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Retrovirology Publishes Five Papers on XMRV and Contamination

Discussion in 'XMRV Research and Replication Studies' started by Countrygirl, Dec 20, 2010.

  1. urbantravels

    urbantravels disjecta membra

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  2. WillowJ

    WillowJ Senior Member

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    also, the important thing to remember is, the good thing about XMRV is that it got us Dr. Harvey Alter in our corner. It's because of Alter that the NIH is listening. He isn't going to change his mind that, when defined properly, this is a "serious, medical condition."

    As I've always said, with our without XMRV, we have all kinds of good, useful science that shows that we have a serious biomedical condition which is treatable.

    However, contamination doesn't explain proteins and antibodies. So I really think the science is going to maintain the XMRV in the end. It's just that newspapers have no idea how to report scientific studies in the first place, and they've tended to have a bad attitude against CFS in the second place. So the press is generally bad for now.

    http://blogs.nature.com/news/thegreatbeyond/2010/12/new_challenges_to_link_between.html
    Nature did better
     
  3. WillowJ

    WillowJ Senior Member

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    right, I checked once and this was a great big conglomerate... ok, glad you're all aware. Probably more than LA Times picked it up and it's being carried in a lot of papers who also did no reporting of their own
     
  4. Carryon

    Carryon Mike Munoz

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  5. Bob

    Bob

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    I just read funinco's comments after the LA Times article...
    http://www.latimes.com/ct-met-chronic-fatigue-xmrv-20101220,0,3617078.story
    It's interesting that Vincent Racainello had such a negative initial reaction to the papers, but on further reading, he now thinks that they aren't so significant... he's now realised that they just point the potential pitfalls of contamination.


    I'm also looking at this comment:
    I don't know, sometimes I seem to be very slow to catch on to things...
    Can anyone tell me if the XMRV DNA integration is new news, or was it published ages ago? Has it even been published?
    I'll have a look at the references in the morning.
     
  6. Ecoclimber

    Ecoclimber Senior Member

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    Virologist Vincent Racaniello clarifies comments on death knell to xmrv and cfs

    Virologist Vincent Racaniello with comments posted here. Also includes comments on WPI's research.

    http://www.virology.ws/2010/12/21/is-xmrv-a-laboratory-contaminant/

    Also posted on this forum under news although the moderator might want to leave it in this section where the discussion seems to be taking place.
     
  7. Snow Leopard

    Snow Leopard Senior Member

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    How much diversity would there be if the virus was spread via contaminated cell culture products - eg vaccines?

    Also, what has WPI been doing research wise? If I were them I would have been investing money in genetic testing - sequencing more virus variants and trying to find evidence of genomic integration. Can someone ask Mikovits what the WPI is doing with regards to this?

    Deliberate timing to reduce the impact of certain recent events (eg Red Cross ban and patient advertisement)?
     
  8. oceanblue

    oceanblue Senior Member

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    Racaniello makes 2 comments that cast doubt on some of the findings in Retrovirology:
    First, he points out that XMRV integration has been shown, which is hard to explain by contamination:

    Bob quoted a comment on the same blog from Eric Klein:
    Then Ranaciello points out that the CFS XMRV isolates are different from the Prostate Cancer XMRV isolates discussed in the Hue paper in one particular context - so that those comment about PCR contamination won't be applicable to CFS XMRV:

     
  9. Marco

    Marco Old blackguard

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    LONG AND SPECULATIVE POST ALERT


    I don't believe that its a good idea to speculate wildly about what these results mean, especially when knowledge and expertise is limited. Best to leave that to the experts.

    But, I just can't help myself.

    Following on from Alex's comments earlier in the thread, I can't help wondering if there is any way of reconciling the findings of 'both sides' if they are both correct?


    For the sake of argument, lets assume all of the following findings are true :

    From the positive studies;


    XMRV found in 22% of patients with aggressive prostate cancer;

    XMRV found in approx 65 to 95% of PWC's;

    A very similar PMLV was found in the Lo/Alter patients but 'not XMRV';

    XMRV found in 4 to 7% of 'healthy' controls;

    While initially there appeared to little genetic diversity in patient samples of XMRV, there are also now indications that the diversity is greater than previously thought.


    From the 'contamination' studies


    Commonly used lab mouse species now known to host a variety of ERVs and MuLVs;

    Contamination of labs working with mice now appears to be more widespread than previously assumed;

    The 22Rv1cell line was created, some time before 1999 as far as I can see, as a 'human prostatic carcinoma xenograft serially propagated in mice';

    the MuLV found in this cell line is, by statistical analysis, ancestral to XMRV;

    the MuLV found in the cell line has greater genetic diversity than that found in the two patient samples.



    I know little about population genetics or retroviruses but from what I can pick up I'm assuming that a retrovirus accumulates genetic diversity by recombination with other viruses and the host DNA and therefore a retrovirus circulating in the population should show greater diversity between patient samples than that found in a laboratory contaminant?

    Statistical analysis can demonstrate where a sample fits on the phylogenetic tree, that is, whether a given sample is derived from or ancestral to another. The 22Rv1cell line virus appears to be closely related to and ancestral to the patient samples.

    Another way of looking at this relationship however is that being ancestral to another sample or other retrovirus is also a function of time. Presumably, once the cell line was created it is then cloned and the XMRV is 'immortalised', that is the genetic structure is 'fixed' at the time the cell line was created and as such is akin to a 'viral fossil'. This being the case, the only thing we can definitively conclude from the Hue paper is that the 22Rv1cell line XMRV dates from an earlier time period than the patient samples (necessarily some time before 1999).

    Further, assuming that contamination is much more prevalent than previously thought and that in 1999 and before the potential for contamination was greater (being unaware of the scale of the problem) it logically follows that contamination of cell lines by MuLVs was fairly common. If we also assume that the incidence of XMRV in aggressive prostate cancer runs at around 25%, then a cell line consisting on a xenograft of human prostate cancer tissues and 'serially propagated in mice' could quite easily contain a 'swarm' consisting of many MuLVs from many mice, the strain of XMRV circulating in the population at the time donated by the PC patient at the time the cell line was created and potentially hybrids of the two. Didn't one of Dusty Miller's papers state 'the virus found in the 22Rv1cell line IS XMRV'.

    Two scenarios spring to mind :


    (a) The 22Rv1cell line XMRV is indeed ancestral to that found in patients as it was introduced into the cell line from the human population at a much earlier time. The XMRV found in patients shows less genetic diversity because :

    there is less scope for hybridisation in a human host compared to the procedure that produced the 22Rv1cell line;

    while the WPI sample came from various regions, at least some of them came from an outbreak cluster where you would expect the same strain of XMRV to be present.


    (b) What happens when you culture patient samples using the 22Rv1cell line and then test for XMRV? Depending on what you are looking for or hoping to exclude you might find :

    the 22Rv1cell line XMRV only suggesting contamination;

    the patient's own strain of XMRV which would be a descendant of the 22Rv1cell line XMRV but should be more dissimilar to it;

    a new hybrid of the 22Rv1cell line XMRV and the patient's own XMRV which would be directly descended from the 22Rv1cell line and also very similar;

    all of the above, a closely related XMRV/PMLV swarm;

    or your controls against MuLV contamination are so broad that they exclude finding any XMRV.
     
  10. eric_s

    eric_s Senior Member

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    I think that's an interesting point, Marco. I have asked myself similar questions too.

    What if you take a limited number of sequences, one old one and the others all younger and then do that type of analysis?

    Wouldn't it be the expected result that the old sequence is deemed to be ancestral to the others?

    But could "the brightest minds" (Source: Wellcome Trust) really make such a stupid statement?

    I have no idea about these things and so i think we just have to wait for the scientists we trust to answer those questions. What i've said above might be totally wrong.
     
  11. CBS

    CBS Senior Member

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    Prostate Cancer v. CFS

    Did a pubmed search for the five articles in Retrovirology:

    • XMRV - All there
    • MLV - All there
    • CFS - All there
    • Prostate Cancer - Nothing
    Seems a bit odd that there wasn't a single article tagged with the search term "prostate cancer."
     
  12. Marco

    Marco Old blackguard

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    I was thinking more along the lines of XMRV is in the population, much more prevalent in ME/CFS and PC, and that's how it got into the cell line.

    So for example, if you tested a well characterised cohort without using the contaminated cell line then you will turn up the 'wild' variant of XMRV. If you culture using the suspect cell line then you may get a swarm of the wild XMRV plus the XMRV/PMLV variants.

    Anyway. Eric's right. We should leave it to the scientists.

    One thing I do know is that is either some strange retrovirus, a strange scientific context (maybe both) or its just this is the first time I have had a personal stake in an unfolding medical science story. Perhaps it always unfolds like this from the 'inside'?
     
  13. oceanblue

    oceanblue Senior Member

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    Hue paper on WPI sequences

    The only CFS XMRV sequences examined by Hue were the two from WPI's original Science paper and not those found by Lo/Alter since "the MLV sequences described were too short to carry out a thorough phylogenetic analysis, and we have therefore not included them".

    And Hue found that the WPI sequences were in the same cluster as all the XMRV sequences derived from 22Rv1 cell line clones. From this they conclude that the WPI XMRV sequences originated form the 22Rv1 cell line and that they are due to contamination.

    This does look like strong evidence for contamination so it's a pity that the WPI statement didn't specifically address this issue.

    Hopefully Lo will be sequencing all his CFS XMRV isolates to see how they compare with the 22Rv1 cell line.
     
  14. oceanblue

    oceanblue Senior Member

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    Hue says 'human cell lines COMMONLY carry XMRV-like retroviruses': he means just 1%

    ... 1% or maybe less

    One other finding of Hue was that
    In other words these cell lines are a ready source of 'XMRV' contamination in labs.

    There are two problems with this statement, based on the evidence in his paper.

    First, 411 cell lines were screened. Just 5 of these (i.e. 1.25%) were positive using a particular XMRV gag-leader primer. And I don't think 1% counts as 'commonly'.

    Secondly, the finding may be irrelevant as it's not the primer used by either of the positive studies (as far as I can tell). Instead, it's the primer used by McClure. And in his same Retrovirology paper, Hue shows that this primer doesn't accurately identify the XMRV sequence it's supposed to identify (a 24nt deletion; sequencing showed that the target deletion was only actually present in 4 out of 12 positive results). So it's possible that NONE of the cell lines actually contain the targeted XMRV deletion - we don't know as they didn't sequence the positive PCR results in the cell line study - and that would make for a very different story.

    So the statement doesn't seem to fit the evidence.

    None of this affect the separate claims about the relatedness of patient XMRV and that of human cell lines
     
  15. Esther12

    Esther12 Senior Member

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    Thanks for those points Oceanblue.
     
  16. free at last

    free at last Senior Member

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    Ocean blue, and all you guys thanks for not accepting there studys as gospel, as some do ( and will continue to do )
    Thanks for trying to get your heads around this complicated paper, i dont understand any of it, i wish i did. But appreciate those that understand more, and are trying real hard not to let them get away with what they have done, the way they have done it. and the damaging long term effect it will produce.

    Its good to be part of a community that understands some of our feelings, and hopes for the future of all of us, Merry christmas Ocean blue, and everybody. Never give in, even though sometimes all feels lost
     
  17. August59

    August59 Daughters High School Graduation

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    I think I'll frame this quote from KDM
     
  18. Ecoclimber

    Ecoclimber Senior Member

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    Dusty Miller Will Be Contacting the Other Researchers for Common Rebuttal to Claims


    I talked to Dr. Dusty Miller. His lab is currently in the stage in testing and experimenting and gathering the evidence to rebut their claims. He states he can refute their claims. He will be getting together with Ruscetti, Silverman, Klein, Smith and others to post their rebuttal as a group against the negative papers.
     
  19. urbantravels

    urbantravels disjecta membra

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    Terrific news! This controversy could wind up being fun, instead of disheartening, to watch. May the best science win!
     
  20. Valb626

    Valb626

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    This is great news, Ecoclimber. Glad that the Contaminants stepped on the prostate cancer research, as well as the CFS studies, this time.

    If we weren't so desperate and sick, watching the science and the associated drama unfold is better than House or any soap opera. The suspense is killing us, though (literally).
     

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