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Retrovirology Publishes Five Papers on XMRV and Contamination

Jemal

Senior Member
Messages
1,031
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...
 

Cort

Phoenix Rising Founder
Of particular interest in this paper is the observation that hypermutation by APOBEC3G is much more prevalent in the cell line versus patients (81 times versus 5). The cell line version of the virus is much more evolved and damaged than prostate cancer XMRV isolates.

They did not discuss the possibility that such ubiquitious XMRV contamination might be itself a source of infection, originally from the cell line 22Rv1, but since this was derived from still earlier cell lines it is hard to say when this all started.

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.
 

Marty

Senior Member
Messages
118
"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.
 

urbantravels

disjecta membra
Messages
1,333
Location
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
Contamination May Have Marred XMRV Studies

Previous studies identifying the murine virus XMRV in patients with chronic fatigue syndrome and prostate cancer may have used contaminated reagents or clinical samples, researchers said.

Four new studies published online in Retrovirology have found that contamination is rampant in laboratory cell lines and tissue samples analyzed in the hunt for XMRV.

...

In an accompanying commentary, Robert A. Smith, PhD, of the University of Washington in Seattle, said the initial studies linking XMRV to chronic fatigue and prostate cancer must be reassessed.

"Collectively, these results cast serious doubts on the PCR evidence used to support claims of murine leukemia virus-related viruses in prostate cancer and chronic fatigue syndrome patients," he wrote.

On the other hand, another prominent XMRV researcher who was a coauthor on two of the Retrovirology papers told MedPage Today in an email that it would be premature to discount the original studies.

"The argument for lab contamination as a source of XMRV is subtle and indirect, and not, in my opinion, conclusive," said John Coffin, PhD, of Tufts University in Boston.
 

Cort

Phoenix Rising Founder
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

The authors went on to compare all XMRV sequences with that of the virus from 22Rv1 cells. The results indicate that XMRV sequences from patients are interspersed with sequences derived from 22Rv1 cells. Furthermore, the virus from 22Rv1 cells is ancestral in evolutionary terms to patient-derived XMRV sequences. There is more nucleotide diversity in viral sequences from 22Rv1 cells than in all the patient XMRV sequences.

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.
 

camas

Senior Member
Messages
702
Location
Oregon
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

But didn't Lo and Alter find that the virus in blood samples from Dr. Komaroff's patients had mutated as one would expect?
 

George

waitin' fer rabbits
Messages
853
Location
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!
 

Cort

Phoenix Rising Founder
Here's the MedPage Today Report

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

Contamination May Have Marred XMRV Studies

By John Gever, Senior Editor, MedPage Today
Published: December 21, 2010
Reviewed by Dori F. Zaleznik, MD; Associate Clinical Professor of Medicine, Harvard Medical School, Boston.
Earn CME/CE credit
for reading medical news


Previous studies identifying the murine virus XMRV in patients with chronic fatigue syndrome and prostate cancer may have used contaminated reagents or clinical samples, researchers said.

Four new studies published online in Retrovirology have found that contamination is rampant in laboratory cell lines and tissue samples analyzed in the hunt for XMRV.

Moreover, DNA sequences used to identify XMRV in samples in previous studies apparently are not specific to the virus, but are also present in other mouse viruses and possibly the mouse genome itself, one of the studies suggested.Action Points
Explain that four studies now raise questions about earlier findings that XMRV, a retrovirus, is associated with chronic fatigue syndrome and prostate cancer; one study suggested that XMRV sequences are found in mouse cell cultures or perhaps even in the mouse genome.

Note that the studies raise the question of whether PCR kits might be contaminated, and whether specimens might have been contaminated with mouse cell culture during testing, but conclude only that previous findings should be reassessed.

"Whilst our observations cannot conclusively prove that XMRV is not a human pathogen, they appear consistent with the hypothesis that XMRV is not an exogenous virus transmitting among individuals," wrote Greg Towers, PhD, of University College London in England, and colleagues in the most extensive of the four papers.

Studies suggesting that XMRV may cause chronic fatigue syndrome have sparked excitement in the patient community and controversy among scientists, particularly because attempts to replicate them at other laboratories have largely failed.

Earlier, researchers had linked the virus to prostate cancer.

The possibility that the original studies had been marred by contaminated samples had been raised as a potential explanation for the discordant results, and these new results clearly bolster that case.

Among the damning findings by Towers and colleagues: XMRV genome sequences appear more diverse in cell culture than in patient samples, contrary to what would be expected for viruses that transmit among individuals.

"Even under the most conservative hypothesis that XMRV undergoes almost no evolutionary change upon transmission, we would expect sequences sampled from geographically-disparate individuals, with no known epidemiological linkage, to exhibit more diversity than sequences derived from a single infected cell line," Towers and colleagues wrote.

Instead, they suggested, the XMRV clones identified in previous studies probably originated in a prostate cancer cell line called 22Rv1. Genomic analyses of different sequences failed to identify any patient-derived sequence that could have served as an ancestor for the others.

A Bayesian statistical analysis of probable ancestries pointed to a cell-derived sequence in every one of 3,000 trials. "The estimated posterior probability that the ancestor of the cluster was not a cell line-derived sequence was <0.001," Towers and colleagues reported.

They also argued that laboratory cell lines often become contaminated with murine leukemia viruses, the family that includes XMRV, as a result of such common practices as passaging them through mice or co-culturing them with mouse cells. They analyzed 411 tumor cell lines from a standard collection, including a range of tumor types, and found murine virus sequences in several of them.

In addition, Towers and colleagues screened different mouse strains with polymerase chain reaction (PCR) primers reported to be specific for XMRV sequences, finding that these sequences could be amplified from many of them.

Along with other data, the researchers suggested that these supposedly XMRV-specific sequences are probably contained in other mouse viruses, or even the mouse genome itself.

The three other Retrovirology papers also reported evidence that cell lines and clinical samples contain non-XMRV genetic material that produces positive results when tested with PCR primers thought to be specific for XMRV. One of the reports suggested that the contamination affected PCR reagents for XMRV testing, rather than the samples.

In an accompanying commentary, Robert A. Smith, PhD, of the University of Washington in Seattle, said the initial studies linking XMRV to chronic fatigue and prostate cancer must be reassessed.

"Collectively, these results cast serious doubts on the PCR evidence used to support claims of murine leukemia virus-related viruses in prostate cancer and chronic fatigue syndrome patients," he wrote.

On the other hand, another prominent XMRV researcher who was a coauthor on two of the Retrovirology papers told MedPage Today in an email that it would be premature to discount the original studies.

"The argument for lab contamination as a source of XMRV is subtle and indirect, and not, in my opinion, conclusive," said John Coffin, PhD, of Tufts University in Boston.

One of the first researchers to link XMRV to chronic fatigue rejected the suggestion that those results were now in doubt.

"Nothing that has been published to date refutes our data," said Judy Mikovits, PhD, of the Whittemore Peterson Institute in Reno, Nev., in a statement.

The statement noted that those data included evidence that patients' serum contained antibodies to XMRV proteins. It also insisted that cell lines and clinical samples used in the institute's studies could not have been contaminated.
 

Cort

Phoenix Rising Founder
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?

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...
 

George

waitin' fer rabbits
Messages
853
Location
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.
 

August59

Daughters High School Graduation
Messages
1,617
Location
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"
 

August59

Daughters High School Graduation
Messages
1,617
Location
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!!
 
Messages
27
Location
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.
 

Crappy

Senior Member
Messages
113
Location
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".

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 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
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
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!

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'? ;)
 

George

waitin' fer rabbits
Messages
853
Location
South Texas
Snort, grins

BTW, George, what is a 'fuster cluck'?

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
 

WillowJ

คภภเє ɠรค๓թєl
Messages
4,940
Location
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.