1. Patients launch $1.27 million crowdfunding campaign for ME/CFS gut microbiome study.
    Check out the website, Facebook and Twitter. Join in donate and spread the word!
Join the National PR Campaign for ME: Power to the Patient (P2tP)
Have you had enough of all the neglect and abuse of ME/CFS patients? Gabby Klein says now is the time for a National PR Campaign for ME/CFS to impress a change. Join the Patient Revolution to restore power to ME patients ...
Discuss the article on the Forums.

Retrovirology Publishes Five Papers on XMRV and Contamination

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

  1. Jemal

    Jemal Senior Member

    Messages:
    1,031
    Likes:
    60
    Journalists have become more and more lazy over the years. The internet is not helping, a lot of websites are parroting each other.
    What isn't helping either are the large press agencies, selling their stories to news outlets. You will see a lot of the same reports on different news outlets, because they simple bought the story and didn't find out for themselves what the story is about. It's all a time and money issue.

    So much rehashed content...
     
  2. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    441
    Raleigh, NC
    One paper found a prostate cancer cell line from 1990 that was producing XMRV. the researchers said he was astonished to find that. The thing was was that the XM RV that it was producing looked like it could have been the ancestor of the 22RV1 cell line. That prostate cancer cell line had been passaged through mice many times and it's been clear for decades that cell lines that pass through mice can pick up viruses. What was really disturbing was how similar that 1990 virus was to the 2008 virus...if the virus had been living out in the human population for that long it should've changed substantially but apparently it had not. Then the WPI reported that their virus was 98% similar to the prostate cancer virus

    This was one of Hue's arguments -and the one that really got me because I studied population genetics in college; Hue is saying that genetically speaking this virus does not look like it's been in humans for very long. ON the other hand the fact that it has been found from samples around the world now would suggest, that if it is not a 'contaminant', then it has been in humans for quite a while; ie it's not slowly spreading in a localized area - it's spread far and has encountered many different humans and it should show, as Hue put it, the scars of those encounters.

    Maybe they just haven't looked at enough samples. I don't know if Hue is going from the five ir six samples from the WPI or if he has a larger sample base. Five or six really wouldn't tell you anything statistically. Its easy to get sampling error from that few.
     
  3. Marty

    Marty Senior Member

    Messages:
    117
    Likes:
    17
    "As you likely saw, there were lots of headlines yesterday saying scientists have found XMRV is not related to CFS. Below are 4 quotes from key scientists and/or news articles (Wall St Journal) stating that XMRV's link to CFS is not dead."

    Great work again, Rivka. When you are awake, you are great. I'd make one change: "not dead" could be "very much alive".

    Good posts from several people. Thanks for your efforts.

    If people want to say thanks to WPI, money speaks louder than words. If people are still wanting to know what to get you for Christmas, birthday, or ask what they can do for you, ask them to contribute to WPI.
     
  4. urbantravels

    urbantravels disjecta membra

    Messages:
    1,333
    Likes:
    507
    Los Angeles, CA
    Medpage Today has published a more nuanced article (we are now seeing *somewhat* more balanced coverage than we were yesterday, when multiple outlets did nothing more than uncritically repeat the "conclusions" drawn by the Retrovirology papers) and check out the quote from John Coffin.

    http://www.medpagetoday.com/InfectiousDisease/GeneralInfectiousDisease/24006
     
  5. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    441
    Raleigh, NC
    The Hue paper is the big problem. It's kind of a weird way to get at it - through evolutionary genetics - as Coffin notes its indirect and subtle - but the genetic evolution of populations and organisms has been well studied.

    From Raccaniello's blog

    Parent populations always have more genetic variation than the populations that spread from them. That's one way they know that we all came from Africa; the genetic variation in Africa in humans is many times genetic variation found in any other continent.

    As I noted in the above blog - if XMRV is an infectious agent spreading in humans it should be highly variable and it should certainly be much more variable than a cell line developed and maintained under very strict laboratory conditions.

    It should also be quite distinct but when they do this kind of ancestral genetic analysis - which they do in populations all the time - to determine where they come from - they found that it appears that XMRV actually came from this cell line. For our purposes XMRV should've looked like it came from a mouse somewhere - but it looks ike it came from this cell line developed in research labs.

    The WPI did do a phylogenetic analysis for the science paper and that analysis suggested that XMRV did not come from inbred laboratory mice. They did the right thing and they followed where the evidence lead them. That analysis was another important check on their results. If Hue turns out to be correct they can't be blamed for missing this.

    As Coffin notes these are 'subtle and indirect' arguments; Hue can't say that XMRV is a contaminant - because he hasn't searched the WPI stocks or samples or whatever for them - all he can say is that XMRV looks like what he would expect to see if it was a contaminant....It's indirect argument...

    Hue is, however, a population geneticist specializing in retroviruses. One of the things he does is determine where viruses come from and what effect their variations have on disease course, etc. He's done alot of work on HIV. Here are some of his papers

    • Schaller T, Hu S, Towers GJ. (2007) An active TRIM5 protein in rabbits indicates a common antiviral ancestor for mammalian TRIM5 proteins. J Virol. Nov; 81(21):11713-21
    • Mens H, Pedersen AG, Jorgensen LB, Hu S, Yang Y, Gerstoft J, Katzenstein TL. (2007) Investigating signs of recent evolution in the pool of proviral HIV type 1 DNA during years of successful HAART. AIDS Res Hum Retroviruses.Jan; 23(1): 107-15
    • Hu, S, Clewley J, Pybus OG. (2005) Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. P.N.A.S. Mar; 102(12): 4425-9
    • Hu, S, Clewley J, Cane PA, Pillay D. (2005) Investigation of HIV-1 transmission events by phylogenetic methods: requirement for scientific rigour.AIDSMar; 19(4):449-50. Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-nave individuals..

    It's the cumulation of negative findings that are hammering XMRV right now; the Hue paper suggests it's derived from a cell line, the Huber and Robinson papers indicate that contamination is more of an issue than previously thought and that some methods of detecting it are not as good as has been thought. Plus there's been the difficulty of replicating the original result by a completely independent group.

    XMRV is not over - as Lipkin pointed out PCR isn't everything and others in the retrovirology community agree. And Coffin is not convinced either - all we have are inferences - there is, as yet, no conclusive evidence that it is a contaminant. Thankfully two really important studies - the Lipkin and BWG studies will continue - they are not convinced.

    It's interesting that the Singh study is using an entirely different assay to look for the virus - that's a whole new element. Bagni at he National Cancer Insitute thinks she has an antibody test that is specific for XMRV - that would be a huge breakthrough in detection. So there are important studies out there that could change the picture.
     
  6. camas

    camas Senior Member

    Messages:
    697
    Likes:
    196
    Oregon
    But didn't Lo and Alter find that the virus in blood samples from Dr. Komaroff's patients had mutated as one would expect?
     
  7. George

    George waitin' fer rabbits

    Messages:
    846
    Likes:
    44
    South Texas
    The interesting thing is that the sequences they are talking about are only the ones listed in the WPI paper and the VP62 clone. There are literally hundreds of sequences that haven't even been looked at so how do they know that there is not more genetic diversity involved?

    In addition in focusing so narrowly on these few sequence sets they have completely left out the both the sequences done by the FDA/NIH as well as ignoring the conclusions regarding the mutations observed by Dr. Alter and Dr. Lo between the blood drawn from 15 years ago and the blood draw during the study.

    As has been pointed out again and again the science really hasn't hurt the forward momentum of the possibility of the HMRV as a potential causative agent for ME/CFS. What has hurt us over and over again is the incredibly well orchestrated fuster cluck by members of the British Scientific community and their press releases that have flat out lied over and over again. I feel like it's 1776 and we are in the fight for our lives!
     
  8. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    441
    Raleigh, NC
    Here's the MedPage Today Report

    http://www.medpagetoday.com/InfectiousDisease/GeneralInfectiousDisease/24006

     
  9. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    441
    Raleigh, NC
    I would think these could loom large...If I understood the BWG correctly the WPI said that they sequence every positive result to ensure that it is was really XMRV? I imagine they just sequence that portion of the gag gene, though, but it would be a huge help to them right now if they could provide evidence showing that XMRV is much more variable than is thought.

    I just looked at the Hue paper: this is what they looked at

    • CFS - 2 full-length samples
    • pol sequences from prostate cancer - 6
    • sequence from 22Rv1 cell line - 1
    • endogenous MLV sequences - 46
    • DG 75 complete genome sequence - 1
    • full length MLV sequences from VP 62 - 28
    • murine C retrovirus - 1
    • MLV complete genome sequence - 1
    • Moloney MLV - 1
    • AKV MLV - 1

    So there were only two XMRV CFS samples - not alot! There was a wide variety in sample numbers - most samples of any virus type were very low and a few were very high; why that is is unclear. It would seem a really good idea, though, for the WPI to get more complete sequences out there. They did 2 1/2; just doing 5 or 10 more, I would think would be really helpful in assessing the genetic heterogeneity...
     
  10. eric_s

    eric_s Senior Member

    Messages:
    1,925
    Likes:
    73
    Switzerland/Spain (Valencia)
    Very good point, George, it seems they have only looked at XMRV from two studies, as it says in this paper http://www.retrovirology.com/content/pdf/1742-4690-7-112.pdf on page six (top). So you say from the Urisman et al. paper they only looked at VP62? Is such a small number of sequences enough to reach a conclusion about where the origin is?
     
  11. George

    George waitin' fer rabbits

    Messages:
    846
    Likes:
    44
    South Texas
    No (grins)

    This is a pretty fast answer to a question that doesn't have enough science completed and published to be looking at these kind of rebuttals.
     
  12. August59

    August59 Daughters High School Graduation

    Messages:
    1,483
    Likes:
    408
    Upstate SC, USA
    It's interesting that the Singh study is using an entirely different assay to look for the virus - that's a whole new element. Bagni at he National Cancer Insitute thinks she has an antibody test that is specific for XMRV - that would be a huge breakthrough in detection. So there are important studies out there that could change the picture.

    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

    Because of ME/CFS being ignored by government agencies and the medical profession (most, but not all) for so long we now have a very large number of very sick patients. Far more than any other disease that I can tell. It is borderline "inhumane that these studies are not published". The antiviral position taken by many in the medical profession is the same situation. The thought to not administer antivirals, to a wanting very ill patient, because it doesn't serve as a reliable statistic to further clinical trials is inhumane. Get these very sick people on a road recovery by whatever means. There are plenty of us that can serve in the clinical trials, if we ever get any.

    Furthermore the government should cover these expenses due to their neglect and corruption for the last 40 years. Most of the very ill have spent 50,000 or 100,000 or more pursuing a relieving treament (not just a cure). They are now bankrupt and can't afford anymore treatment and by no fault of their own. If the government had handled this correctly in the beginning these people would not be suffering and bankrupt.

    The NIH should purchase every pending study from reputable researchers and publish a book and give the proceeds to help PWC that need it!

    Okay, I feel better now!! Hope everyone has a "Merry Christmas"
     
  13. August59

    August59 Daughters High School Graduation

    Messages:
    1,483
    Likes:
    408
    Upstate SC, USA
    It's a growing problem!!

    Based on new CENSUS figures (308.1 miilion) there are now 21.56 million healthy people in the US infected with (or carrying ?) XMRV!!! :eek::oops::eek:

    Where does that put the ME/CFS population? Add in fibromyalgia? Add in breast cancer? Add in MS? Add in Autism? Add in prostate cancer?

    It is all pretty nauseating, to say the least!!! The picture here is pretty bleak, but the worst part is that it should have never made it this far

    The bright side!! Where would we be if Dr. Judy Mikovits had not gotten involved with the NCI and Cleveland Clinic study. Can't quite remeber, but the odds of CFS patient blood samples being included in a prostate cancer study seems like long odds! Who would of thought!!

    Merry Christmas!!
     
  14. Revday

    Revday

    Messages:
    27
    Likes:
    0
    Atlanta, Georgia
    We need more links to journalists andf build a network of Dr.'s that will quickly and widely refute this political kind of horse play. Maybe someone will be well enough to follow the money and find who or what is behind these efforts to dismiss ME/CFS as legitimate? I know... I know... something that has some C's and a D in it. Great thread.
     
  15. pamb

    pamb Senior Member

    Messages:
    168
    Likes:
    20
    Edmonton, AB, Canada
    Ditto everything August59 said :thumbsup:
     
  16. lancelot

    lancelot Senior Member

    Messages:
    324
    Likes:
    2
    southern california
    Yes it did
     
  17. Crappy

    Crappy Senior Member

    Messages:
    110
    Likes:
    9
    TX
    I beg your indulgence, I realize this is not the present topic, however, the current subject is a part of the parent topic "Chronically Inadequate Funding".

    The post from August59 struck a reoccurring chord. In an effort to gain visibility for the need to act, I elected to post here, along with other actions. I see several others here advocating action to foster change. I don't know if we can act concertedly, but we need to.

    A portion of my rant in parallel with August59's statement:

    I protest the disproportionate diversion of resources to national security, drawing away from other deadly issues like food, water and disease. The FDA, CDC, NIH and nongovernmental organizations including the AMA are ineffective bureaucracies that have become impotent and highly political. Failing to disband these organizations will likely cause such a drain on resources; proportional to contributions, society will collapse down to a less advanced form, weakening civilization. Simple minded over-commitment of resources to Military Might ignores other serious, but far more deadly threats to existence. In fact, the vast majority of people die from causes other than war or violence. Currently my life’s value is nothing even close to a violent persons’ who receives unlimited Gov. Funds, for example, bin Laden; absurd.

    Presently a perverted motivation exists globally to exterminate others that are not like minded. Those of us stricken by chronic illness have been betrayed by our fellow citizens. The minority members of the world; violent, angry and dogmatic are SOCIOPATHIC MANIACS bent on dominating and controlling everyone worldwide. Why do we let our leaders continually revisit this same tired agenda (build society-inflated egos tear society down; build society-inflated egos tear society down; endless loop…). Famously quoted; failing to recognize these historical disasters, dooms us to repeat them. Haven't we repeated this loop enough yet? Society at large is behaving like mindless Lemmings, allowing the agenda of the Fear/Defense complex to dictate the direction of society. Disproportionately allocating resources to the Science of Killing rather than the Science of Advancing Humanity.

    Spending for defense in 2009 was $494 Billion, AIDS research spending was $3 Billion, and spending on my type illness, Chronic Fatigue, research was $3 Million! As this catastrophic illness gains understanding, the affected population is predicted to be much larger than HIV, but comparatively only receives one tenth of one percent (%.1) in research spending. It is predicted to be a much larger killer than previously realized (implicated in heart failure and numerous other energy related illnesses) killing considerably more people than war, yet funding for stopping this killer is so miniscule it cannot be compared to defense spending (six ten thousandths of one percent, %.0006), paltry insurance.

    Hope no one takes offense.
    Merry Christmas
     
  18. Bob

    Bob

    Messages:
    8,912
    Likes:
    12,618
    South of England
    Yes, that's what I've been thinking...

    Judy has reportedly found a number of XMRV strains now, but hasn't published anything about them yet, as far as I know.

    Wouldn't it make sense that the first XMRV strain that she discovered in ME patients was the most similar to the original strain of XMRV that was found in prostate cancer patients? After all, this is the strain that she was looking for?

    I don't know how different the various strains of XMRV are from each other, but it might satisfy the questions posed by the Hue paper.

    Did Judy first detect XMRV that had a low genetic variability, and then later she detected XMRV with more genetic variability?

    All the details of the science are beyond me here, but it seems that the Hue paper just raises more questions for us, as usual, than actually giving us any answers.

    Did the Hue paper actually detect any XMRV at all, or are they just denying the existence of it altogether? If they didn't isolate or sequence XMRV, or whatever MLVs they think they detected, then it seems like a weak study.

    XMRV has been genetically sequenced, and it is not mouse DNA, so doesn't that answer the question about XMRV being a mouse DNA contaminant? Hasn't the DNA/RNA of XMRV been checked against all of the mouse genomes that the Hue study looked at? If not, why not? Isn't this contamination issue as simple as that to answer?

    Questions Questions Questions, but very few answers.
    Let's hope that we have some better answers during 2011, because 2010 has been a bit of a disappointment for us hasn't it?
    I had really expected that we'd have a few answers by the end of 2010.


    oh, I'm just catching up with the thread, and realise that I've just repeated a load of stuff here!


    BTW, George, what is a 'fuster cluck'? ;)
     
  19. George

    George waitin' fer rabbits

    Messages:
    846
    Likes:
    44
    South Texas
    Snort, grins

    What bad people do to good chickens. (grins)

    I keep reading the Hue paper and I know something is off but I haven't figured it out yet. Maybe tomorrow. There is something that just keeps nagging at me. But on another note I like Crappy's rant. I'm in a bit of a ranty mood myself. I am just so tired of politics trumping the science. As for the lovely well orchestrated attack this holiday season I was looking at information regarding Wellcome Pharma company. They have been absorbed by Glaxo and Smith Kline since then but here is an interesting diagram from 1994 that shows just how easy it is to get everybody in bed together. even the chickens. (grins)

    wellcome-trust.jpg
     
  20. WillowJ

    WillowJ Senior Member

    Messages:
    3,149
    Likes:
    2,851
    WA, USA
    http://www.latimes.com/health/ct-met-chronic-fatigue-xmrv-20101220,0,5986876.story

    LA times is quoting PR. They selected only discouraged quotes. The reporter's email address is available.

    They misrepresented the Lo/Alter/Komaroff paper again. That seems to be their favorite meme at LA Times. Maybe if someone has time, they could pull the quote out of the PNAS paper which specifically states the paper confirms Lombardi et al. and email it to the reporter and to the editorial board, and maybe someone who is registered there could post it there as well (someone already posted a nice response but didn't say this in particular).

    They published Mikovits' conclusion but nothing about proteins or antibodies, reducing this to "multiple ways." No UW citation like in Amy DM's article, either.

    I'm sorry; I have some other projects and don't have time to deal with this.
     

See more popular forum discussions.

Share This Page