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Paolucci et al: 2 out of 12 CFS patients positive for MuLV

Discussion in 'XMRV Research and Replication Studies' started by natasa778, Jul 31, 2012.

  1. natasa778

    natasa778 Senior Member

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    http://www.ncbi.nlm.nih.gov/pubmed/22842604

    New Microbiol. 2012 Jul;35(3):341-4. Epub 2012 Jun 30.
    Xenotropic and polytropic murine leukemia virus-related sequences are not detected in the majority of patients with chronic fatigue syndrome.

    Paolucci S, Piralla A, Zanello C, Minoli L, Baldanti F.
    S.S. Virologia Molecolare, S.C. Virologia e Microbiologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
    XMRV and polytropic MLV-related virus have been controversially associated with chronic fatigue syndrome (CFS). Subsequent reports failed to detect XMRV and MLV-related virus in CFS patients, and the previous results have been interpreted as a massive laboratory contamination by mouse DNA sequences. Among 12 sequential CFS patients, two were positive for XMRV/MLV sequences. In contrast, 40 selected control subjects were negative. CSF patients and controls were negative for mitochondrial mouse-specific DNA sequences. These findings do not confirm the high frequency of MLV-related viruses infection in CFS patients, but also contrast the widespread laboratory contamination previously suggested.
     
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  2. natasa778

    natasa778 Senior Member

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  3. natasa778

    natasa778 Senior Member

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    The finding of two related, but different, virus sequences
    (polytropic MLV and XMRV) in two CFS
    patients, does not confirm the high frequency of
    MLV-related virus infection in CFS patients reported
    in previous studies (Lombardi et al., 2009).
    On the other hand, our results are in contrast
    with the reported massive and widespread laboratory
    and reagents contamination (Robinson et
    al., 2010; Oakes et al., 2010; Tuke et al., 2011). In
    fact:
    i) all samples were negative for mitochondrial
    mouse-specific DNA sequences;
    ii) all the several negative reaction controls were
    consistently scored as negative;
    iii) all blank reagent controls were consistently
    scored as negative.
    These results would exclude the presence of contaminating
    mouse or plasmid DNA in reagents. In
    addition, the two positive amplicons showed different
    retrovirus sequences, thus excluding amplicon
    carry-over contamination. The data here
    reported are relevant to a small group of CFS patients,
    and studies in larger patient cohorts have
    not attributed an etiologic role for XMRV or MLVrelated
    viruses in CFS (Erlwein et al., 2010;
    Switzer et al., 2010; van Kuppeveld et al., 2010;
    Simmons et al., 2011). It is however intriguing
    that the only positive results were obtained in
    these patients. ...
     
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  4. JT1024

    JT1024 Senior Member

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    Thanks for posting this natasa!

    A few sentences in the article jumped out at me.

    The opening line of the article states: Chronic fatigue syndrome (CFS) is an uncommon clinical condition of unknown etiology characterized by persistent fatigue in association with malaise, multiple joint and muscle pain, unrefreshing sleep and severe mental and physical exhaustion.

    The presence of so many patients on this forum alone indicates it is not as "uncommon" as the authors state.

    During 2010 the presence of XMRV and polytropic MLV-related provirus was investigated in 12 sequential CFS patients.

    This was carried out in 2010 using PCR with careful consideration for contamination. At least nucleotide sequencing was performed on the two positive patient's samples. The macaque studies performed to date have indicated that viremia is transcient so sample selection (blood vs tissue) and timing is critical.

    Also, cohort selection impacts outcome as well. If they authors had 1000 "CFS" patients diagnosed by non-CCC criteria, that alone would skew results. I may need clarification on the definition of "sequential" in this context. If they are testing patients "sequentially", eg. #23 through #35, without taking into consideration sudden onset, length of illness, severity of illness, etc., that impairs the ability to draw conclusions. Poor cohort selection = poor study design.

    The data here reported are relevant to a small group of CFS patients, and studies in larger patient cohorts have not attributed an etiologic role for XMRV or MLV related viruses in CFS (Erlwein et al., 2010; Switzer et al., 2010; van Kuppeveld et al., 2010; Simmons et al., 2011). It is however intriguing that the only positive results were obtained in these patients.

    The study was indeed small but referencing other flawed studies does not eliminate the significance of the small study's findings. The larger studies are guilty of the same errors as many others: poor cohort selection, poor sample selection, poor methodology selection, etc. etc.

    More work is needed IMHO!
     
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  5. JT1024

    JT1024 Senior Member

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    I believe it had to do right cohort selection and exceptional attention to detail in study design. The clearer you are on what you are looking for, the higher the probability you will find it. While viremia is transcient, free cell dna/rna (? from apoptosis?) could be detectable.

    Sorry I can't go further right now. When I can, I will dig deeper. My brain is in shut down mode.
     
  6. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    This is a positive study. 2 out of 12 is not insignificant, particularly given the vagaries of the testing procedures. The language of the study is interesting, almost as if the researchers are begrudgingly having to acknowledge there is something there. We should be able to cite this paper in support of MRVs, against the contamination researchers. That alone is a significant point.
     
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  7. JT1024

    JT1024 Senior Member

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    Very true RustyJ.

    Now why would they entitle the paper in such a negative fashion?
     
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  8. Bob

    Bob

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    I haven't read this paper properly yet, but the wording in Hanson's paper is similarly apologetic for finding sequences, giving the appearance of attempting to explain the results from the point of view of contamination, even though the apparently rigorously designed study failed to find any links to contamination.
    My own interpretation is that the authors wish to avoid attracting too much controversy, seeing as what's happened to Judy, and so use wording that downplays their results.
    Hanson's paper can also be interpreted as a positive study, if unrepeatable positive results are counted as positive, rather than negative.
     
  9. barbc56

    barbc56 Senior Member

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    Hypothetically speaking, not if the 2 out of 12 turn out not to be significanare as the outcomes of these samples could happen by chance. That's where the statistics come to play in studies. I haven't had a chance to look to see if this is what the paper is saying or not.

    I don't think most scientest are apologetic about what they find, nor should they be. What they find, they find and any information adds to the big picture, even if it eventually turns out that the study is not correct.

    I think, but am not absolutely sure, that it's only in the Lipkin study where any positive is counted as a positive study. This way these samples can be studied further to see if the finding is genuine.

    Barb C.:>)
     
  10. Bob

    Bob

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    If it's not contamination, then it's significant, however low the numbers.
    (i.e. if you find a novel human retrovirus, then it's significant.)
    But I haven't read it yet, so I can't comment on it further yet.

    There isn't any rule about this. In scientific papers, authors present their results/data, along with a discussion about their own interpretation.
     
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  11. barbc56

    barbc56 Senior Member

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    There are certainly "rules", for lack of a better term, per study. You can find these in the methods section of a study.

    Barb C.:>)
     
  12. JT1024

    JT1024 Senior Member

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    This study had no methods section and it published no statistical analysis so good luck finding this study's "rules".

    With of 16.67% (2/12) positive for a non-descript cohort of "CFS" patients and 0% (0/40) positive among the control patients - that is a positive finding. Especially since contamination was taken into consideration.
     
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  13. Mark

    Mark Acting CEO

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    As regards the statistics, there are various ways one could look at this, but one is to say that given that two positives are found out of 52 samples total, the chance that both of them are found in the 12 CFS patients is 12/52 * 12/52 = 5.3%.

    However, to make sense of questions like this, and make use of the power of statistics, it would be necessary for all registered scientific experiments to publish their data openly, whether the experiments are successful or not. So, for example, if any studies have been done which found a couple of positives in controls but not in patients, and which decided not to publish the findings but instead ignore them or run some more tests to look for contamination, those initial results too should have been published with full data, and the same applies to any positive studies which are not deemed acceptable for publication in a major journal - they should all be published somewhere, with full data, so that the sum of the data can be objectively assessed.

    That's partly why I support Open Access and Open Data, along with many other long-overdue reforms to scientific practice like open peer and public review and pre-registration of studies. Scientists, of all people, should understand the importance of not requiring people to form their beliefs about reality based purely on trust and appeals to authority: they should be vigorously campaigning for the capability of science to provide the evidence (the data) directly to the people who are expected to believe in their findings, and they should understand the importance of not introducing gaps in the evidence base by discarding or suppressing evidence or data that is judged to be inconvenient, anomalous, irrelevant or simply not particularly career-enhancing. Sadly, a significant proportion of scientists are more concerned with their own reputations and financial rewards than with the purity of the scientific method and the integrity of science itself, and so bad practices and the corruption of science by commercial interests persist and the public continues to lose faith in the integrity of modern science - but hopefully those that stand up for Open Access, Open Data and reforms to scientific practice will win out in the end...
     
  14. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    Barb, it is not a matter of statistics that MRVs were found. Only where they were found. Forget about pathology atm. This study is another that has found MRVs in people. If we take the wider view, then this study calls into question, again, why the negative studies did not find MRVs in controls or patients.

    At this stage we should move past the question of whether MRVs are in people, and start looking at which people they are in and what is the pathology.

    Take the narrower view, then it becomes another study that found MRVs to a greater extent in patients.
     
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  15. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    By the way, this is not a false positive. They have found different viruses. They ruled out contamination. You can't just balance out all the positive studies with the negative ones. You can't say that a bunch of negative studies which can't find anything balances out a bunch of positive studies where people are describing new viruses.
     
  16. alex3619

    alex3619 Senior Member

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    Politics? If they sound too enthusiastic they might have more resistance and more difficulty in continuing research.

    On the other hand, it could be normal scientific caution. Scientists like to be careful, or they should. Bold hypotheses and careful study make for good science in my view.

    As for only two positives, this is not an unexpected result given the macaque studies. On the other hand I suspect from the WPI/Mikovits story that it was patient samples that were presumed contaminated. Controls would then be normal - and in this type of circumstance we could again have the results like this study. A subset of patients contaminated (this is possible even with different viral strains) and controls normal. It could go either way, nothing is conclusive.

    Even presuming this is accurate though, and MLVs were found, it still does not answer the important question: are they just opportunistic infections or something causal?

    Science marches slowly, but as long as its moving somewhere its probably a good thing.

    Bye, Alex
     
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  17. Firestormm

    Firestormm Guest

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    Or because they haven't been able to find contamination and are frustrated or explain their results to their own satisfaction? You know it is as feasible that whatever checks they used to detect contamination, that they were not adequate and the authors 'caution' (if that is a more conducive word to what is being deemed 'negativity') is because they have - as I said - been unable to determine/explain these results. Whatever 'we' might feel about all of this I would imagine that scientists generally are very conscious of the prevailing - dare I say it - consensus. Any 'positive' findings need to be explained thoroughly and if they can't be, if there remains an element of doubt, then perhaps they will feel uncertain about what their equipment and tests have 'found'. Until such time as 'MLV's' for example ARE linked to human disease or even confirmed as being present in humans; every single one of these studies I would suggest will be similarly phrased in cautionary terms. But, it's only an opinion of course.
     
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  18. currer

    currer Senior Member

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    Finding any MLVs in humans is a serious matter if you take gene vector technology into consideration.

    The "wild" MLV would not even need to cause disease. There would always be the theoretical possibility of recombination in humans of an introduced gene vector and a wild MLV.

    If the retrovirology community is responsible, they have no choice but to get to the bottom of this.
    So we ought to see much more research on MLVs and human infection, even if MLV s are benign and not causing disease.

    This will be a good thing for us but the motive may be nothing to do with CFS/ME.

    Maybe this is why there is so much willingness to believe Paprotka.
    The viriologists can see their research funds and patented MRVs fading away.....

    From information I have come across it seems that patented viruses are worth a vast deal of money
    $$$$$$$ :alien:$$$$$$$
     
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  19. RustyJ

    RustyJ Contaminated Cell Line 'RustyJ'

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    Would this be the same caution exercised by those researchers who couldn't find MRVs, who promptly announced to the world that they aren't in humans, or perhaps those researchers who introduce their papers with the statement that "Xenotropic murine leukemia virus-related virus (XMRV) is a virus created through recombination of two murine leukemia proviruses under artificial conditions during the passage of human prostate cancer cells in athymic nude mice." http://www.sciencedirect.com/science/article/pii/S0006291X12013903
     
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  20. Firestormm

    Firestormm Guest

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    No. I was expressing an alternate opinion of what might explain your reference to 'negativity' and others reference to some sort of apologetic nature in the paper about which this thread is concerned. But, neither would it be the 'caution' employed by Dr Mikovits either if you wish to go down this route. Why not - seriously - contact the authors and ask? I have found in the past (with the exception of Ruscetti - though there were reasons for that I believe) that in general they are very receptive to polite enquiries. Give it a whirl, see what they say.
     
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