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Frequent detection of infectious XMLV in human cultures from mouse xenografts

Discussion in 'XMRV Research and Replication Studies' started by Jemal, Jun 30, 2011.

  1. RedRuth

    RedRuth Senior Member

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    Yes, LnCAPs, the cell line that the Mikovits lab uses in the Science paper for viral transmission, they've also infected LnCAP cells with the VP62 plasmid (supplementary figure 3.A)
  2. currer

    currer Senior Member

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    But Jace pointed out to you, redruth that the WPI have stated that they do not use the infected cell lines in their lab.
    You are harping on continually about contamination in the WPI's research. Can we explore some other ideas please? We are aware of the contamination arguments and they have been going on for some time.

    For the sake of argument, let us suppose it is not contamination. What then? What would that mean?
  3. RedRuth

    RedRuth Senior Member

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    Who's Jace? The WPI do use LNCap cells, it's in their methods section of the Science paper, they also use the VP62 construct. Anyone who's ever done PCR will tell you the easiest way to contaminate it is with a plasmid.


    Ok, from what point of view? If XMRV is present in the Human population then it's a potential problem. But you have to remember that correlation doesn't imply causation. Do you mean, if it's in the population how could it be a factor in ME?
  4. currer

    currer Senior Member

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    Redruth I have tried to be helpful to you as you are not a patient and seem to have come recently into this debate.
    But I cannot repeatedly go over things that have been discussed here before. I am afraid it is tedious - and not just tedious for me but for others reading this thread too.

    Can I politely suggest that you read some of the earlier threads and get your information from them?
    There is a lot of information archived on this website, I am sure you will be able to find what you need.
    Correlation and causation, how XMRV could be a factor in ME have been discussed at great length before. There is a useful video of the JM talk on XMRV I think it was the Prohealth one. You might like to start there.
  5. RedRuth

    RedRuth Senior Member

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    All I'm trying to do is understand what you mean by this question and then answer it

    I thought you might mean, what would that mean to people like me who work with cell cultures, I don't know, you're not very clear. If you mean the wider context then I don't know and I'm not qualified to comment. I try to confine my opinions and comments to subjects I have some understanding of.
  6. currer

    currer Senior Member

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    I think you have made a useful point there.
    We do need to debate the implications of the contamination problem, and by we I mean the wider public, not just a small scientific elite.
    Why? Because decisions made by scientists affect us all, as do mistakes. Those who pay for the mistakes may not be those making them. Profit and loss from scientific innovation is not evenly distributed in society and important decisions are made on scientific subjects by politicians who do not necessarily have any more scientific background than those here, and who will be subject to pressure from lobbies who have significant financial interests in a decision.

    Why do you express such reluctance when asked to think about the wider implications of your scientific work? This may be speculation, but is speculation forbidden once one starts work in a laboratory?

    Concern has been expressed about the XMLV contamination by virologists too, so it is a valid concern as can be seen from my previous post with quotes from the CROI conference.
  7. ukxmrv

    ukxmrv Senior Member

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    Redruth,

    The WPI do use LnCAP cells and I have checked with them and discussed this with them previously. It was one of the first things I thought about in 2009.

    The WPI do not have contaminated LnCAP. There is no argument that some labs have been careless and some contamination has occurred. No one has any problem with this.

    The WPI LnCAP is not contaminated, they do run regular checks. Harvey Alter has been running checks for contamination - he's clear.

    Dr Hanson said that she has checked for contamination and she is clear. So that's three groups that have searched for contamination and stated in public that they cannot find it.

    I can't understand why this is still a problem. If it is not contaminated then it is not contaminated.

    We need to move on and work out

    1. How did the virus get into the patients

    2. Is it in any way causal for symptoms that patients have

    3. How do we treat it
  8. RedRuth

    RedRuth Senior Member

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    Well, stating they're clear is easy but clear of what exactly? What did they look for? And how did they do it? There's also the fact that they've used the VP62 plasmid in their lab and their submitted sequences look just like VP62 sequences.

    Move on from what? The contamination question certainly hasn't been answered yet.

    I think we have to establish 1. before trying to answer 2 and 3. I think where we're talking at cross purposes on this thread is that you're taken 1. as a given whereas I would say the jury is still out.
  9. currer

    currer Senior Member

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    Here we go, back to the beginning again.
    Redruth, you are arguing that XMRV has to have the characteristics of a wild, replicating virus.

    Such a virus has been found by Switzer http://www.plosone.org/article/info/:doi/10.1371/journal.pone.0019065#abstract0

    But if XMRV is being introduced into the population by artificial means as suggested by Gkikias Magiorkinis, you do not need the same evidence of mutation. http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(11)70081-0/fulltext?...

    So here you have both types of evidence available, but you will not accept either. If Switzer found any XMRV, and he believes he has, then XMRV is in the human population as a wild, replicating virus.
    If he is wrong, you still have a plausible hypothesis as to how XMLVs could have transmitted from Magiorkinis especially as his hypothesis has been supported by the further paper on widespread contamination of cell lines by Zhang et al.

    Are we missing the obvious here? XMRV is a lab created virus. To find ANY ANYWHERE is highly disturbing and should be seriously investigated.
    Even unconnected with ME, even benign, this virus should not be in people at all. It is an artificial virus created from mouse zenografting.

    Please stop arguing with us and go to the papers themselves. If you disagree, write to the authors of those papers. If you really wanted to find out more you would show some evidence of reading the references we give you.

    I think what worries me most is the rush to stifle debate and scientific enquiry on this matter.
    Redruth, you seem very threatened by the implications of this research too, if it is correct. Arguing with us wont stop it.
    The publicity about XMRV is that it is over. That is what the public is told.
    But the science shows that so far it is not disproven.
    I want the WPI and all the other researchers, good, reputable scientists to be given the opportunity to prove their case.
    People on this website understand the political motivation to stifle this work.
  10. ukxmrv

    ukxmrv Senior Member

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    Redruth,

    But the contamination question has been answered by the WPI, Lo/Alter and Dr Hansen. They have all said in public that they have tested for contamination and it is not there.

    That's why we should be moving onto causality.

    We can't go around believing one side of the story and not the other. Unless Coffin and co can prove contamination then we need to move on.
  11. currer

    currer Senior Member

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    This is called - placing an unreasonable burden of proof onto the proponents of an hypothesis.

    ANY hypothesis can be destroyed if an ever increasing burden of proof is placed on one side and not the other.

    Why should Dr Coffin be able to freely claim "contamination" and have this universally accepted when his own theory is so weak, while the WPI cannot get their papers published, no matter how much evidence they put forward?
  12. RedRuth

    RedRuth Senior Member

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    Well that' easy for them to say, other research has called this very much into question.


    Which is why I'm saying the jury is still out. There has to be a reason why the ME/XMRV results aren't reproducible, the most likely reason at the moment is contamination. If you want to speculate on the hypothetical transmission of an MLV to the human population then fine. I'd be interested to know how Mikovits thinks a retrovirus that evolved in the lab got into the general population.
  13. RedRuth

    RedRuth Senior Member

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    Gkikias Magiorkinis is saying that IF the results are real and not just lab contamination then the most convincing explanation is that the infection is from a common source and not from Human to Human. I'm not arguing with this it seems a reasonable conclusion.

    EDIT: BTW do you accept then that the phylogenetics data infers it can really only be one of these two scenarios?

    EDIT EDIT: If I can just clarify what I'm trying to say. The subject of the OP is the contamination of cell lines with MLVs and how easy this appears to be (I have made the point elsewhere that I happen to know that prostate cancer cell lines often don't express tetherin, but anyway). This is primarily of concern because of the effect it could have on work using these cells but also as a potential health risk to people (including me) who use these cells. However, infecting a dish of cells is a very different matter to a retrovirus infecting a multicellular organism with an innate and adaptive immune system, especially given what we know about the transmission of retroviruses. A zoonotic source is entirely plausible (given the obvious example of HIV and the fact that about 9% of our genome is of retroviral origin) but doesn't seem to fit the data.
  14. currer

    currer Senior Member

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    Hi Redruth,

    Seems like just you and me here.

    To take your three points in order:

    I. Yes. This is an hypothesis.

    2. No. I dont see why we should limit ourselves to just two scenarios at this stage. It seems a little early. The research is just beginning and I hope this important research, (important for us, but only of theoretical importance to non sufferers like yourself) will not be prematurely curtailed.

    3. Yes, I do understand that there is a difference between infecting a cell line and contamination spreading around the lab in this way, and infection in a living multicellular organism with a normal immune response.

    However the paper we are discussing on this thread expresses clear concern for the health of lab workers and suggests they are tested for antibodies to XMLVs. So the authors must feel there is risk, even if you do not.

    They do not suggest that lab workers could transfer XMLVs to their contacts, so I suppose they assume that the risk of more than a transient infection from contact with tissue culture is small.
    However we do not know for certain, because no work has been done on XMLV infection in people exposed in this way yet.
    This is why it would be nice if the WPI could get on with their research, so that we could find out whether XMLV infection really exists in the population and whether it is a danger to human health.
    I hope you do not want this research to stop.

    The work I have read recently on restriction factors is done in cell lines, though.
    Looking through some of the restriction studies you posted I note that many of the details of the interaction of the virus with the cell are not understood.
    I wonder how much of this research can really be extrapolated to infection in the living organism which would be much more complex, dynamic and unpredictable.
    I think there will be a lot to learn with a new retrovirus (XMRV) and a new host. Just like the early days of HIV. A new virus in an entirely new ecosystem (the human body) for it to evolve in.
    So scientists need to be humble and not make assumptions in this novel situation.

    I seem to remember reading that it is thought that the last time a retrovirus endogenised (XMRV has not done this yet) in us, we were still at the stage of sharing a common ancestor with the chimp.
    There isnt much data yet, lets wait and see.
  15. RedRuth

    RedRuth Senior Member

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    I didn't say there isn't a risk just that it's a very small risk and given the inconsistency of testing I don't see any point in looking for antibodies in people who work with potentially infected cell lines just yet.

    Possibly, but at the moment the only known host of XMRV is prostate cancer cell lines so comparisons with HIV are a little premature.
  16. eric_s

    eric_s Senior Member

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    They have been reproduced. Dr. Alter called Lo et al. "highly confirmatory" of Lombardi et al. in the phone conference after publication, where they talked about the study and reporters could call in. And there have been other groups than this one. Also the CFIDS Association of America has recently posted that there will be more positive (and negative) papers in the foreseeable future.
  17. RedRuth

    RedRuth Senior Member

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    They haven't been reproduced consistently, there are far more negative papers and the sequences from the Lo paper indicate probable contamination http://forums.phoenixrising.me/show...es-Relationship-to-XMRV-and-MLVs-in-Human-DNA plus multiple cell lines have been shown to be be contaminated by MLVs and lab reagents like Taq polymerase are contaminated with Mouse DNA (genomic Mouse DNA has endogenous retroviral sequences that will be picked up by PCR).
  18. eric_s

    eric_s Senior Member

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    I agree that they haven't been reproduced consistently and that there have been more negative papers than positive ones. I don't know why and also i'm no scientist, so i can't speculate on this too much. My guess would be that this virus is very hard to find and that maybe the WPI also deliberately didn't share all the details with everybody. But that's really just a guess and might well be totally wrong.

    The paper in the thread you mentioned is the one by Coffin, i was already aware of it, but i think i never read all of it. I know that this is what he thinks. But other scientists think otherwise. So far i rather believe the other side.
  19. currer

    currer Senior Member

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    Hi Redruth,

    I hope you had a nice weekend.

    You misunderstand my point.

    I was not comparing XMRV to HIV. What I said was that a new pathogen in an entirely new host would behave unpredictably and virologists will not be able to predict what it will do, particularly if they can only rely on data from cell line experiments

    At the moment I am reading the transcripts of some FDA meetings and when they are alone these virologists freely admit that retroviruses exist all the time in their cell lines. Most are not replication competent, but recombination in a cell line is possible.

    Please do stop reiterating the same argument that the WPI cannot do its tests right..
    Why are you so afraid of admitting that cell lines will be contaminated? Virologists themselves admit this and the paper we are discussing found XMLV contamination in a quarter of the cell lined tested.

    It is entirely possible that this "contamination" has got into humans and could cause disease.

    If such a thing were thought possible we should investigate it properly because it would pose a new risk.
    It seems highly irresponsible to argue that a potentially dangerous event should be prematurely dismissed.
    I cannot understand why you want to stop us thinking about this.
  20. RedRuth

    RedRuth Senior Member

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    It's not a matter of getting the tests wrong (though they should probably get themselves a qPCR machine) it's that they're picking up contamination.

    I'm not! I know they are, I have a cell line in the lab that's contaminated with an MLV. I've read the Paprotka paper on the origin of XMRV and the paper that's the subject of this OP, in fact it's possible it's these contaminated cell lines that have caused contamination at the WPI.

    It's possible but unlikely, I'm not unduly worried about it in fact I'm more concerned about the Human tissue and blood samples we get in the lab than the cell lines. It's something we should take into consideration but I'm not going to rush off and get a dubious test done for antibodies or viral DNA.

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