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Recombinant Origin of the Retrovirus XMRV (2nd Science article)

Discussion in 'Media, Interviews, Blogs, Talks, Events about XMRV' started by Jemal, May 31, 2011.

  1. Jemal

    Jemal Senior Member

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    http://www.sciencemag.org/content/early/2011/05/31/science.1205292.abstract
    http://www.eurekalert.org/pub_releases/2011-05/nci-oox053111.php

  2. Mark

    Mark Acting CEO

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    So as we suspected, the major new publications that were anticipated are just the work of Coffin et al that we knew about several months ago, and there is no new evidence presented here. Moreover, putting aside the deeper scientific arguments about the sequence identity, both the paper's conclusions and the press reports make wild speculative leaps with no supporting evidence, and this illogicality demands distrust.

    This paper claims to show that it is likely that XMRV - indisputably a novel human retrovirus - was created in the laboratory, unintentionally. It shows how XMRV probably got into human prostate cancer cell lines.

    These findings clearly do not imply the conclusion that the authors drew:
    "our results suggest that the association of XMRV with human disease is due to contamination of human samples with virus originating from this recombination event". As I've found to be the case almost universally with papers from those opposed to the concept of an XMRV-CFS connection, the last sentence of the abstract in no way follows from the rest of the paper, and merely demonstrates what the authors wanted their results to show.

    Finding the recombination event during which XMRV was created, and showing its presence in widely-used prostate cancer cell lines, does not imply that "the association of XMRV with human disease is due to contamination". It should not be necessary to spell out this latest illogical leap of faith, but I'll just observe that the authors are positing that somehow human samples got "contaminated" with the virus, rather than humans themselves getting "infected" with it, though there is no evidence presented as to how this transmission of XMRV may have occurred, nor why it affected the samples taken from patients and not those in healthy controls.

    The argument seems to run like this: We have tracked down the origin of XMRV. It is indeed a novel human retrovirus. It was created in the laboratory by mistake in about 1992. It is now present in cell lines that are widely used all over the world. Therefore it can't be associated with human disease, and any detection of it must be contamination, because...why, exactly? Because it was created in the laboratory? And because the idea that retroviruses created accidentally in the laboratory could be harmful to humans is just...unthinkable?

    It's also going to be very noticeable, I expect, that the news reporting of this story will show no interest in the revelation that novel human retroviruses are routinely created in the laboratory by accident and spread around the world through unknown means. This was news to me, and it seemed significant...but the media doesn't seem too bothered. Eurekalert seems to show no interest in this point. Instead, it leaves the last word to Pathak:

    "due to the time and resources dedicated to the understanding of this virus by researchers at NCI and NIH as well as others, scientists can now concentrate on identifying the real causes of these diseases".

    What on earth does that sentence even mean?!

    It would be lovely to dream that scientists really are going to "concentrate on identifying the real causes of these diseases" - or, at the very least, to investigate these diseases in some fashion. But that just sounds like more pie in the sky to me: I'll believe it when I see the money going in and when I see serious research into "these diseases" begin at long, long last. Until then, that garbled sentence of Pathak's will imply to me a confused attempt to construct a logical argument that XMRV was created in the lab, by mistake, so it can't be very important, and we should all just ignore it now and return to business as usual.

    If that 'business as usual' included genuine research into ME/CFS, then maybe people with ME/CFS would be more inclined to listen to this sort of stuff with greater respect.
  3. Bob

    Bob

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    Great post Mark,

    Yes, their conclusions are too simplistic.

    The authors believe that the same combination event is highly unlikely to have happened on two separate occasions, so that XMRV could only have been created in this cell line.

    But that is only a belief, or a calculation of probability (I don't know the details), and not a known fact.

    They also believe that the virus could not have escaped the lab into the wild, but again, that's only a belief, and it could have escaped in a number of different ways.

    Some of the thinking behind the contamination theory is that there is not enough variety in the known XMRV sequences, but new sequences are being found all the time, including by the CDC. But even if there wasn't much genetic variety, this might only suggest that the virus behaves differently to other known retroviruses or that we haven't discovered the entire range of XMRV-like viruses yet, or that the virus spreads through another route, other than infection, such as through vaccines.

    This paper is a bit out of date now, because even the CDC are finding XMRV in the wild, in prostate cancer patients, and treating it as a human virus.
  4. floydguy

    floydguy Senior Member

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    It reminds me of the OJ Simpson trial.... You must acquit so that OJ can help find the "real" killer.

    When they say this the translation for me is I have a lot pressure to to this f$#^&** work on CFS B&*%$. Now that I've done this half a$$(* study can't I get back to my cushy work on X where people don't pay attention to the nonsense that I produce....
  5. toddm1960

    toddm1960 Senior Member

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    You said a &%#@! mouthfull Floyd.............lol.............i agree 100 &%$@# percent
  6. Cort

    Cort Phoenix Rising Founder

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    The key argument for XMRV being a contaminant has nothing to do with how XMRV was created or where it came from. These people aren't idiots...they know that dangerous viruses can and have been produced in labs before http://news.bbc.co.uk/2/hi/health/3719990.stm

    The key factor is that the XMRV found in the WPI samples is so genetically similar to that found in the 22RV1 lab strain that it simply could not have made it into the human body. If it had made it into the human body it would have shown signs that that had happened.

    If the XMRV samples from the WPI and from prostate cancer samples were more genetically distinct it wouldn't matter where they came from. The fact that researchers can show XMRV was probably produced in a lab in the 90's simply explains things...it helps to tie things together.

    The NCI just posted a statement on their website that they have isolated strains of XMRV from the original samples and those strains, contrary to the WPI's assertion, indicate that XMRV has never entered the human body.
  7. Mark

    Mark Acting CEO

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    But that link is not at all relevant to the significance of the way that XMRV was created.

    The link you give describes a deliberate and controlled experiment in which a flu virus was genetically modified in such a way as to make it deadly. The argument about how XMRV was created says that it turns out that a human retrovirus was accidentally created during a standard laboratory process, and that this retrovirus has spread worldwide through cell cultures, in such a way that many laboratories are contaminated with it...and the precise routes of such contamination remain mysterious.

    Scientists may, perhaps, have all been well aware that standard laboratory work has been creating novel human retroviruses, spreading them around the world, and contaminating laboratory experiments (at least) through unknown vectors, but it was news to me and I think many people would be very interested to learn that this is the case - especially those still curious about the origins of the HIV virus.

    As a general proof of concept, it's surely significant that such previously undetected retroviruses have been created and spread through laboratories in this way...especially to someone who is wondering what might be the cause of unrecognised new forms of neuro-immune disease, and especially to someone who is wondering whether a contaminated vaccine may have been what made them or their child sick.

    But I'll repeat that the implications of the idea that any such retroviruses may have been responsible for human disease, and/or may have been transmitted in vaccines, are so dramatic and unthinkable that they are hard possibilities for scientists to face up to - even though such possibilities are perfectly plausible and demand further investigation.

    This genetic similarity is presumably in reference to the 2.5 XMRV samples that the WPI sequenced fully, and now (but not when the argument was originally advanced as definitive) in reference to the sequences subsequently submitted by the WPI, which do show some variability.

    The argument requires several assumptions, of course: that those 2.5 samples are representative of all the XMRV detected by the WPI; that the specific tests employed by the WPI are not just picking up a well-defined subset of the strains present; and crucially, that if XMRV had made it into the human body it would have reproduced and mutated just as expected, and does not exhibit properties of sequence conservation. There may be a cast-iron argument proving the latter assumption, but I haven't seen it yet, and we do need to see that argument. What I have seen is a convincing assertion that slow-replicating retroviruses, viruses exhibiting sequence conservation properties (as proven for XMRV under APOBEC3 editing), and viruses with short genetic sequences, can be expected to show much lower levels of mutation than other viruses. And it's always made sense to me that a virus defined by such a short genetic sequence is likely to show relatively low levels of variability.

    So while this argument does seem strong, it also seems to be statistical, and based on assumptions, and does not seem at all conclusive to me. Ranged against arguments like the absence of any known vector for contamination of WPI samples, the absence of any evidence of XMRV contamination of any product used by the WPI or other labs that found XMRV, and of course the consistent differential rates of detection between patients and controls, it still leaves a lot of questions to be answered.

    Of course there's a Catch-22 here: the strains of pMLVs sequenced by Lo and Alter are genetically distinct from XMRV - though less distinct than different strains of HIV-1 - and were therefore said to be nothing to do with XMRV. Heads I win, tails you lose?...

    I read that but I didn't see the reasoning behind this assertion. Is that also based on them finding that all the strains they isolated had the same low levels of genetic diversity, or on some other evidence? And did they detect the same kind of variants that the WPI have shown in the sequences recently submitted to GenBank? Those details seem to be crucial to this argument, so I guess we'll need to see those in order to be convinced...


    While I'm on...am I right in saying that the entire question of "mouse contamination" is a complete red herring, and that all those tests for mouse contamination, IAP tests etc, were barking up the wrong tree? Because the contamination that is alleged is from cell lines in laboratories, which are themselves systematically infected with XMRV, and it has nothing to do with mice at all except that XMRV itself was originally created inside a mouse. In which case, I don't understand why Dr Coffin was recently speculating about mice roaming around and carrying lab material from lab to lab on their fur, because his own argument makes that vector for contamination seem quite irrelevant now. And the suggestions that the WPI's labs themselves are contaminated also seem irrelevant, along with all the tests for mouse DNA, because there's no reason at all to suggest that such contamination would be a factor if the XMRV is all supposed to come from cell lines.

    It's been said before and it will be said many times again I'm sure: this will not be over until all the details are fully explored, explained, and accepted by the WPI. Having got so far, the job of explanation should - must - be completed: leaving crucial questions hanging will only fuel a thousand conspiracy theories for decades to come. So the next job for the contamination theorists must surely be to identify the source of contamination in the WPI's process, and to explain the contamination's preference for samples from people with ME/CFS? Given that others have detected XMRV in WPI samples, in multiple labs (including Blomberg's notable detection of XMRV in a WPI sample), it remains the case that the only plausible source of contamination was during the blood collection process, most likely via contamination of the specific type of collection tubes used by the WPI. So XMRV now has to be sought in those tubes: if they contain XMRV to start with then this needs to be understood.

    And critically, what remains to be explained is how the WPI are consistently finding differences in XMRV detection between different groups. Supposing that the tubes they used are all contaminated with XMRV, it would still be possible that some property of ME/CFS patients' blood is responsible for the different levels of detection of XMRV by the WPI. That would be vital to understand and could be a breakthrough in itself. So the absolute bottom line for me remains: the WPI remain solidly convinced that they are detecting different results from ME/CFS patients as opposed to healthy controls, and there is still no reason whatsoever to imagine this is due to incompetence on their part, and so this difference in detection rates demands a full explanation - after everything we've all been through with this, it would be completely crazy to just stop now and walk away from all those unanswered questions.
  8. Bob

    Bob

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    Question regarding Mouse DNA contamination tests, with reference to the Paprotka, Pathak & Coffin preXMRV paper

    Can anyone help me with something that I don't understand?

    In the Paprotka et al. (includes Pathak and Coffin) paper, they detected two endogenous viruses preXMRV-1 and preXMRV-2, which have almost identical genetic sequences to the VP-62 strain of XMRV for over 3.2 kilobase stretches of their genome. The authors propose that XMRV was created by a recombination of preXMRV-1 and preXMRV-2

    The pre-XMRV's are endogenous mouse viruses, and so they will be encoded for in the mouse DNA. So would it not be the case, that if you ran a mouse DNA contamination check on any samples containing XMRV, then the samples would show positive for mouse DNA contamination, because XMRV contains sequences almost identical (99.92% identity) to mouse DNA (preXMRV-1 and preXMRV-2)?

    I don't know much about mouse contamination tests, but I know that they test for mouse mitochondrial DNA. If they only test for mitochondrial DNA, then I suppose that would answer the question.

    Anyone got any thoughts about this?
  9. alex3619

    alex3619 Senior Member

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    Hi Bob, I don't think it works like that. The mouse DNA contamination tests would be looking at specific sequences, not at all sequences. If XMRV or an analog (preXMRVs) were present it probably would not show up. They are looking for either mouse genomes or mouse mitochondrial genomes, not specific DNA sequences of endogenous mouse retroviruses. They probably have select target sequences that are typical of mice and not humans.

    My understanding is that XMRV contamination from a cell line would not show up as mouse DNA.

    Of course it is equally true that if wild XMRV is present in the sample, then it would not show up as mouse DNA.

    The thing about this theory of contamination is that it cannot be easily tested for by any simple test. Two lines of evidence are used instead - which have been discussed at length on these threads. The first is the use of controls - if controls were also being contaminated, you would expect equal probability or maybe a little lower (to account for extra handling). Instead what we see is a lot lower, which does not fit contamination whether by mouse DNA or lab derived XMRV.

    The second line of evidence is genomic variation. Highly similar sequences may indeed be contamination. The problem with this is that this approach is validated on high viral loads, with such low viral loads its almost useless as a single test. Instead, it relies on the accumulated evidence from many tests, from many labs, over time. In the end the genbank sequences may accumulate to the point a pattern is very clear. I think that it is still premature to claim that, as there are so very few attempts at sequencing.

    Several people are also wondering about whether or not XMRV should show a huge variation. We should be looking at HTLV as a model, not HIV. I have not read enough on HTLV to say anything definite, but I think it might have reduced variation.

    We still need the BWG and Lipkin studies, whether you are pro- or anti- the Lombardi XMRV/CFS hypothesis.

    Bye
    Alex
  10. heapsreal

    heapsreal iherb 10% discount code OPA989,

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    Even if the retrovirus was made in a lab, wouldnt antibody tests confirm that the retroviruses has infected humans. Then the boof head who is making these viruses should be shot, can u shoot a government organisation for making viruses?????????
  11. Bob

    Bob

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    Judy has said that some mouse contamination tests (specifically IAP) can show false positives. I wonder if this could be related to my question. I don't know much about the IAP test.

    Also, if a researcher was testing for contamination from MLV's, then wouldn't there also be a chance of XMRV showing positive because XMRV was created by a recombination event from MLV's?
  12. alex3619

    alex3619 Senior Member

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    Hi Bob, isnt the IAP test a mitochondrial test? I do not recall the details. The point of my comments is that such a test should not be positive for XMRV. They still might react to other things. The point of testing for XMRV is that you should pick sequences that are not in common with other MLVs, but it depends on the test used.

    My earlier comment is about mouse DNA, not MLVs. I do expect that testing for MLVs could be problematic. It all depends on what PCR primers you choose, and what assumptions you make - if you rule out the turkey (avian, not the country) MLV-like virus in your selection, and the patient ate a turkey with the sequence for example (I do not know how likely this is, or if turkey MLLVs containing many cross-reacting sequences), very small traces might be detected if there is a partial sequence match. Any PCR primer to be used must be checked against all known MLVs before selection, but I am not sure that is happening.

    BTW, MLLVs are MLV-like retroviruses, an even larger gammaretrovirus family.

    Bye
    Alex

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