity” of these persons, why haven’t at least some of them corrected this apparenty damaging mistake publicly?

  4. Pet101

    The evidence already shows VP62 was not in any samples at the WPI or NCI. Hanson said no such thing at the conference, so those twitters have terrible memories. They probably don’t know who Hanson is and I doubt they can follow the details.

    The work you keep referring to is not from the BWG and has not been published. You’re like a broken record with your uninformed personal pleading.

    The positive patients in the BWG were not screened by Ruscetti or WPI.

    Lo in the BWG used primer combinations and cycling times that were used in Lo et al and found no evidence of a MuLV of any kind in samples which tested positive with their other assay using diff nested primers and cycling conditions. It is a fact!

  5. Anonymous

    It is obvious that the gammaretroviruses discovered by Ruscetti and Mikovits in the blood of people with ME are not related to VP-62. Some of them however may turn out to display a xenotropic pattern of host infections and hence we may have several XMRVs on our hands as well as PMRV’s

  6. Anonymous

    It is obvious that the gammaretroviruses discovered by ruscetti and mikovits in the blood of people with ME are not related to VP-62. Some of them however may turn out to display a xenotropic pattern of host infections and hence we may have several XMRVs on our hands as well as PMRV’s.  Xentropic are now recognised as having the largest host range.

  8. RRM

    They are related. Do you have a comparison of the WPI sequences with the Lo sequences? They are not as closely related as the WPI/VP62 sequences are. 

    Attachment (c) erv. 😉

  9. Anonymous

    Again, Mr RRM you have no right to question Frank Ruscetti or Judy Mikovits integrity.  Outrageous. Who do you think you are? VP62 has been proved to not be infecting their samples and has no relationship to the HGRVs findings. VP62 has never been in their labs.

  10. RRM

    You have just shown through this wall o’text that you understand very little about validating assays and very basic scientific methodology. Using VP62 as a control does not mean that you have calibrated your assay against VP62.

    So no, I don’t agree. You should really take this up with the editors of Science though, because:

    – convincing me won’t help your cause
    – the Science editors could use a good laugh

  13. Anonymous

    Silverman if asked does not say that.  They are not Silverman and I am going to say they cannot speak for Silverman.  

  16. Anonymous

    Using VP62 as a control means you have not optimised your assay to detect any virus in nature, as VP62 is not found in nature.  It was constructed from 3 sources not one.

  17. RRM

    Lo’s team using the assay from Lo et al. that failed to detect the POSITIVES.””The positive patients in the BWG were not screened”Backtracking much? ;-)Also, from the Lo paper, regarding the PATIENTS. I repeat, not the controls, but the PATIENTS:using EITHER the previously reported PCR primer sets (first
    round: 419F/1154R; second round: GAG-I-F/GAG-I-R) (3, 4) or
    our in-house–designed PCR primer set (first round: 419F/1154R;
    second round: NP116/NP117) (Fig. 1), we detected a high frequency
    of MLV-related virus gag gene sequences IN PATIENTSYou see that EITHER and IN PATIENTS? And the primer set 419F/1154R (first round) GAG-I-F/GAG-I-R (second round)

    – You don’t actually believe what Judy Mikovits was saying there? Are you suggesting that Mikovist was lying in that talk? And if you don’t rely on unpublished evidence, then I take it you dismiss the presented VP62 plasmid dindings by Mikovits as well? But no, you have actually already used that unpublished “evidence”  (that she refuses to share with Science) in the first paragraph. Do you happen to have any consistency in your arguments? 

    – The nice thing about Twitter is that you  can do it LIVE. You don’t need a good memory for tweeting. 

  18. Anonymous

    Here you go again RRM.  It is obvious that the gammaretroviruses discovered by Ruscetti and Mikovits in the blood of people with ME are not related to VP-62. Some of them however may turn out to display a xenotropic pattern of host infections and hence we may have several XMRVs on our hands as well as PMRV’s.

  20. RRM

    Wierd formatting. Here’s a picture quote from Lo et al. that shows they detected positives in patients, using the primer set as in the BWG (as well as another)

  21. RRM

    Those quotes are  just literal quotes from Gerwyn (also known as jhk). I am sure you agree with his logic.

    I only inserted the bit about the VP62 plasmid.

  22. RRM

    Why don’t you ask him and post his response? 

    In the meanwhile, I will go with the official response from the Clinic officials as correctly reflecting the opinion of the scientist(s) who did the investigation into the contaminant.

  23. Pet101

    Lo in the BWG used primer combinations and cycling times that were used in Lo et al and found no evidence of a MuLV of any kind in samples which tested positive with their other assay using diff nested primers and cycling conditions. It is a fact!
    You are missing the point as usual.

  24. Jack

    I see Cohen has reconfirmed what he said in his article:

    ‘WPI did use VP62, in contrast to claims posted here.’

    Oh and also: ‘XMRV is, without a doubt, dead. The viral sequence reported in Lombardi et al. is the result of a contaminant. If other gammaretroviruses prove to have links to CFS/ME, they will not be the virus described first by Silverman as XMRV. It’s no more complicated
    than that, a point that John Coffin made clearly in his Ottawa debate
    with Judy Mikovits. I think confusing XMRV with other possible viruses
    clouds the waters for everyone.’
    http://news.sciencemag.org/scienceinsider/2011/09/insider-looking-out-how-people.html#sci-comments

  25. Pet101

    Lo in the BWG used primer combinations and cycling times that were used in Lo et al and found no evidence of a MuLV of any kind in samples which tested positive with their other assay using diff nested primers and cycling conditions. It is a fact!
    You are missing the point as usual.

    What talk are you now inventing ?

    Hanson has said no such thing. There cannot get there memories straight when listening.

    VP62 is not involved in the Lombarding findings of HGRVs.

  26. Anonymous

    What quotes?  

    VP62 was never used by the WPI or NCI.  

    “Neither 22Rv1 nor any of the cell lines reported to be contaminated with XMRV or cell lines growing the VP62 infectious molecularly cloned virus was in the laboratories where the patient cells were isolated.”  
     
    http://www.wpinstitute.org/news/docs/FinalreplytoScienceWPI.pdf  
     Response to the Editorial team

    Be a good boy and email Frank Ruscetti. Unless you continue to question his integrity.

  27. RRM

    No, I am not “personally setting”. The WPI/VP62 sequences are about as related as different cultures from 22Rv1 are “related” to eachother. I hope you agree that different cultures from 22Rv1 are related?

    You have a weird defintion of “the same”. When two items share a common feature, that DOES NOT prove these two items are the same thing. It’s like saying “this ball is round, the earth is round, so the earth and this ball are the same thing”. No, they’re different things that happen to share some feature(s).

    Similarly, even if two sequences share some common feature (being “polytropic for one”), this does not mean the findings are the same thing. In fact, the Lo/WPI sequences vary more from each other than the VP62/WPI sequences do, indicating that if you do not consider the VP62/WPI sequences to be related, you must also reject the idea that the Lo/WPI sequences are the same thing.

    Even Alter and Lo don’t agree with this anymore, by the way.

  29. Anonymous

    No Cohen has that wrong.  He is free to contact Frank Ruscetti who’s integrity I don’t think he will question when he confirms that Cohen is wrong.  

    Cohen may have a personal wish for whatever reasons, but the fact is that VP62 has nothing to do with the Lombardi data.  They found HGRVs as Lo and Alter did.

  32. RRM

    “Evidence for integration of HGRVs in people with ME is for later research to discover.”
    That is not what Drosha was saying. (S)He was saying that even if you think that not using Trizol will kill all the virus, you should still be able to detect it if the rest of the blood sample stays intact. 

    Because the BWG showed that the blood sample stayed “intact”. the (integrated) virus should have been detected (if it was present). This has nothing to do with showing integration itself.

    If even a fully untrained layman like myself can understand what Drosha was arguing, how can a “trained” person like yourself completely fail at that?

  33. RRM

    – Lo used the same primers. I showed you that through referring you to a quote and a figure from the paper. You screaming the opposite “is a fact” is not evidence that your assertion is true.

    So, pretty please, can you provide evidence for the assertion that Lo used primers that weren’t able to detect positives in the Lo et al. study? It should be simple if true. 

    – I am “inventing” the talk where Mikovist showed the secret data from the secret lab. You accept unpublished evidence when it suits your purpose, and reject it when it doesn’t.
    – Were you at the talk of Hanson? If  not, what source do you have that these posters are wrong, other than your pathological belief in HGRV’s?

     – VP62 is very likely involved in the “Lombarding” (I like that verb) of the results. Of course, with Mikovits is refusing to share her data with Science, we might never conclusively know.

  34. Anonymous

    RRM you are suggesting that the BWG found integrated virus.  LOL  What do you think you mean by intact blood? LOL Why are you discussing matters that you have no training in?  The assays were prevented from working because the virus was degraded.

  35. Jack

    I do not believe that Jon Cohen would confirm what he had already said without having established his facts. Not in this journal and not this writer.

  36. Anonymous

    Because it you who is questioning Frank Ruscetti’s integrity.  You won’t trust a post of mine as proof so you must do the contacting.  He will be informed if you lie.

  38. Anonymous

    The sequences you are referring to are  the ones where Silverman mistakenly sequenced VP62 in his lab.  The samples have been proven to not contain VP62 before they the WPI or NCI.  

    State in scientific terms, which I know you are incapable of doing, what would make the viruses different?  What percentage is requited and why?  This is where you agreement has no validity, as you provide no argument.  Both detected polytropic gag sequences. 

    Lo and ALter have never stated they disagree, you are lying again.

  39. RRM

    No, I don’t trust a post of yours of proof. In fact, so for, you posting something is an indication something isn’t true.

    So apologies for not believing your vouching for the truth over a statement by CC officials.

  40. Pet101

    Your not reading my comments. You are missing what the issue is. They couldn’t identify the other positives. I have several colleagues who heard Hanson talk, she never said her results were contamination. Stop lying Mr RRM.

    No one has refused to share all data is public. You like lying don’t you. Go and seek some help.

    VP62 has never been in the WPI or NCI lab

  41. Anonymous

    He has definitely not confirmed it with Frank Ruscetti, Judy Mikovits or Robert Silverman.  He is being tricked by someone.  Cohen should name who it is.  I think that person should be held accountable for spreading this lie.  

  42. Anonymous

    How is it that two people on this site think that VP62 has unnatural powers of teleportation.  The WPI and Rusceetti labs have never had that clone in their facilities.  They then don’t blink one eye when negative papers that have looked for VP62, even though it has no relationship to the HGRV findings, use that clone but have no contamination in any samples or controls.   This group are acting like a VP62 religious cult.

  43. RRM

    That quote from you does not carry the conlusion that you derive from it. WPI merely stated that VP62 was not “IN THE LAB WHERE THE PATIENT CELLS WERE ISOLATED. Oh. My. God.

    This means that:

    1. VP62 WAS probably in their possession – otherwise they would have stated that it wasn’t instead of “just” stating VP62 wasn’t in the same lab as the patients’ samples

    2. WPI don’t deny that VP62 could have been in the lab where and when experiments other than ISOLATION (i.e. PCR for gag) were performed. Again, if it was not present with EVERY experiment, why did WPI only name the ISOLATION experiment?

    Thank you very much for this very revealing statement from WPI.

    Now I know why you usually don’t substantiate your claims with evidence: when you do, it proves you wrong.

    PS: If you read back, you’ll see that my former post was made within quotation marks. I wanted to make sure that everybodu could see that  it was not my “logic” that I was posting.

    Therefore, you attacked Gerwyn’s logic, not mine. I thought it was a pretty neat “set-up” to debunk Gerwyn’s “logic” as well as your lack of consistency, but apparently even this went way over your head. 🙁

  44. Anonymous

    Then contact Silverman and Ruscetti.  You won’t because you cannot argue against there statements. 

  45. Anonymous

    I know what quote states.  You can email Ruscetti yourself, or continue to lie.  They have not had VP62 in their labs.  Refusing do so is proof you know you are lying.  It is outrageous that you are attacking his integrity and that Mikovits.

  46. Anonymous

    It is not an accurate blog, so why do that?  Why not speak to the scientists who are involved in the research?  

  49. RRM

    You know what that quote states? Then you must agree that this quote does not say, AT ALL, that Silverman did not send VP62 to WPI. Or do I read ISOLATION wrongly? 

    How would Ruscetti know what was happening in the WPI’s lab? I’m not going to mail Ruscetti or any other scientist involved, but that does not mean that I am lying – that part is only in your head. 

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