Due to the following fact - is contamination even possible?

[omerbasket]

Look at the following article by Cort, summarizing the "demystifying medicine" broadcast with Dr. Alter and Dr. Lo:
http://phoenixrising.me/?p=5158

It says:

Dr. Lo reported that they sent some positive samples to the CDC lab – which came up negative and that the CDC sent a negative to Dr. Lo’s lab – where it came up positive. The negative sample was notable because the CDC has repeatedly tested it and it came up negative every time yet every time Dr. Lo tested it – it came up positive.

Look at the sentence in bold letters. Now, the contamination theory cannot explain that sentence - because even if the samples were contaminated, then the CDC's test, if it's indeed good at finding XMRV/MuLVs as they say it is, should have come back positive - because the test doesn't care if it's contamination or not (and only other tests, like the mtDNA tests, would have shown that the result is probably due to contamination). One explanation could be that the tests were being shipped at wrong conditions - but I guess that both the scientists from the FDA and from the CDC insisted that the tests would be shipped in conditions which they believe are sutiable - and since all of the scientists that came up with negative results refuse to recognize that it's very possible that some variation, which seems not important to them, from the original methods described in the "Science" paper, are resposible for the discrepant results - it would seem that they would also think that this is not the case here, meaning that the shippment conditions are not responsible for the CDC not finding any positives in samples that the FDA found all of them to be positive. So, that leaves us with a very high probability that the following is the reason for the dicrepancy here: The CDC's tests, performed on the samples sent by the FDA, couldn't find a virus that was actually there (contamination or not).

 

[In Vitro Infidelium]

Dr. Lo reported that they sent some positive samples to the CDC lab – which came up negative and that the CDC sent a negative to Dr. Lo’s lab – where it came up positive. The negative sample was notable because the CDC has repeatedly tested it and it came up negative every time yet every time Dr. Lo tested it – it came up positive.

If there was contamination in Lo's lab - equipment, reagents etc, but not in the samples - then what is quoted is exactly what one would expect -the positive would be in Lo's process, but not in the CDC's process. Of course other explanations are possible - the CDC process is not up to the task - Lo's process is finding a 'phantom' artefact where something created by an idiosyncracy of the processing is prducing the positive result, but contimation of reagents especially can not be ruled out.

IVI

 

[Wonko]

playing devils advocate here

its perfectly possible - even likely - if lo's tests are detecting contamination as positive and the CDC is using a better test which doesnt.

not very likely IMO but it would explain it.

of course if the CDC isnt detecting contamination in the samples..........then things may be a little different.

 

[omerbasket]

If there was contamination in Lo's lab - equipment, reagents etc, but not in the samples - then what is quoted is exactly what one would expect -the positive would be in Lo's process, but not in the CDC's process. Of course other explanations are possible - the CDC process is not up to the task - Lo's process is finding a 'phantom' artefact where something created by an idiosyncracy of the processing is prducing the positive result, but contimation of reagents especially can not be ruled out.

IVI

I think it's highly, highly highly highly unlikely, since Lo has control negatives - If it's not the samples that are contaminated, why wouldn't the negative controls show as positive also? Plus, all of the samples, including the 44 from healthy blood donors (which only 3 of them came up positive), should have come back positive.

Wonko, your explanation is not a good explanation for the CDC. It would mean that although they claim that their test finds XMRV/MuLVs, it doesn't find anything which is close enough to those - it finds only XMRV, or known MuLVs - but than it would miss all of the sequences found by Lo/Alter, which are not 100% identical to VP62, and also not 100% identical to known MuLVs (and still, there is no reason to think that they are contamination. Actually, had they been 100% identical to MuLVs, there would be more of a reason to think that, although it still doesn't say that it is contamination). Anyway, they cannot perform a test that wouldn't detect contamination and would still detect XMRV and MuLVs - what they can do is to check for contamination with other tests (since the lab can, theoretically, be contaminated with XMRV or MuLVS, and they say that their method detects XMRV and MuLVs. Do they addmitt that it does not detect MRVs? Because I'm under the impression that what they tried to say is that it would detecet XMRV and anything close to it - and the PMRVs are very close to it).

 

[kday]

So, that leaves us with a very high probability that the following is the reason for the dicrepancy here: The CDC's tests, performed on the samples sent by the FDA, couldn't find a virus that was actually there (contamination or not).

What makes you think the CDC actually tested the samples. And even if they did, what makes you think they would report positive results? Wouldn't that be against the goals of the Center of Disease Proliferation.

Look, my sister set up lab equipment to the FDA and CDC (primarily PCR). All she ever talked about is how incompetent they are. Apparently, she sold them hundreds of thousands of dollars in PCR equipment. However (excuse me if I get some technical details wrong), but they never touched these machines for years since they had to call the company to activate them with some type of key or something. They also didn't get all the necessary equipment to get the machines running anyway, and when inquired why, they said they didn't have the funding.

She said the scientists that "worked" in the labs were apparently incompetent as well.

So spend hundreds of thousands on medical equipment, and never use it.

I remain HIGHLY skeptical of these government bureaucracies, their intentions, and their actions. I am not arguing that XMRV is a contaminant or not. I'm just saying from history they can do a lot more harm then good, they are incompetent, and they aren't to be trusted.

So what do I do when I see a gov't study? I pretty much ignore it.

 

[WillowJ]

I think it's highly, highly highly highly unlikely, since Lo has control negatives - If it's not the samples that are contaminated, why wouldn't the negative controls show as positive also?

That's a really good point.

 

[toddm1960]

Far be it from me to be CDC bashing..............but............could this be part of the BWG findings? This round might point the finger at who's not trying to find XMRV? I can't wait for the BWG to report, it could be explosive stuff.

 

[omerbasket]

What makes you think the CDC actually tested the samples. And even if they did, what makes you think they would report positive results? Wouldn't that be against the goals of the Center of Disease Proliferation.

Look, my sister set up lab equipment to the FDA and CDC (primarily PCR). All she ever talked about is how incompetent they are. Apparently, she sold them hundreds of thousands of dollars in PCR equipment. However (excuse me if I get some technical details wrong), but they never touched these machines for years since they had to call the company to activate them with some type of key or something. They also didn't get all the necessary equipment to get the machines running anyway, and when inquired why, they said they didn't have the funding.

She said the scientists that "worked" in the labs were apparently incompetent as well.

So spend hundreds of thousands on medical equipment, and never use it.

I remain HIGHLY skeptical of these government bureaucracies, their intentions, and their actions. I am not arguing that XMRV is a contaminant or not. I'm just saying from history they can do a lot more harm then good, they are incompetent, and they aren't to be trusted.

So what do I do when I see a gov't study? I pretty much ignore it.

Very important. Did you consider telling this to Dr. Mikovits? Perhaps it would make her arguments stronger. Perhaps it would expose that the king is naked.

Did your sister tell you what is the situation with scientists that do not work for the government? Do they do everything right, or is this incompetence spread among most or all of the scientists?

I think it is very important to do it all right, and not forget that these are machines - one wrong thing and your result is wrong, and you don't even know that it's wrong.

Anyway, if I return to the subject of the thread here: I think that these results show us that there is a good chance that the CDC's test wasn't able to find PMRVs even if they were there. And the NCI found XMRV in the FDA/NIH samples that they checked (8/9 if I'm not mistaken), so apparantely the FDA/NIH couldn't find XMRV, and the CDC couldn't find XMRV and PMRVs.
That is why it's cruicial to replicate the original study: To minimize the chances of wrong negatives as much as possible.

 

[WillowJ]

WPI is well aware of the CDC's incompetance, although they might find this true story scarily amusing.

The best-received criticism (of this sort) of CDC, however, will come not from their nemesis but from a third party.

More to the point would be for the sister to ring up her Senators and tell them, and to tell a cartoon artist from the Washington Post (in the latter case, probably after the BWG results come out).

The best show of the CDC's incompetance to come from WPI, assuming XMRV is real (as it would appear at this moment, and as much as I hate the idea of a retrovirus, a specific etiology is useful to us and this model has a lot of explanatory power), is the BWG results.

But some cartoons in the Post and a GOA (Government Office of Accountability) investigation or Congressional Inquiry would be a lot of help... both to us for a bit of restitution (de facto apology in the form of major research funds for all biomedical aspects of the Disease, quick access to social support, blitzing physicians with true education, true education for the public at large, and so on, perhaps even a formal apology) and to prevent this sort of thing (the whole entire 50-year story) from happening again.

 

[Bob]

Hi omerbasket,

I think that your first post, on its own, isn't such a solid argument because, as In Vitro says, it might be that any contamination entered during the testing, and not during the taking or processing of samples.

However, I think including your later point about the negative controls makes your point much stronger.
As you say, if contamination was entering the study during testing, then we'd expect the negative controls to be testing positive at an equal rate to the CFS samples.

What Lo also said in his presentation, that in my opinion made his case even stronger, was that he consistently and repeatedly tested one of the CDC's negative controls as positive, even though it was a blind coded control. Lo emphasised this during his presentation, and seemed to think it was very significant. The fact that he consistently and repeatedly tested the same negative control as positive, he suggested, showed that it was in fact a positive sample. It was the consistency of testing this one particular coded blind sample that was so significant.

Alter said in the presentation that if Lo is consistent during the Lipkin study, then this will be the evidence that they need.

 

[*GG*]

What makes you think the CDC actually tested the samples. And even if they did, what makes you think they would report positive results? Wouldn't that be against the goals of the Center of Disease Proliferation.

Look, my sister set up lab equipment to the FDA and CDC (primarily PCR). All she ever talked about is how incompetent they are. Apparently, she sold them hundreds of thousands of dollars in PCR equipment. However (excuse me if I get some technical details wrong), but they never touched these machines for years since they had to call the company to activate them with some type of key or something. They also didn't get all the necessary equipment to get the machines running anyway, and when inquired why, they said they didn't have the funding.

She said the scientists that "worked" in the labs were apparently incompetent as well.

So spend hundreds of thousands on medical equipment, and never use it.

I remain HIGHLY skeptical of these government bureaucracies, their intentions, and their actions. I am not arguing that XMRV is a contaminant or not. I'm just saying from history they can do a lot more harm then good, they are incompetent, and they aren't to be trusted.

So what do I do when I see a gov't study? I pretty much ignore it.

This doesn't surprise me, I worked for gov't and I see incompetance all around me!

 

[Mark]

As Bob says, the argument about Lo's positive samples testing negative at the CDC doesn't conclusively end the argument in itself - but what it does do is show that any alleged contamination in relation to Lo would have to be in their equipment and not in the samples themselves.

We have discussed all these possibilities ad nauseam in the past and several times we have come to the conclusion that any alleged contamination must be in the samples themselves. The samples themselves have to be 'contaminated' with XMRV, in the WPI's case, not only because the ongoing difference between controls and patients doesn't make any sense of a 'contaminated equipment' theory, but also because of the Swedish findings. A little-noted aside in the Swedish negative study (Blomberg et al?) was that before running their full test, they tested 3 positive samples from the WPI to use as controls, and they tested one of them positive before going on to find no positives at all in their own samples. Thus if the explanation for alleged 'false positive' detection of XMRV were contamination, then that contamination would have to be in the samples themselves, and not just in the primers or other part of the detection process.

So the contamination theory is driven, I think, to the position that says that WPI samples themselves are contaminated (and the patient samples are far more contaminated than the control samples due to some aspect of the way the samples are collected), but that Lo's contamination is in his lab and not getting into the samples themselves. The whole thing is not completely logically ruled out by all these various bits and pieces, I think, but the contamination theory does seem to require a fairly extraordinary set of different explanations for the same results by different labs - and until all those details can be proved, the 'contamination theory' remains very much unproven - and that contamination theory should be treated with at least the same degree of scepticism as has been applied to the original findings.

 

[omerbasket]

I generally agree with you, Mark, but I would think that had Lo's eqiupment been contaminated, he would have found the MLV-related viruses in every test he made - all of the tests of the patients, all of the tests of the healthy controls, and all of the tests of the negative controls. Not to mention that he wouldn't have gotten 86.5% in the sick people as opposed to 6.8% in the healthy controls and 0% in the negative controls.

I'm not a scientist and I might be missing something, but what I say is from common sense.

 

[toddm1960]

OB you have it exactly correct, if the contamination was in the equipment 100% of Lo's sample would test positive. If Lo's lab contaminated the sample it sould have tested positive at the CDC. They can't have it both ways, blame equipment contamination when it fits theior story, but blame sample contamination for everything else. It shows a clear willingness to descredit XMRV research if you ask me.

 

[CBS]

I know that this is not a human study but the contamination argument is that XMRV is a non-viable RNA/DNA viral sequence that is not capable of causing an infection and that therefore we need to stop looking at potential disease associations.

If that's the case, can anyone explain this away as contamination? What are the odds that you'd get that anti-body overlapping profile in the animals from a contaminant?! My guess is that the odds are well over 1/10 to the 16 power.

J Virol. 2011 Feb 16. [Epub ahead of print]
Infection, viral dissemination and antibody responses of Rhesus macaques exposed to the human gammaretrovirus XMRV.

Onlamoon N, Das Gupta J, Sharma P, Rogers K, Suppiah S, Rhea J, Molinaro RJ, Gaughan C, Dong B, Klein EA, Qiu X, Devare S, Schochetman G, Hackett J Jr, Silverman RH, Villinger F.

Abstract

XMRV was identified in association with human prostate cancer and chronic fatigue syndrome. To examine the infection potential, kinetics, and tissue distribution of XMRV in an animal model, we inoculated 5 macaques with XMRV intravenously. XMRV established a persistent chronic disseminated infection, with low transient viremia and provirus in blood lymphocytes during acute infection. Although undetectable in blood after about a month, XMRV viremia was reactivated at 9 month confirming the chronicity of the infection. Furthermore, XMRV gag was detected in tissues throughout, with wide dissemination throughout the entire period of monitoring. Surprisingly, XMRV infection showed organ specific cell tropism: CD4 T cells in lymphoid organs including the gastrointestinal lamina propria, alveolar macrophages in lung, and epithelial/interstitial cells in other organs, including the reproductive tract. Of note, in spite of the intravenous inoculation, extensive XMRV replication was noted in prostate during acute but not chronic infection, even though infected cells were still detectable by FISH in prostate at 5 and 9 months post infection. Marked lymphocyte activation occurred immediately post infection, but antigen specific cellular responses were undetectable. Antibody responses were elicited and boosted upon reexposure, but titers decreased rapidly suggesting low antigen stimulation over time. Our findings establish a nonhuman primate model to study XMRV replication/dissemination, transmission, pathogenesis, immune responses and potential future therapies.

Fig. 5. Time course of antibody response to the XMRV transmembrane protein p15E (anti-p15E) (a) and capsid protein p30 (anti-p30) (b) in three monkeys post-XMRV infection and immunization. Antibody responses were determined by recombinant protein (p15E and p30)-based indirect chemiluminescence immunoassays (CMIAs). RLU, relative light units. (c) Neutralizing antibodies were tested against the inoculating XMRV with dilutions of sera of three monkeys, 12 days prior to infection and 114 days postinfection. Virus inhibition was expressed as RT values from supernatants of cells infected with viruses exposed to the indicated dilutions of preimmune sera versus sera collected at day 114 collected from each of the three monkeys. Data are from average RT activities of triplicates of single-well infections.

 

[ixchelkali]

It seems to me that there are still too many questions that remain unanswered by the contamination theory for anyone to reasonably say it's proven. I think that the responsibility for answering those questions rests with those proposing the contamination hypothesis.

I think if I were Harvey Alter I'd invite John Coffin to come find the contamination. I'd say "I've run every test I know and I can find no contamination in our lab. Why don't you try? Come show us." And Bob Silverman could say the same to Greg Towers. And whatever they find or don't find, publish the results.

 

[Navid]

IX:


your plan is just too rational and common sensical, therefore i predict it will never happen.......too bad.

 

[ukxmrv]

Is it possible that Coffin could bring a contamination into the lab with him and obviously, I mean by accident, i.e. on his clothes or something else he would bring in?

 

[omerbasket]

Possible, but not likely, as it would have probably cause the first tests that they did to come up positive (and they came up negative), I guess. However, perhaps there are other ways in which it would cause the misunderstanding.

 

[alex3619]

Hi everyone,

There are two words that I don't see enough in this argument: specificity and sensitivity.

Alteration of PCR parameters, even when using the same test, can affect both sensitivity and specificity. Typically as sensitivity goes up ("did we find anything") specificity goes down ("did we find the one thing we were looking for"). Alteration of such things as reagent concentrations and PCR annealing temperature are just two factors I am aware of that affect this.

Here is one solution to the problem, and in this nearly ALL the data is correct, potentially:

The CDC could (not do, has to be proved) have low sensitivity and high specificity. They are using a very specific test looking for a known strain of XMRV. It isn't there.

Lo and Alter, plus WPI, have learned (I suspect, not proven) to adjust parameters for sensitivity not specificity. Indeed, now they use parameters that will detect PMLVs and not just XMRV. So they find what is there, but it might not be anything like the original XMRV strain - indeed they may be finding multiple strains and related but different viruses, as they have claimed.

The CDC is operating from the assumption that there is a very narrow range of genetic diversity in the target virus. The WPI are operating from the assumption that there is a huge genetic diversity in the target virus family. These assumptions drive different parameter selections.

So the CDC can't find anything, and the WPI is finding it all over the place, even with the "same" test. This is just an hypothesis, but it explains the data. All the labs need to actually sequence the viral strain they are finding - just saying it is there is not enough. I do realize this uses up resources, and there is not enough funding - so the blame for this is still lack of funding in my view.

Coffin's hypothesis of a culture origin of XMRV is something else - personally I suspect it was infected by an XMRV positive lab worker, and did not originate there, but I do think it likely that he found two murine endogenous viral strains that may be related to the viruses that did give rise to XMRV, originally.

Bye
Alex