William Switzer - CDC looking for XMRV and MLV in lab workers!

[CBS]

CBS
thought Stoye was meaning he'd been testing himself for HIV due ot his reseatch, not XMRV?

That was not my impression. In the tape he says "there are some of us who've been working with XMRV, murine related viruses, I've been doing it for 35 years and I know that I'm negative, at least the last time I looked."

 

[Dr. Yes]

Look at how complex and odd this is. They are still not saying its in CFS patients - the CDC has looked twice for it in CFS patients and has not found - even in the 'real CFS' patients.

That's not true - see the CDC's Phase IIa results from the BWG. They found CFS patient samples positive for XMRV and what they called "MLVs" using two new PCR assays that they hadn't used before. Inexplicably, they immediately afterward abandoned using those assays!

The researchers appear to be leaning to XMRV being a real virus that escaped from the lab which somehow contaminated the WPI's samples but which did not infect the patients.

Whoa, whoa! That's not what they're learning!! Be careful how you interpret science, Cort. There is evidence that it may be a virus that was created in a lab, but that is by no means definitive yet. There is absolutely ZERO evidence that it contaminated the WPI samples. In fact, the vastly different positivity rates between CFS patient and negative control sets in the WPI and other groups' studies is evidence against contamination (that is one of the purposes of having controls, after all). Then there is the issue of the PMRVs and M-PMRVs being found by the WPI, NCI, NIH/FDA, and Hanson at Cornell... those are distinct from one another and from XMRV as defined by Coffin et al. What about those? How many different recombinant contaminants are we talking about?

The WPI can go a long way to proving actual infection by showing that the virus is integrated into human DNA. I honestly don't know why they or Alter/Lo haven't done that yet - that would turn the conversation in a different direction.

You obviously haven't asked them. The reason they haven't yet is because it's really, really difficult in the case of XMRV. There may only be one cell in which integration has occurred out of millions; finding such cells (and finding the virus in those cells and sequencing the provirus and its flanking sequences) takes a very long time, and is a major commitment of laboratory resources. I'm sure they're working on it, but resources are in short supply thanks to a lack of funding, among other things.

 

[Christopher]

Cort, be careful not to give more weight to short-term trends over long-term research (recency effect might be kicking in for you).

Much more research has to be done, and is currently being done, to determine the importance/existence of XMRV. Until such research is conclusive either way (which it is not currently), look for studies to continue to be published arguing both for and against.

It is entirely too soon to say one way or the other how this is going to play.

 

[Cort]

WOW! That's new to me. When do they think that happened? Under what circumstances? And who was responsible?

It was an accident and they believe it happened between 1993 and 1996.

 

[CBS]

Who is talking about entire health agencies?

We're talking about the resources the HIV branch of the CDC has put into XMRV. I say they've put substantial resources into it. You say they've only starting caring about XMRV since they found out their worker might be infected.....I disagree. This is a very specific instance - one part of one agency working on one problem.

This doesn't have anything to do with Tuskegee, Enron, the financial crisis, global warming or any other national or world crisis you want to bring up.

First, this is not what I'm saying. I'm saying that they seemed more than ready to take a quick look and then dismiss this as another CFS dead end. That tune seems to have changed.

As for Enron, Deep Water, Tuskegee, etc. comments. That was in response to your reassurances that those things only happen in the olden days when people were ignorant and the government didn't provided sufficient oversight. I'm saying good luck with that view. There is plenty of evidence to question blind faith in government oversight. And again, it doesn't malice, just self-interest.

 

[Dreambirdie]

There is absolutely ZERO evidence that it contaminated the WPI samples. In fact, the vastly difference positivity rates between CFS patient and negative control sets in the WPI and other groups' studies is evidence against contamination (that is one of the purposes of having controls, after all).

HELLO! Very important, Cort! Please get that straight.

Thanks Dr Yes, for your well informed posts on this thread.

 

[Lynn]

It was an accident and they believe it happened between 1993 and 1996.

How would a date of 1993-1996 explain people who became ill in the 1980's?

Lynn

 

[Jemal]

When I watched the video, I was astonished. Stoye was saying, "this means that XMRV is just contamination and it doesn't cause disease" out of one side of his mouth, and, "we're concerned about our lab workers" from the other. Guys, you can't have it both ways!!! I wonder if he knows how obvious this was.
:headache::Retro mad::Retro mad:

Oh man... I laughed out loud when I read this. It does look they want to have both ways.

 

[Otis]

That's not true - see the CDC's Phase IIa results from the BWG. They found CFS patient samples positive for XMRV and what they called "MLVs" using two new PCR assays that they hadn't used before. Inexplicably, they immediately afterward abandoned using those assays!

Whoa, whoa! That's not what they're learning!! Be careful how you interpret science, Cort. There is evidence that it may be a virus that was created in a lab, but that is by no means definitive yet. There is absolutely ZERO evidence that it contaminated the WPI samples. In fact, the vastly difference positivity rates between CFS patient and negative control sets in the WPI and other groups' studies is evidence against contamination (that is one of the purposes of having controls, after all). Then there is the issue of the PMRVs and M-PMRVs being found by the WPI, NCI, NIH/FDA, and Hanson at Cornell... those are distinct from one another and from XMRV as defined by Coffin et al. What about those? How many different recombinant contaminants are we talking about?

I explored this a bit on another thread. Better placed here.

One connection, I guess is Dr. Silverman since he discovered the virus. Could materials have been passed from the Silverman lab to the WPI that contained the virus....that, I suppose is a possibility.

And on to every lab finding a positive? That's where this starts stretching a bit thin.

I'm not sold in the idea but it makes for some interesting speculation. If we're dealing with a lab creation, then we need to be thinking in terms of this happening repeatedly creating and thereby different viable infectious retroviruses. They started with the "answer" the the form of the XMRV sequence and went backwards and found two endogenous strains that appear to have combined to "make" XMRV, apparently without too much trouble. C=A+B. Well there's a helluva of a lot of possible substitutions for 'A' and 'B' and even more for 'C' as a result of all the possible combinations of 'A' and 'B', recognizing that we're talking about roughly 8100nt sequences for each.

And although we don't have a complete sequence from Lo/Alter if they're seeing a recombination artifact it's different in significant ways - e.g. 9nt deletion vs. 24 seeming to add some weight to the diversity of these viruses - made by nature or man.

So if we accept the idea that recombination may have have created an infectious virus in the one case where we started with the result and backtracked and happened to find the answer, how many times has nature found a way to take advantage of these xenografts (and other means of such recombination) and created something viable. And how many times have lab workers come in contact with them over the last 3-4 decades? It seems a little light bulb went on here. As CBS mentioned the concern seems to be for their own, not the public at large.

It's ironic how caviler people can be until it's their own asses on the line, which in the case of Stoye is one large ass even discounting his charming personality. If Stoye thinks this is contamination or perhaps now a non-viable recombinate, I find it quite amusing he's testing himself for XMRV.

 

[Cort]

That's not true - see the CDC's Phase IIa results from the BWG. They found CFS patient samples positive for XMRV and what they called "MLVs" using two new PCR assays that they hadn't used before. Inexplicably, they immediately afterward abandoned using those assays!

Whoa, whoa! That's not what they're learning!! Be careful how you interpret science, Cort. There is evidence that it may be a virus that was created in a lab, but that is by no means definitive yet. There is absolutely ZERO evidence that it contaminated the WPI samples. In fact, the vastly difference positivity rates between CFS patient and negative control sets in the WPI and other groups' studies is evidence against contamination (that is one of the purposes of having controls, after all). Then there is the issue of the PMRVs and M-PMRVs being found by the WPI, NCI, NIH/FDA, and Hanson at Cornell... those are distinct from one another and from XMRV as defined by Coffin et al. What about those? How many different recombinant contaminants are we talking about?

You obviously haven't asked them. The reason they haven't yet is because it's really, really difficult in the case of XMRV. There may only be one cell in which integration has occurred out of millions; finding such cells (and finding the virus in those cells and sequencing the provirus and its flanking sequences) takes a very long time, and is a major commitment of laboratory resources. I'm sure they're working on it, but resources are in short supply thanks to a lack of funding, among other things.

Actually I just asked them in an interview.

I agree that there's evidence that is was created in a lab and its not definitive - that's why I said 'leaning'....its all circumstantial at this point - but it is mounting. Regarding the controls we all know the problems with controls and different sampling and storage techniques. That is why the BWG study is the key to this whole thing. If the WPI can pick out the positives from the healthy controls that changes everything.

 

[Esther12]

Seriously Cort, have you ever heard W. Switzer or anyone else at the CDC utter the words "we share your concern" when talking about ME/CFS?

I agree with Cort that there's genuine concern about finding the truth as regards to XMRV (too big a risk not to)... but I certainly don't think there's much moral imperative with CFS though.

 

[asleep]

Oh man... I laughed out loud when I read this. It does look they want to have both ways.

Yes, and Cort is trying desperately to convince us that these two incompatible realities are one and the same. Hilarious.

 

[Cort]

First, this is not what I'm saying. I'm saying that they seemed more than ready to take a quick look and then dismiss this as another CFS dead end. That tune seems to have changed.

As for Enron, Deep Water, Tuskegee, etc. comments. That was in response to your reassurances that those things only happen in the olden days when people were ignorant and the government didn't provided sufficient oversight. I'm saying good luck with that view. There is plenty of evidence to question blind faith in government oversight. And again, it doesn't malice, just self-interest.

A quick look??? All that work?

 

[Cort]

Cort, be careful not to give more weight to short-term trends over long-term research (recency effect might be kicking in for you).

Much more research has to be done, and is currently being done, to determine the importance/existence of XMRV. Until such research is conclusive either way (which it is not currently), look for studies to continue to be published arguing both for and against.

It is entirely too soon to say one way or the other how this is going to play.

Good point Christopher - these studies have not been replicated yet and we will surely see more.

Trying figure out one part of this -concerning the 22RV1 cell and its connection to all this - this is what I've come up with

The 22RV1 cell line was created in 1999 (Study published)

Nine months after the Science paper Dr. Dusty Miller found that the 22RV1 prostate cancer cell line was producing XMRV.

“ Here we describe the detection of multiple integrated copies and high-level production of XMRV from 22Rv1 prostate carcinoma cells, which were derived from a primary prostatic carcinoma (14, 15)”.

Cloning of the gag gene revealed nearly exact matches to XMRV clone VP42, and phylogenetic analysis revealed that the 22Rv1 sequences clearly cluster with all previously cloned XMRV sequences by Silverman from his prostate cancer find. From these data, we conclude that the 22Rv1 virus is XMRV. In the addendum to the paper Miller added that further work showed that the virus produced by 22Rv1 cells is similar to XMRV over its entire length and not just over the gag region that we sequenced, further supporting our conclusion that the 22Rv1 virus is indeed XMRV.

Given his finding Miller warned of possible virus transmission to laboratory personnel and to other cells cultured in the lab.

In the Science paper the WPI also agreed that in ‘all positive’ cases ‘the gag and env sequences were 99% similar to those previously reported for the same prostate tumor-associated strains of XMRV (VP62, VPf35, and VP42)’ and that the entire genomes of two XMRV strains they sequenced (CFS XMRV strains 1106 and 1178)…”were >99% identical in sequence to those detected in patients with prostate cancer.”

The 22RV1, VP62, VP42 and WPI strains appeared to be essentially the same virus.

The similarity of a lab strain (22RV1) to viruses putatively found in the human body, however, raised some red flags because viruses usually change significantly genetically after encountering the harsh environment of the human body. Groom came out with a paper indicating that APOBEC editing had, in fact, altered the composition of XMRV in the blood stream.

In Dec 2010 Hue sequenced 22RV1 XMRV strain and compared it to that found in the prostate cancer and the two strains found by the WPI. They found, to their surprise, that the XMRV produced by the 22RV1 cell line was more diverse genetically than the XMRV found in the prostate cancer and CFS patients despite the diverse geographic origins of the patients.

They did leave open the possibility that the virus in the cell line had undergone more replication that that found in the patients but ultimately concluded that XMRV probably arose from mouse contamination as the prostate cancer cells were being passaged through mice to produce the 22RV1 cell line.

In Feb 2011 Towers, of the MRC Centre for Medical Molecular Virology at the University College in London, presented evidence that the integration sites of prostate cancer tissues also suggested XMRV was a contaminant. Dr. Raccaniello agreed that in all previous cases this has indicated contamination.

In Feb/March CROI Conference, Cingoyz of the National Cancer Institute presented evidence suggesting that all existing XMRV strains (prostate, two CFS samples from the WPI) were derived from a recombination event that occurred when the prostate cancer cells were grown in mouse tissues. He put XMRV’s creation between 1996 and 1999 - the date the first 22RV1 study appeared.

You can see the problem. The XMRV the WPI found appears to be almost exactly identical to the other strains. If that's true then its hard to imagine how XMRV was not a lab escape and and got into CFS samples and prostate cancer samples instead of CFS patients and prostate cancer patients.

That's because of the low genetic variability of the samples thus far. I have asked Dr. Mikovits about this and about the potential for other more variable strains to be present. It is also possible that XMRV is acting very oddly and has less variability in the wild than it does in the lab.....there are alot of possibilities but this would be really surprising. Basically with XMRV there is alot of circumstantial evidence......

 

[CBS]

A quick look??? All that work?

Yes, a relatively quick look given the potential consequences and no, they haven't been interested in the same cohort nor in replicating the original methodology or that of Lo/Alter.

 

[August59]

Is it possible that the assays developed to screen out "contamination" could have in fact been screening out the "lab created XMRV"? The one that is "extraordinarily infectious"?

 

[Cort]

Yes, and Cort is trying desperately to convince us that these two incompatible realities are one and the same. Hilarious.

No. I'm not desperate at all. I'm trying to methodically work my way through this.

 

[Jemal]

Why are there so many conspiracy theorists amongst us? Is that another symptom of CFS?

I don't think people are trying to do a coverup on XMRV. I do believe egos are involved though and that obviously impacts (objective) science.

It's all very confusing for me, things seem to be far more complicated than they are presented. At first it looked like everyone was screaming "contaminant" yet significant resources go into further research. There's definitely a few folks that want to close the book on XMRV, but many more that are continuing their work, even though they themselves are reporting about possible contamination.

 

[Cort]

Is it possible that the assays developed to screen out "contamination" could have in fact been screening out the "lab created XMRV"? The one that is "extraordinarily infectious"?

That is a different question but it is an interesting one. My guess is that Dr. Mikovits may feel that way based on her questions about the IAP test. Coffin, of course, would reject that. If that was true then we'd have three or four positive studies instead of one - because they did all think they found XMRV at first.

However the Huber positives were in the healthy controls - not in the CFS patients. That finding was what made her think contamination might be present.

The McClure and the other studies are a possibility.

 

[Dr. Yes]

I agree there is a difference. Instead of being evidence for infection, Raccaniello stated there has never been a case in which findings like Paprotka's did not indicate contamination.

I don't know if that's correct; even Miller in his comment to Retrovirology about Garson et al states that he'd like to see evidence to support that assertion. In any case, and I repeat, Garson et al's observations only apply to two of the fourteen integration sites identified in prostate cancer. They could not explain the other 12 as contamination.

Hue found that the XMRV in the human population had less variation than the XMRV in the lab - if you know anything about population genetics you know what a red flag that is...that finding suggests but does not prove that XMRV came from the 22RV1 lab creation and was spread around labs and somehow ended up in both the Silverman and WPI samples.

I know quite a bit about population genetics, as it happens! :Retro wink: Enough to have seen that Hue et al used a tiny sampling of extremely closely related human XMRV samples.. remember, until recently very specific primers have been used and only small amounts of the genetic diversity that's out there had been detected. Also, the claim that XMRV came from 22Rv1 kind of clashes with the other contamination argument that it came from DU145, doesn't it?

Contamination? - Actually at three labs thought they found XMRV and then concluded that it was contamination - all from different sources. So theoretically - there are at least 3 ways to explain the positive studies.

Not exactly - those three labs that found that their samples were contaminated did not find the wide difference in positivity rates between test subjects and controls that the WPI and others have. Similar results between test subjects and controls suggest contamination. Major differences suggest no contamination (and disease association).

This is not to say that that happened in the WPI - I don't think those situations applied to them - but it did show that there are multiple ways to mistake XMRV for some thing else.

It showed that those labs managed to contaminate their samples. Everybody knows contamination can happen; avoiding it is the trick.

Just think about that for a moment. We've been saying the CDC just can't find XMRV - and now these reports suggest that maybe they actually can! but not in the place we or they were expecting.

Again, the CDC HAS detected XMRV in the Blood Working Group before, using samples from WPI pedigreed positive patients. But that was using different PCR assays that they have since abandoned...

Infection? - What we have now is evidence that XMRV is in blood samples but I think what the research community now wants is evidence of 'infection'; ie XMRV integration into human DNA. There's no mystery about what Alter/Lo and the WPI need to do to turn this around....show XMRV integration into human DNA (and then passing the BWG blinded tests).

It is not necessary to show integration to prove infection. Integration was not the yardstick for determining whether an agent was infectious or not for the vast majority of viruses that are accepted to cause human disease. A principal way to demonstrate that a virus is infectious is to look for an immune response to it. That is precisely what the WPI and NCI have done, and they have already reported these results at conferences (take their UK study, for instance, as reported at the BPAC and XMRV Workshop). Of course those results haven't been published yet, nor have the ones about cytokine profiles specific to XMRV positive patients, but we have seen the abstracts discussing these results.

MIA - where are XMRV's supporters? the 'other side' is pumping out paper after paper yet we've heard little or nothing from Ruscetti over the past year (two review papers) and Silverman....I imagine everyone is waiting for Ruscetti to come out with his paper and has been. It was rumored ready to come out last year.

Make no mistake - there are 'sides' in this thing, and it's politically very ugly. And the reason there have been no other publications yet are that, as I'm sure you know, they have had a great deal of difficulty getting published, just as Alter and Lo did, and as Lombardi et al did early on.. only it's gotten even harder, as a direct result of the paper after paper being pumped out by those arguing for contamination.

Talk about wearing rose colored glass and wanting to see fuzzy bunnies! Take those glasses off!

You talking to me, or CBS? Or the HUGE majority of other patients who think far less of the CDC than you appear to? I guess you're the only one who can see clearly! (That's usually a 'red flag' of sorts...)