McClure's XMRV Contamination Conversation

[Mark]

i agree with all your points. i am just trying to see if there is any even remote chance of a screw up here, and it's hard to find.

Sure Jim, I can relate to that. I keep coming back to that myself, I'm in a similar situation actually, that's why I read Weiss' article carefully in full, to try to see if there's any contamination scenario that could make sense. But try as I might, no matter how much I read about the complexity of contamination possibilities, I just can't make any kind of contamination scenario fit all the facts.

I don't think there's anything wrong at all with keeping looking out for it, and trying to keep an open mind, I try really hard to be honest about it but I just can't make sense of the sceptical arguments. They all just seem to boil down to no more than "Oh no it isn't!" at the end of the day.

Yet no matter how many times I go over and over that same ground and conclude "no, there's just no way", nevertheless the nagging doubts keep coming back. Very frustrating. For me, it's testament to the power of a whisper campaign: repeat something often enough, stick to those guns, keep slinging the mud, keep denying it's all true, come across confident and knowledgeable, and that drip-drip-drip effect just keeps putting those doubts in people's minds.

on the other hand, i have to say, as a lay person, it is also confusing how supposedly reputable research scientists don't know which test tubes to use (e.g. not heparin).

I think the point here is that the whole heparin point, and also the issues around length of storage and nature of storage, time from blood draw to storage, etc etc, those things are new science. There's something strange going on around the collection and preparation of the samples, and that has to be the case with the PC studies as well. The big progress over the last few months, I think, has been to absolutely nail down that the answers to the big discrepancy in results have to lie in that area - on whatever side of the argument - and not in the cohort selection or detection methodology.

The failure by so many groups to detect anything at all has to be in the sample preparation I think; it can't just be in the PCR methodology. Numerous arguments show that to be the case, most recently the Swedish study. There has got to be something novel about XMRV in relation to the storage tubes, and I'm hoping that when that's explained it will reveal something very useful about XMRV. There's already a thread with somebody trying heparin injections as a therapy, for example...that has a certain logic to it...

Even on the other hand, as Dr Yes and I have both mentioned, there are several reasons why any contamination has to be in the drawing, storage and preparation of the samples. Lab contamination theories just don't fit the evidence. Weiss' idea that the patient samples may have been more frequently handled is the closest to a rational explanation I've heard, but it's speculation and he admits himself it's not a satisfactory explanation; it remains a mystery even regarding studies that "came to nothing" in the past.

and i don't think poor patient selection can explain it all, as u have to figure even the cdc picked some pwc's and should have found at least 1 positive.

I have always believed that: logically patient selection was always extremely unlikely to explain all the observations. And yet there are some potentially very surprising possibilities here. It really is possible that the CDC cohort contained not a single case of ME. If their exclusionary criteria - excluding neurological symptoms for example - remove all XMRV+ patients from the cohort, that could work. If the WPI's very strict criteria define XMRV, and that strain of XMRV defines the most aggressive form of MRV-induced disease, whereas Lo/Alter's Fukuda cohort define the more widespread variations, that would work too to explain that apparent mystery of the X vs P variants, given that the WPI say they too have found the same P variants since publishing in Science. When you look at the patient criteria, knowing the subtleties of those distinctions, those who are knowledgeable on that would have always argued that these are distinct and different criteria.

It's very possible that our natural assumption that we know nothing, really, about CFS, and that all the diagnostic criteria are vague, and that the whole phenomenon of ME/CFS is vague and ill-defined and probably not a well-defined criteria...all of those assumptions actually could be wrong! It's quite possible that we understand rather more than we think. And even if CFS is complex and made up of distinct clusters, that doesn't mean there is no common factor as well. It's well worth reflecting on this and trying to imagine how this really could be true, that we all of us have XMRV, as do many others with neurological conditions, but that different clusters have other things going on as well. It seems amazing, but it really could be true IMO.

To illustrate how this can be the case, note that ME/CFS is itself merely one particularly well-defined "tip of an iceberg" of lots of similar immune and neurological conditions of unknown cause. GWI, MCS, FM, IBS, MS, autism, rising rates of allergies, and indeed mental illnesses in general...all of these are remaining medical mysteries and are related conditions with unknown causes. So: ill-defined as ME/CFS may be, those who have actually obtained an official diagnosis are doing pretty well! My only official "diagnosis" is "ideopathic immune dysfunction", for example (and MCS via others), even though I did fit the Fukuda criteria once upon a time. So from the wider perspective, ME/CFS can itself be seen as a fairly tight subset of something much, much wider: modern, ideopathic neuro and immune dysfunctions. Within the ME/CFS world, it all feels fairly diverse and ill-defined - but perhaps that's just because it really is a condition with a lot of variability (this must be true, or there are 50 or so similar patterns of symptomology with masses of overlap but 50 different causes! That would be even weirder when you think about it...surely all this has to have some common factors?).

With regards the CDC study, there was one little intriguing detail: Lo/Alter found very small suggestive traces of MLRs in about 10% of the CDC samples they tested. Now that could be the last faint surviving traces of the MLR+ samples from the general population, which are supposed to be there at around 10%. That would mean: they had no "real ME" patients at all in their cohort, and in addition, their preparation methodology all but destroyed the evidence of the background infection as well. For me, there is a consistent picture emerging which can explain all the results...and one has to be looking for that, if one's looking for the truth...well, that picture can be constructed, there is not much that is confusing me these days, I can't think of any anomalous results that don't fit the explanation I've sketched.

either way, i think our answers will come within a few months, and i think the wpi/nih/cc/fda will be vindicated.

I agree with that too, on both counts. "It'll all be over by Christmas"...or soon after. It should be, anyway, there are multiple lines of inquiry under way that ought to resolve the issue from a scientific point of view. However: then there are the political factors. If the scientific answer is "contamination", then unless the WPI et al were obliged to hold up their hands and accept that, I think an awful lot of people are going to see that answer as merely a cover-up. If there's no adequate scientific explanation (and it would have to be a really good and thorough explanation), the XMRV theory can't be debunked: it will go on, and some patients and some researchers will continue to believe in it. I wouldn't personally be trusting the authorities in such a case unless their evidence and explanation was really, really strong; I can't imagine that scenario really. Whereas, if an explanation for the negative studies that confirmed XMRV were found, then things ought to really take off big time in that case. And the whole question is so crucially important, and both answers are so politically unacceptable to different parties, that one can see it all being kept under wraps for ages and ages, no matter what turns up, pending absolute certainty...

Still, I find myself saying, yet again, that we are surely, surely only a few months away from the decisive moment...so I hope I'm right this time!

 

[eric_s]

Hey Eric
when do you think our physician will be obligated to try to help us with xmrv? I told mine and his response so far was to send me a cbt exercise study on Fm being successful.
seems like its going to be years until they are "obligated"?

Hey xrayspex

I'll try to give you some answers now, but it's not a very good moment, sorry. I arrived in Barcelona (Spain) yesterday in the morning. Now, in 2 hours i will have to check out at this hotel and take the bus to another city (Valencia).

So, first of all, i have to say that i don't know the american legal system. In the anglo-saxon countries they have a tradition of case law, as far as i know, and we (continental europe) basically only have codified law.

What you have asked me, was a bit different from what i was referring to, in my post above. There i was not talking about a doctor not treating someone diagnosed with XMRV, i was thinking about a doctor saying XMRV does not matter at all. In the crazy situation we're in right now, this might be worse than refusing treatment.

First of all, of course you can never tell a doctor what he has to do, unless he's your employee. But what he does or does not do, might have legal consequences for him.

Basically 3 different kinds, i think

- civil law (mainly damages)

- criminal law (a sentence)

- "professional law" (don't know if you say it like that in english) (he/she might lose the licence etc.)

A doctor (or anyone) might have to pay damages to you (under our legal system) if he hurts your health, property, etc. or breaches one of his duties out of a contract with you (as you have with your doctor) and this leads to damage of your property (this includes you losing money) or even immaterial damage, in some cases.
For someone to be liable in this way, that person has to have had intent to cause the damage or there has to be negligence that was causal for the damage.
Plus there are some more requirements, like it was not done in self defense, etc., the person causing the damage was not mentally ill, heavily drunk or anything of that sort, and so on.

Basically it's the same for a sentence according to criminal law. I can only see physical injury as being relevant here (intentional or by negligence), and in case of this offence, there has to be physical maltreatment or a damage to a persons health (not psychological health in our legal system, i don't know about the USA). And this has to be caused intentionally or by negligence.
Also here the same things i've mentioned above are true, as far as self defense, mental illness, etc. are concerned. There are some more requirements than what i can now quickly list here.

Now, i don't suspect many doctors actually have the intent to harm their patients, so i will leave this out and just comment on the cases where there is negligence.

So, the big question is, when does an action by a doctor constitute negligence? I can of course not predict how a judge will answer this question, i guess no one can do that with certainty, as each situation is different, and different judges will not decide in the same way. So there's a lot of uncertainty, especially in a case like CFS where basically no one knows anything for sure at this moment.

I would say that at this moment, it is impossible for a doctor to act in a negligent way by not prescribing ARVs to a person who has CFS and is XMRV+, because
a) the tests for XMRV are not approved yet
b) the role of XMRV in CFS is not clear
c) the therapeutic effect of ARVs in the case of an XMRV infection is not clear

But i was thinking about different cases than a doctor not prescribing ARVs.
Let's say a doctor says XMRV does not matter for CFS, even regardless of wheter you have it or not. In a situation where XMRV might well be the cause of CFS and thus of course is a reason for hope, i would say it can constitute negligence to deny that possibility. Since a doctor has a "garantor position" in regard to the patient, he has duties. If a patient is emotionally unstable, such behaviour by a doctor might have all sorts of bad consequences, which might include physical injury or worse.
So i can imagine cases where a doctor would have to pay damages to a patient (or his relatives) or be convicted for physical injury resulting from negligence or even manslaughter through negligence.

Or let's say a doctor says XMRV does not matter and then a CFS patient goes out and pays money for all sorts of useless therapies that don't do anything, because it later turns out XMRV is the answer.
I can imagine cases where that action by the doctor is a breach of his duties out of his contract with the patient to inform and advise that patient correctly, and this might lead to the doctor having to pay for the monetary losses that the patient has suffered because of the doctor's action.
Plus you might not have to pay the doctor's bill or not all of it.

This was a quick answer, and it's not very serious to answer that kind of questions in this unsystematic way, in bad shape, out of a hotel room. And i don't have time to read through it for more than some minutes to correct mistakes etc.
So please only take it with caution.

 

[ukxmrv]

I'm a little stumped on how they could explain contamination for the UK Ashford 50 results.

The bloods were collected in a UK NHS hospital, then sent straight to the USA for testing in 2 separate labs, where I am told no testing with mice has been carried out.

The contamination would need to have been in the blood tubes, not sure who supplied these but assuming the NHS, or the culture medium (LnCAP) or similar?

 

[Snow Leopard]

And how she can argue that the mutation of viral sequences in samples from the same patients taken 15 years apart can be explained by contamination is beyond me.

In principle, the original cellular source of the contamination would have multiple variants of the virus. Lo and Alter have not yet demonstrated substantial genetic variation. So that particular point doesn't discount the possibility of contamination.

The Alter study found pMLV only, and only in PCR and therefore is much more suspect of contamination than the Lombardi study.

I think the contamination suggestion should still be taken seriously and all of the reagents, tubes etc used should be screened. If not least, to avoid further doubt.

 

[Cookie Monster]

The Alter study found pMLV only, and only in PCR and therefore is much more suspect of contamination than the Lombardi study.

Hopefully some more papers to follow - Dr Lo answers McClure's response letter in PNAS yesterday and his last sentence stated "Our recent collaborative studies with a National Cancer Institute group have shown that we can detect antibodies in most patients
with CFS with positive gag sequences and not inmost PCR-negative "

 

[Mithriel]

Andrew said

I think the contamination suggestion should still be taken seriously and all of the reagents, tubes etc used should be screened. If not least, to avoid further doubt.

If any of these were contaminated, the results for patients and controls would be much the same. That is one of the reasons you use controls.

I find it telling that Huber found her results were contamination when her patient positives 2 from three were much the same as her controls about 30 out of 40 or something like that.

People wonder why McClure and Weiss should put their careers on the line by claiming contamination, but it is actually quite sneaky. When the evidence becomes overwhelming they can claim they were just being cautious as good scientists ought to be. Weiss in particular, as someone who is very politically savvy, is framing everything in terms of "it even happened to me". Yet this is like saying "I used to drink and drive so your accident must be caused by drinking and driving"

This continual drip feed of disinformation, much of it untrue so we can only assume that McC, for instance, has not actually read the papers casts doubts and will be dragged up every time anyone thinks about giving money for research.

It cannot be a coincidence that the multi million pound PACE trial into CBT and GET for CFS is due to be published. If the HMRV link was taken as proven then this would get laughed off, but enough fog is being cast that they will get away with it.

As people have said, the media have not taken much interest in the XMRV story so these things are being written for another reason.

Plausible deniability and disinformation was brought to a fine art by the UK government in NI.

Mithriel

 

[Wildcat]

"This continual drip feed of disinformation, much of it untrue so we can only assume that McC, for instance, has not actually read the papers casts doubts and will be dragged up every time anyone thinks about giving money for research.

It cannot be a coincidence that the multi million pound PACE trial into CBT and GET for CFS is due to be published. If the HMRV link was taken as proven then this would get laughed off, but enough fog is being cast that they will get away with it.

As people have said, the media have not taken much interest in the XMRV story so these things are being written for another reason.

Plausible deniability and disinformation was brought to a fine art by the UK government in NI.

Mithriel"

Thoroughly agree, Mithriel. There's something very familiar about the disengenuity/denier/disinformation style and patterns of reporting etc in the last months re XMRV, that we are so familiar with in UK ME politics.... the Lancet editorial definitely reads like 'one of those', familiar phrases..... smoke and mirrors, fog and fudge. What goes on is as much/more about manipulation of language, as science.

Wildcat

 

[asleep]

The big progress over the last few months, I think, has been to absolutely nail down that the answers to the big discrepancy in results have to lie in that area - on whatever side of the argument - and not in the cohort selection or detection methodology.

Mark, in all fairness, you may be overlooking the likely role the CDC's methodology played, whereby they flip a coin for each sample and declare it negative if it comes up heads or tails and positive if it lands on its side... :Retro wink:

Edit: In seriousness, I completely agree with your assessment.

 

[Dr. Yes]

In principle, the original cellular source of the contamination would have multiple variants of the virus. Lo and Alter have not yet demonstrated substantial genetic variation. So that particular point doesn't discount the possibility of contamination.

The Alter study found pMLV only, and only in PCR and therefore is much more suspect of contamination than the Lombardi study.

Hi Andrew1,

The contamination argument does not explain Lo's et al's report that the older Komaroff patient samples had one set of gag fragments while the new samples from the same patients had very similar sequences but with slight mutations. The only clear way to explain this is by a mutation over time of a virus infecting those patients. If the source of those sequences was contamination, it would not be selective for the set of samples (old vs. new); it should not differ between them. Also, for your speculation about contamination to be correct, the contaminants in the newer set would have to, by a remarkable coincidence, just happen to be only from strains that are mutated descendants of the strains that happened to contaminate the older set... and this would have to occur independently for each of 7 patient samples, i.e. the descendant of the strain that contaminated the sample from patient 1 would have to somehow selectively contaminate the matching freshly drawn sample from patient 1, and the same in turn for the strains in the samples from the other six patients. The improbability of this scenario is staggering.

Furthermore, I wonder why you think the original source of the contamination would have multiple variants "in principle". It is in fact less likely that it would (unless you are contending that there are multiple, distinct sources of cellular contamination) hence the contention by Lo that the presence of genetic diversity among their samples argues against contamination, which would be expected to have very limited genetic variation (because of the limited amount of cellular material and sources). Also bear in mind that the sequences identified by Lo et al appear to be distinct from known MLV gag sequences, thus necessitating that the alleged contaminants each be previously unidentified MLVs.

I also don't understand what you mean by "Lo et al have not yet demonstrated substantial genetic variation". If you look at either the phylogenetic analyses of their gag fragments or at the sequences themselves in the supplementary section, you can see that they have actually found fragments with greater genetic variation between them than was found between the comparable fragments of XMRV identified in the Lombardi study. If you are referring to the genetic diversity between the samples taken from the same patients 15 years ago and the freshly drawn ones, one would of course expect that to be small rather than 'substantial'.

We don't know for certain if the Alter study found PMLV only. As they isolated gag fragments (and only two env fragments), we don't know the host range within lab mice of the viruses in question. Due to viral recombination, many MLV and MLV-related viruses, such as XMRV, are hybrids of different viruses. In the case of XMRV, the envelope and part of the gag derive from an X-MLV, while the rest of the gag and the pol derive from a P-MLV. And even if the fully sequenced viral genomes turn out to be polytropic, that would not make the Alter study more suspect of contamination. You are correct that the Lombardi study was much more thorough and therefore potential contamination is even less capable of explaining its results. But in either case the improbability is very high. (Note also the comment by Lo et al in their letter to PNAS that they are now finding an antibody response, as the WPI/NCI had, in CFS patients with positive PCR for gag sequences, though they were vague as this is unpublished research.)

I think the contamination suggestion should still be taken seriously and all of the reagents, tubes etc used should be screened. If not least, to avoid further doubt.

I think if one carefully considers, for example, the arguments raised by Lo et al, Mikovits and those summarized in the blog by cfssufferer and elsewhere, one will find the contamination argument extremely weak, lacking sufficient explanatory power and requiring too many suppostions to form a tenable hypothesis. Such a hypothesis would have to explain, for example, the differences in results for test versus control subjects. Of course, all necessary precautions to prevent contamination should be taken in any study on MLVs, and assays for mouse cellular contaminants are useful to dispel doubt; indeed, both the Lombardi and Lo studies took these steps.

As for screening of reagents, etc, consider also the following from Lo et al's letter to PNAS, in response to those by Erlwein et al and Martin:

"We were aware that the SuperScript III One-Step RT-PCR System (cat. no. 12574–030; Invitrogen) had come under question for contamination with mouse DNA. For that reason, we rigorously examined the Platinum Taq polymerase we used (cat. no. 10966–034, lot 727463; Invitrogen) for any possible mouse DNA contamination. First, as stated in the article (3), no murine leukemia virus (MLV)-related gene amplicon was produced in more than 300 negative controls tested in parallel. Second, we tested the polymerase and our PCR assay system repeatedly using the highly sensitive mouse DNA-specific seminested PCR targeting the mitochondria DNA described; we never detected any mouse DNA contamination."

 

[Snow Leopard]

Screening for mouse DNA is insufficient, since this only rules out the direct contamination (eg mouse cells in the tubes). Secondly, viral infections aren't necessarily homogenous - infections aren't necessarily just of a single genetic variant, but a group of closely related viruses including that 'slight mutation' you refer to. The level of variations themselves depend on the evolutionary dynamics of the virus. So we can't yet be more specific on the expected levels of genetic variation.

I'm not saying contamination is likely, but weird things can happen in science. It is possible and similar cases of contamination have occurred before.

"Also bear in mind that the sequences identified by Lo et al appear to be distinct from known MLV gag sequences, thus necessitating that the alleged contaminants each be previously unidentified MLVs."

For the contamination to occur in an indirect way (eg there were no mouse cells), I would expect such distinct variants in the first place. I wonder what non-mouse cell cultures these variants can infect...

Mithriel - Unfortunately the controls of the Alter/Lo study weren't blinded and so some will question the results on that basis.

 

[Dr. Yes]

Hi Andrew1,

Screening for mouse DNA is insufficient, since this only rules out the direct contamination (eg mouse cells in the tubes).

You could argue that screening for mouse mtDNA is insufficient, but I'm not sure what the alternative is to screening for mouse genomic DNA, since the only other contaminant DNA would be retroviral. And in that respect, again, Lo et al's gag fragments did not match that of known MLVs, including from vectors. I don't know for certain if they compared their sequences to those of every known murine ERV, but I would be rather surprised if they did not.

Secondly, viral infections aren't necessarily homogenous - infections aren't necessarily just of a single genetic variant, but a group of closely related viruses including that 'slight mutation' you refer to. The level of variations themselves depend on the evolutionary dynamics of the virus. So we can't yet be more specific on the expected levels of genetic variation.

Indeed, retroviral infections in particular are rarely homogenous, though contaminants tend to be. If you are suggesting the possibility that contamination took place by a batch of viral variants, then the question is: how did they manage to sort themselves out such that the parent strain gag fragments were only in the old set of samples from Komaroff's patients and their variants in the new set? [I am going on Lo's statement in the press conference and Alter's elsewhere that they found mutations in the individual strains suggestive of viral evolution, and of course on the assumption that these researchers would not have missed the fact that the second set of sequences were incompatible with the first set.]

"Also bear in mind that the sequences identified by Lo et al appear to be distinct from known MLV gag sequences, thus necessitating that the alleged contaminants each be previously unidentified MLVs."

For the contamination to occur in an indirect way (eg there were no mouse cells), I would expect such distinct variants in the first place. I wonder what non-mouse cell cultures these variants can infect...

Am I correct that you are suggesting the existence of at least one unique MLV-related virus (including a set of variants) that has infected the cell lines used to produce reagents, etc? If so, which reagents in the Alter/Lo study do you postulate as the source of these contaminants?

One last point before I crash - even if there somehow was contaminant DNA in the FDA/NIH samples, it would have shown up in the CDC's assays when they shared positive samples - yet the CDC found them all negative. Either the CDC assay is hopelessly flawed, or those samples had no contaminant.

 

[Mithriel]

Reading these posts, it seems to me that nothing will convince doubters that the virus is not contamination as, in the end, it comes down to "these viruses were found in the samples, were they there before the blood left the patient or did they become part of it afterwards."

Looking at things from the opposite side is the obvious solution. Did these patients have anything going on in their bodies that was indicative of HMRVs being present?

The answer is a resounding "yes".

Patients show the same neurological and immunological abnormalities as are accepted as being caused by MULV infections in animals.

If you are trying to prove that tapeworms can be found in people with a wasting syndrome. You could argue that specimens were introduced as contamination. But if the same wasting is found in animals with a tapeworm then it is perverse to discount the evidence.

Science is never finished. There can always be something unexpected. To move forward we have to go with the most likely explanation until such time as it is proved wrong. Newtonian physics is not the whole story but it works well in day to day life. Quantum physics has given us a lot of modern society but it is not the whole story either. We do not say let's not use computers as there may be something we do not know yet.

It is time to move on and research how HMRVs can affect us, what is their role in the body, how they are transmitted.

That is how science works

Mithriel

 

[Snow Leopard]

You could argue that screening for mouse mtDNA is insufficient, but I'm not sure what the alternative is to screening for mouse genomic DNA, since the only other contaminant DNA would be retroviral. And in that respect, again, Lo et al's gag fragments did not match that of known MLVs, including from vectors. I don't know for certain if they compared their sequences to those of every known murine ERV, but I would be rather surprised if they did not.

It is possible for MLV contaminants to come from cell cultures other than those from mice. Indeed I would expect the viruses which are adapted to those particular cultures to be unique.

But the (small number currently) of viral sequences uploaded by Lo et al. do not actually show enough variation for this hypothesis to yet be considered implausible.

Am I correct that you are suggesting the existence of at least one unique MLV-related virus (including a set of variants) that has infected the cell lines used to produce reagents, etc? If so, which reagents in the Alter/Lo study do you postulate as the source of these contaminants?

I don't know what reagents were used in the first place, so I don't know.

One last point before I crash - even if there somehow was contaminant DNA in the FDA/NIH samples, it would have shown up in the CDC's assays when they shared positive samples - yet the CDC found them all negative. Either the CDC assay is hopelessly flawed, or those samples had no contaminant.

Which tests did they use? Testing for mouse DNA is not sufficient. All this does is narrow down the possibilities.

I'm not saying that the results are due to contamination, simply that the argument (for this study at least) is plausible until more substantial data is published - including recently mentioned serological data, evidence of genomic integration etc.

 

[Dr. Yes]

Greetings, Andrew1,

It is possible for MLV contaminants to come from cell cultures other than those from mice. Indeed I would expect the viruses which are adapted to those particular cultures to be unique.

Okay, so which non-murine cell cultures are you referring to that have relevance in Lo et al's study?

I don't know what reagents were used in the first place, so I don't know.

It seems that your argument for the plausability of contamination now hinges upon infected cell lines (which you have now limited to non-murine ones, if I understand you correctly). If that remains your concern, you might try to contact the researchers and find out what cell lines they might have used (however indirectly) and suggest that they screen them for MLV or MLV-related sequences.

But the (small number currently) of viral sequences uploaded by Lo et al. do not actually show enough variation for this hypothesis to yet be considered implausible.

Again, I ask how these speculative contaminants could have sorted themselves out into just the right patient tubes to produce the observed sequence results. That is enough to regard the contamination argument as implausible in the extreme, at least in the case of the 7 Komaroff patients who donated fresh samples.

(Me): "One last point before I crash - even if there somehow was contaminant DNA in the FDA/NIH samples, it would have shown up in the CDC's assays when they shared positive samples - yet the CDC found them all negative. Either the CDC assay is hopelessly flawed, or those samples had no contaminant."

Which tests did they use? Testing for mouse DNA is not sufficient. All this does is narrow down the possibilities.

See here: http://regist2.virology-education.com/1XMRV/8_September.html for the slides used in the oral presentation by Dr. Lo; click on the link "Pres." next to his name. Slide 17 shows the results of the reciprocal testing wherein the CDC and FDA (Lo) exchanged samples and ran their respective assays for detecing XMRV/MLV on one another's samples. It doesn't say on the slide which type of assays they used, though I assume it was PCR (Lo didn't have a serology test at the time they published; Alter mentions only the NIH collaborating with the NCI to do serology testing). Anyway, using their assay, the CDC found zero positives on any of the Lo et al's positive samples, although they could detect "MLV" in spiked control samples. If Lo et al's positive samples were contaminated with rogue MLV sequences, the CDC should ostensibly have picked them up.

I'm not saying that the results are due to contamination, simply that the argument (for this study at least) is plausible until more substantial data is published - including recently mentioned serological data, evidence of genomic integration etc.

Plausibility contingent upon an extremely improbable set of events is hardly plausibility, but few things are impossible, and as I said all precautions to prevent contamination should be taken in every study on MLVs or MLV-related viruses. That doesn't mean the likes of Myra McClure should wield that relatively tiny probability like a blunt instrument against all authors of studies that found XMRV, or that her argument be given anything approaching equal weight and coverage, or allowed to slow down recognition of a potential public health problem (especially in the UK). Unfortunately, that has been the effect (but hopefully not the intent) of the contamination argument by its most vocal proponents. It can have (and likely already has had) a chilling effect on research funding, as well, at a time when new funding is of great importance. I have been comparing the anti-contamination protocols of the Lombardi and Lo papers with those of various studies in MLV research published between the 1980's and the present, and I must say that the two CFS-related studies actually included more internal checks for contamination - and certainly more detail in the publications about these checks - than any of the others. The increased demand for precautions is obviously related to the potential significance of positive findings, and is certainly justified, but also to their political implications, which is not justified.

Caution and skepticism are necessary in science, but not to the point that they begin to paralyze the science itself, and not if arguments that do not stand up to scrutiny are repeated ad nauseam with limited and diminishing basis and without a practical experimental proposal that will answer the questions raised. The anonymous reviewer asking that the FDA/NIH paper be held essentially until Lo et al could demonstrate genomic integration of provirus is an example of this argument paralyzing the scientific process; among other things, this would have required the researchers to find integration sites for their MLV-related viruses, and in so doing would have delayed publication of a paper that will trigger more interest in and swifter funding of critical research (such as the effort to find integration sites!). I am a steadfast proponent of good science, regardless of the outcome, and firmly believe that this is something that should never be sacrificed or subverted, especially not in the attempt to learn about my own disease. I am also aware of the politics involved in science and research funding, and their potential impact on good science. I try to be aware of both considerations when I analyze the situation before us.

 

[eric_s]

Hopefully some more papers to follow - Dr Lo answers McClure's response letter in PNAS yesterday and his last sentence stated "Our recent collaborative studies with a National Cancer Institute group have shown that we can detect antibodies in most patients
with CFS with positive gag sequences and not inmost PCR-negative "

That's very good news. I hope we will get to see more results from this group (Alter, Lo and others) soon.

 

[xrayspex]

Hey somehow this thread fell off my radar, super interesting debate

just wanted to say thanks eric for responding, that was plenty thorough enough of an answer, I figured everything is too hazy yet to say any doc obligated to treat based on xmrv, but I do feel like saying at some point, nicely of course, ugh, if I get cancer down the road and the best advice you could come up with for cfs/me/xmrv was cbt exercise therapy, I will be talking to my lawyer, perhaps to no avail, but I am not one to quietly go down. I guess its premature to say that now as if xmrv doesnt pan out will look like a hothead.

urban travels I do have an fm dx too but I dont know if it really fits, got it in 96 and didnt even have the tender point thing, just PEM and spinal pain, I think when there is pain they used to think fm for sure.

Mark says he has "ideopathic immune dysfunction", i am starting to wonder if trying to chuck the cfs and fm dx out of my chart and just go with OI or something would be better til the viral part is sorted out....

anyway, sorry went a bit off topic here

 

[jace]

Mithriel's post deserves repeating. Andrew1, do you think her points have merit?

Reading these posts, it seems to me that nothing will convince doubters that the virus is not contamination as, in the end, it comes down to "these viruses were found in the samples, were they there before the blood left the patient or did they become part of it afterwards."

Looking at things from the opposite side is the obvious solution. Did these patients have anything going on in their bodies that was indicative of HMRVs being present?

The answer is a resounding "yes".

Patients show the same neurological and immunological abnormalities as are accepted as being caused by MULV infections in animals.

If you are trying to prove that tapeworms can be found in people with a wasting syndrome, you could argue that specimens were introduced as contamination. But if the same wasting is found in animals with a tapeworm then it is perverse to discount the evidence.

Science is never finished. There can always be something unexpected. To move forward we have to go with the most likely explanation until such time as it is proved wrong. Newtonian physics is not the whole story but it works well in day to day life. Quantum physics has given us a lot of modern society but it is not the whole story either. We do not say let's not use computers as there may be something we do not know yet.

It is time to move on and research how HMRVs can affect us, what is their role in the body, how they are transmitted.

That is how science works

I'd just like to add that the shortcut to proving causation is to treat the supposed cause, in a controlled manner, and observe if there is clinical improvement of the disease in vivo, in humans. There's many of us that would volunteer for well designed and supervised clinical trials.

 

[Snow Leopard]

I feel a bit silly debating the subtleties when no clear picture has yet emerged. The picture is still very much hazy and the only way it will become clearer is with a lot more funding spent on research. The immunological abnormalities of MLV in other species is still poorly understood also.
Some people will never be convinced eg HIV-AIDS deniers (despite massive and overwhelming evidence), but that level of evidence is currently a distant dream for us.

I remain unconvinced either way and will do so until a substantial number of us on this forum have tried several targeted strategies and the results become clear.

Unfortunately, the test results for many (50%) were negative on viral culture, at least according to the poll. Maybe the tests sensitivity isn't that high, maybe there are blood processing/storage issues even for patients. Maybe the reported results on the poll are false (I've just asked Cort about this..). There are many maybes. Or maybe XMRV/MLV at best is a contributing factor only to a proportion of cases, rather than most.

On a personal level, I'll put the results of my (VIPDx) serology test in my profile when the results come back.