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XMRV CFS UK study #II

Discussion in 'XMRV Research and Replication Studies' started by Orla, Feb 15, 2010.

  1. usedtobeperkytina

    usedtobeperkytina Senior Member

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    random thoughts....

    I recall that the Defreitas virus would show for six days and then suddenly disappear. Very sensitive little virus.

    I recall that freezing the samples would make it so you wouldn't find the DeFrietas virus.

    Now, as was said, Peterson said the blood of a person who was sick 25 years ago was tested and found positive. But I don't remember which of the four different tests they used on that sample.

    Additionally, the antibody test depends an an immune system that is able to form antibodies. Considering our defect is in the immune system, I guess it is possible that the antibody production system is flawed. Coffin mentioned this as a possible problem.

    Not drawing conclusions, just throwing out a few more factors for discussion.

    Tina
     
  2. usedtobeperkytina

    usedtobeperkytina Senior Member

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    And, just a side note, the editorial response concerning this study is ENCOURAGING MORE STUDY INTO XMRV AND CFS.

    This is my excitement, we have a non-CFS person (doctor or patient) urging more research for us. YEAH!

    tina
     
  3. Hope123

    Hope123 Senior Member

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    This is a good point. If XMRV had absolutely nothing to do with the illness (i.e. a random factor), it would make sense that roughly the same proportion of XMRV+ (i.e. 4%) would be seen in CFS group. I guess it might be missed perhaps because of the size of the study -- i.e. less than 200 in each arm - which is large for CFS but small compared to other illnesses studied.

    Also, I have not read the article in full yet but what is the point of adding or not getting rid of neutralizing antibodies in a sample when you are trying to see if those cells could be infected? Perhaps I'm understanding this incorrectly as I have to take some time to review the piece.
     
  4. Marco

    Marco Old blackguard

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    You may recall this response to a Written Parliamentary Question published in Hansard on 7 December 2009.



    Written answers for 7 Dec 2009 :
    Column 46W

    Biomedical Research

    Paul Rowen: To ask the Minister of State, Department for Business, Innovation and Skills what biomedical research into myalgic encephalomyelitis and xenotropic murine leukaemia virus-related virus is being undertaken. [304330]
    Mr. Lammy: The Medical Research Council (MRC) is one of the main agencies through which the Government support medical and clinical research. The MRC is an independent body which receives its grant in aid from the Department for Business, Innovation and Skills.

    In 2008-09 the MRC's total expenditure for research relating to Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) amounted to 728,000. This supported four projects including a 164,000 research programme led by Dr. C Clark at Queen Mary College, London on the general and specific risk markers and preventive factors for chronic fatigue and irritable bowel syndromes. CFS/ME continues to be a strategic priority area for funding and the MRC remains committed to supporting scientific research into all aspects of CFS/ME including evaluations of treatments and studies into the biological basis of the condition.

    The MRC recently held a CFS/ME research workshop where the recent xenotropic murine leukaemia virus-related virus (XMRV) findings were among the items discussed. A note of the discussions will be published on the MRC website in due course.

    The MRC's National Institute for Medical Research are leading a programme on infection and replication of retroviruses (including XMRV). One study within the programme is looking at how XMRV reproduces in the cell, its interaction with host cell factors and how it subverts the host immune systems.


    There appears to be no mention of the study under discussion. How long does it take to approve funding of such a study? Surely the MRC would have had to decide on funding such a proposal and, given the flak it received from ME charities for not funding biomedical research, wouldn't they have wanted to publicise it, not to mention being required to be full and open in a response to a parliamentary question?
     
  5. Gerwyn

    Gerwyn Guest

    all i,m saying as it was infective it could not have been a herv I dont think that group of controls was selected by accident and the pcr phase only contained 48 patients the potential for misdianosis is huge clinically feduka does not and cannot distinguish between ME and idiopathic chronic fatigue--the canadian criterea can UK doctors do not as a rule look for post exhertional malaise.I dont think that WPI used the same cell line for transfection---my point is that you cannot get viruses from those cells 18 hours after transfection or RT and this is well documented so why try.The "XMRV" clone used was "messed about with" in the very region that makes XMRV unique so the clone was a incomplete and b more like a herv so they used DNA which was not in any way complimentary to WT xmrv why
     
  6. Gerwyn

    Gerwyn Guest

    That is the key point It was infective so exogenous the last active herv was millions of years ago and it shared the same unique base sequence as a virus found by other independent researchers.No other assay has been able to find it but other people using tissue isolates have.Anyone using whole blood hasn,t.It takes about three months to be able to detect aids in blood even with its rapid replication rate yet this team tried to find xmrv a few hours post transfection.PCR is highly problematical in detecting aids as well.
     
  7. guest

    guest Guest

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    http://www.virology.ws/2010/02/15/x...itional-uk-chronic-fatigue-syndrome-patients/

    "...A second method was then used to search for evidence of XMRV: the patient serum samples were examined for the presence of antibodies that could block infection of cells with the virus. Cells were infected with XMRV in the presence of serum from CFS patients or control patients. Included were sera known to block XMRV infection to ensure that the assay functioned normally. None of 142 CFS samples contained antibodies that could block XMRV infection of cells. In contrast, 22 samples out of 157 controls (14%) were identified that contained neutralizing activity. One of 28 CFS serum samples from a separate cohort was found to contain XMRV neutralizing activity; none of the 12 control sera could block XMRV infection...It’s time to put aside arguments over the competence of laboratories to carry out polymerase chain reaction and work towards understanding the role of XMRV in human disease. The three laboratories who have published their findings on XMRV in humans should exchange their samples to confirm the findings. Compelling answers will only come from far more extensive global studies of the prevalence of XMRV in CFS and control populations are clearly needed."

    What now?
     
  8. Mithriel

    Mithriel Senior Member

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    This study wasn't designed to back up the biopsychosocial view, it was a rough and ready thing using blood they already had to see what was there. If it wasn't ME/CFS that was involved this would have been uncontroversial no matter the result.

    All they showed was that this new virus is not easily found by any old PCR method but needs a very specific process to find it and even then it doesn't always work. This just shows the characteristics of the virus and is not unusual when something new is discovered.

    You have to discover which tissue is best and if blood, how best to collect it, store it, which chemicals to use. The WPI is doing all this and the people working on prostate cancer are too. It was mentioned on this forum that new work has shown that the tissue culture cells used by one study that found very little XMRV are now known to be very bad for growing it in. It is all new knowledge.

    Unfortunately for us, every negative study will be used to deny we have a proper disease are and as confirmation that we just enjoy being sick.

    The WPI isolated virus from one old sample, but this doesn't mean that it is easily found from old blood. When people are getting tested the blood is collected in an optimal way, so you would expect better results and that is what is happening.

    Every time the psyches here have opened up the definition of CFS there has been a tenfold increase in numbers, the same thing happened with Reeve's new empirical definition which made US numbers similar to the UK. This means it is possible for only 1 in a hundred of samples to be ME or the same disease as WPI looked at.

    If the existing evidence for the biological pathologies of ME/CFS was accepted and not ignored by the medical establishment, all this new research would be interesting but not have the importance we are giving it.

    Mithriel
     
  9. Gerwyn

    Gerwyn Guest

    The freezing bit bothered me also snap with antibody test
     
  10. Gerwyn

    Gerwyn Guest

    the other thing that really bothers me is the control group all the illnesses in that group were associated with endogenous gammas you would not try to find the prevelance of xmrv in a population swimming in endogenous gammas the antibody tests would pick them up.also they knew or should have done -that the cell line used to transfect the clone could not produce Rt untill 7 days or virus ibside two weeks so why only wait 18 hours?
     
  11. Guido den Broeder

    Guido den Broeder *****

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    Indeed, this is very important to remember.

    This is a validation study, trying to confirm the WPI results with a different method. It would be of major significance if they had validated the WPI findings, but the fact that they failed to do so means near to nothing. Given the complications that WPI encountered in detecting the virus, it is extremely unlikely that any random validation study will succeed.

    Add to this the often dubious way that patients get diagnosed, especially in the UK, and possible problems with how the samples were kept. For a validation study, I think it is absolutely necessary that it includes a LMW RNaseL test to identify the patients.
     
  12. Dr. Yes

    Dr. Yes Shame on You

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    No and Yes...

    This study did not confirm the existence of XMRV in the UK; first of all, they did not do an 'antibody test' as one is used to thinking of the term. They did neutralization assays, giving hypothetical antibodies in the patients' sera the chance to prevent XMRV from infecting cells, and compared the results to a previous run of the same assay with known XMRV-specific antibodies (not from these patients' blood) which they feel they had established really COULD specifically block XMRV infection.

    Some controls and one CFS patients' samples were able to reduce the overall level of XMRV infectivity according to this neutralization assay, so they tried to see if this was really due to an antibody genuinely against XMRV in these patients or to an antibody (or antibodies) that just happened to block XMRV but was produced by the patients to some other virus that merely "resembled" XMRV in some places. After this further test, it seems that using their basic assay methodology, the prepared (known) antibodies were specific for XMRV, but those in the patient sera were not; the latter blocked all the viruses the team threw at 'em.

    They took this result and, combining it with their negative PCR results, concluded that the patient sera very likely did not contain antibodies to XMRV, but to some other virus that merely shares some key sequences (and therefore key antigen/s) with XMRV. That interpretation means NO solid evidence of XMRV even among the controls.

    Whether their interpretation is correct is open to some question, mainly because it hinges on the quality of their PCR test. (Did they allow enough time to culture the 'virus'? etc)

    Also, as the authors themselves said, the fact that more controls were 'positive' for neutralization was odd, so they threw out a hypothesis I find a bit questionable:

    Is the bolded statement necessarily true? It assumes that XMRV will always replicate at a higher level when immunity is compromised in that special CFS way. No one has demonstrated this to be the case, to my knowledge.

    [I also wonder which other virus they believe those neutralizing sera were responding to, i.e. how common are viruses that share XMRV, MLV, etc sequences (not limited to those that code for the retroviral envelope protein, either)? I'm not a virologist, so I really don't know; in absence of that knowledge I just find it odd that XMRV would be neutralized so noticeably by antibodies to some other virus.. if it's an ERV, it's a bit strange that the antibodies would also neutralize the VSV-env MLV pseudotype.]

    Anyway, even if XMRV is involved in just a subset of cases as they propose, then it is all the more necessary to select patients that match the WPI cohort as closely as possible, incl. using the Canadian criteria and sampling patients from a wider geographic distribution.

    I agree with everyone, including the authors of this paper, that the key now is to find out why the different labs' techniques are yielding such different results. Is it the methodology or the samples? Collaboration, especially in testing known positives from the WPI vault, is the only answer. And in that regard the best nearest hope is the collaboration already underway under the auspices of the DHHS, with Dr. Mikovits on the Task Force (see Jennie Spotila's post earlier in this thread!) THAT is what I'm really waiting for.

    (Btw, as others have mentioned, whatever happens it does seem most likely that the WPI found SOME virus, so even if it is established that XMRV is not what they found, the DHHS should not be able to avoid the question of what then was found... and then we'll have another round of 'fun' ! So we should not get manic this early in the game folks -- the terrain will keep shifting, so each of us needs to seek a comfortable equilibrium. :angel:)
     
  13. Dr. Yes

    Dr. Yes Shame on You

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    Just thought that this from Mithriel bears repeating:

    I'd say it would still be very significant, but not the make-or-break we are increasingly being forced into, and should resist publicly and otherwise.
     
  14. Esther12

    Esther12 Senior Member

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    Isn't it likely Kerr and Mikovits would have been in contact with each other regarding their own study, and Kerr would have discussed the results from this study with Mikovits when they were available?

    I'm still hopeful the WPI's paper will lead on to something interesting, but I'm surprised the WPI were so dismissive of the IC study if they knew this one was coming. It looks like honest attempts to find XMRV can fail, or else there is some problem with the WPI's results. I wonder how they'll respond to this one.
     
  15. Gerwyn

    Gerwyn Guest

    I haven,t actively been involved in virology for a long time but the entire methodology is strange, As I understand things these healthy controls would have a great deal of expressed endogenous DNA, because of the herv element in causation of these illnesses the controls suffered from, at least as now widely expected..You would expect unusually high concentrations of anti herv antibodies in the control population . with the env sequence of XMRV played about with this "XMRV" viruses probably had no unique sequences and was more similar to a herv i agrre about the hypothesis I think it would be the other way round poor immune response more virus integrated lower antibody response to xmrv
     
  16. Bob

    Bob

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    Dr Yes, thanks for your clarification on some of these points...
    When we look at the implications of this study closely, like we are, it does seem to throw up more questions than answers... that's why I'm still not disheartened.
    And at least these authors do seem to be taking their research seriously, and aren't being dismissive, unlike the Wessely authors.
    However, their explanations for their 'neutralising' test results just seem to be made-up because they haven't a clue what's going on here...
    it just shows that no one can draw any conclusions from this study, including the authors.
    (And what's with these 'neutralising' tests anyway? Where did these come into the WPI research? Why didn't they just replicate the WPI study and be done with it instead of all this messing around with 'neutralising' tests?!?)
     
  17. Cort

    Cort Phoenix Rising Founder

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    Whethe Kerr and the WPI talked is a very interesting question. I would guess that they did; this team wanted to find the virus. When I was reading Osler's Web b the CDC and DeFreitas talked frequently about why they weren't getting the same results. Gow (the second study not to find the virus) also talked frequently. Not knowing any better I would assume, given that this was a 'friendly' team that they were in communication.

    My understanding is that the WPI is using an antibody test developed by Dr. Singh in Utah and that test is not only picking up XMRV infectin but its showing increased rates of positivity. It really is a conundrum; the WPI appears to be getting more and more internal evidence that they're right these papers are coming out suggesting that something went wrong. The first question always appears to be if what the WPI found is an endogenous retrovirus - a piece of junk DNA from an old mouse retrovirus in our genome. They sequenced 2 and a half strains of the virus and compared what they found against our entire genome against our entire genome and found nothing. Thats one of the reasons Science took the paper - they convinced them it was not an endogenous retrovirus.

    I still don't see how they could be wrong. It think hey've still done more to show that the virus is real than anyone has shown that its not..but the twists in this story are amazing.

    I wish wMy understanding is that the WPI is now using Dr. Singh's antibody test specific to XMRV that shows INCREASED not decreased rates of positivity. It really is a conundrum; the WPI appears to be getting more and more internal evidence that they're right these papers are coming out suggesting that something went wrong. The first question always appears to be if what the WPI found is an endogenous retrovirus - a piece of junk DNA from an old mouse retrovirus in our genome. They sequenced 2 and a half strains of the virus and compared what they found against our entire genome against our entire genome and found nothing. Thats one of the reasons Science took the paper - they convinced them it was not an endogenous retrovirus.

    I still don't see how they could be wrong. I think they've still done more to show that the virus is real than anyone has shown that its not. How could they be wrong? (How could they be right?) The twists in this story are amazing.
     
  18. Bob

    Bob

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    KFG, I take your point, and I still have faith in the WPI. Like I said before the XMRV genie can't be put back in the bottle! (not even by Wessely)
    But you must understand why we all get frustrated by this... we've had decades of not being able to rely on the science... science has been against us in the form of psychiatrists!
    So you must forgive us if we are all a little untrusting, cynical and frustrated.
     
  19. Robin

    Robin Guest

    There doesn't seem to be scientific consensus on how to detect the little bugger. I just wish that issue was resolved before XMRV was implicated in ME/CFS -- it would be so much less trauma for all of us.

    I'm waiting for the CDC working group report because they are specifically assigned to work on the problem of testing.
     
  20. Cort

    Cort Phoenix Rising Founder

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    Bear in mind that we have yet to see a 'replication study'; no one has yet followed the WPI's study to the letter. Different groups are doing different kinds of PCR and different kinds of antibody tests. Theoretically they all should match up but they're not; the twists to this story are amazing and unsettling but the WPI has the National Cancer Institute and the Cleveland Clinic behind them; they produced 'the best' first paper possible and it landed in the most prestigous journal in the world. Other groups are doing more comprehensive analyses of the WPI results; Dr. Klimas said this was going to be an up and down process - she was clearly right!
     

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