Switzer - Publishes new XMRV varieties, and challenges Coffin's recombination theory

[eric_s]

Ruth, does it really not make a difference wheter the control is a sample spiked with genetic material or an actual clinical sample of the same kind like the samples studied?

 

[Bob]

I would say that one of the biggest problems is that all of the negative studies have been able to pick up the positive control at extremely low copy number. This means there isn't anything wrong with the PCR conditions or the qPCR conditions which leaves sample preparation or patient selection (unlikely given that the virus is supposed to be in the general population)

This is not the case if the patient samples have even lower copy numbers than the spiked positive controls.
There may be other reasons why spiked positive controls are easier to detect than wild virus.

Patient cohorts might be a significant issue. Judy Mikovits doesn't select ordinary CFS patients. She has further selection criteria.

I don't think they are. They're saying the lack of sequences variation is evidence for the contamination theory. They also say that what little variation there is in the sequences put's them as derived from 22RVI As Cort says................ Since the WPI must given GenBank their most variable sequences - and they obviously have the biggest store of CFS-related XMRV sequences of anyone - - the fact that that attempt didn't work is troubling. My guess is that we've seen the limits of XMRV variability in the blood in CFS and its very low (Unless an analysis is being done right now on those additions that has positive results.)

I haven't yet seen a peer reviewed analysis of the newest XMRV genbank sequences, so can we actually comment on them in an informed way?

Why do you think they're trying to 'have it both ways'? Perhaps I've misunderstood your argument?

A lack of gene variability says nothing about whether someone is infected with a virus or not, for a couple of reasons that I am aware of.
The apparent high frequency of lab culture contamination and xenograft contamination suggests a higher possibility that humans are exposed to these viruses via contamination.

This is an excellent point. I really don't think conspiracy theories are very helpful here.

There might not be a wider conspiracy, but there is definately an attempt from some individuals in the scientific community to move the science community away from XMRV research, especially in relation to CFS. I don't know how deep and wide the influence of those individuals is.

 

[RedRuth]

Ruth, does it really not make a difference wheter the control is a sample spiked with genetic material or an actual clinical sample of the same kind like the samples studied?

No, it really doesn't and anyway the Levy paper spiked the control DNA into a negative sample, this is to make sure that having genomic DNA in the sample or anything else in the sample doesn't inhibit the PCR reaction. DNA is DNA is DNA it's the binding of the primers to the target sequence that's important and getting the right conditions for the buffer, dNTPs, enzyme.

 

[RedRuth]

This is not the case if the patient samples have even lower copy numbers than the spiked positive controls.
There may be other reasons why spiked positive controls are easier to detect than wild virus.

Patient cohorts might be a significant issue. Judy Mikovits doesn't select ordinary CFS patients. She has further selection criteria.

But the positive controls are extremely low copy number which means the PCR is very sensitive why would the Mikovits' lab PCR be more sensitive than say the Levy lab's PCR? Not very likely especially as they did qPCR. The point about patient selection is valid but is muddied by the fact that they find positives in healthy controls.

I haven't yet seen a peer reviewed analysis of the newest XMRV genbank sequences, so can we actually comment on them in an informed way?

I was just repeating Cort's comment, I assume he keeps up with the current research. What new genbank sequences are you talking about?

A lack of gene variability says nothing about whether someone is infected with a virus or not, for a couple of reasons that I am aware of.
The apparent high frequency of lab culture contamination and xenograft contamination suggests a higher possibility that humans are exposed to these viruses via contamination.

It comes down to method of replication. Generally retroviruses use their own reverse transcriptase for the first stage of infection of a host cell, this enzyme is error prone so sequences between patients and even from the same patient will vary considerably. If however the retrovirus has become endogenised into a Human cell line then replication will only be via the host error checking machinery. So high sequence variability is evidence of an infective, replicating virus. Low sequence variation is evidence of a contamination of lab reagents with the DNA from an endogenous retrovirus.

 

[eric_s]

No, it really doesn't and anyway the Levy paper spiked the control DNA into a negative sample, this is to make sure that having genomic DNA in the sample or anything else in the sample doesn't inhibit the PCR reaction. DNA is DNA is DNA it's the binding of the primers to the target sequence that's important and getting the right conditions for the buffer, dNTPs, enzyme.

I think Judy Mikovits said it does make a difference, but i have no background in these things, so i will just have to take your statement and hers and leave it open.

I just find it very hard to believe that a number of labs would find XMRV/MRV in different kinds of samples with different types of methods, more often in cases than in controls, and not figure out it's caused by contamination for such a long time. At least some of the studies were blinded, which makes it even harder to explain, if there is not truly an infection.

 

[Jemal]

I disagree that some want to bury the research because of its putative origin in a lab. The paper and others suggesting so have been published, some by NIH funded scientists- and that aspect has been freely discussed with the National Cancer Institute even producing a video explaining how they thought that happened. Even after those papers were published there were no media reports that I saw exclaiming "lab creates virus!"; which suggests the media doesn't think that's a hot topic at all.

I am not sure what kind of state the US media are in... but over here (Netherlands) they are in a bad shape. They mostly recycle the content of the big press agencies, like Reuters or they lap up easy stories. This is not an easy story to cover. Far from it: many scientists are disagreeing with each other and I am sure the few journalists that might be interested (still talking about the Netherlands) think it's a hornet's nest. So that the media are not reporting on it, doesn't mean it's not a hot topic, or at least I think so.

There might not be a wider conspiracy, but there is definately an attempt from some individuals in the scientific community to move the science community away from XMRV research, especially in relation to CFS. I don't know how deep and wide the influence of those individuals is.

I fully agree with this.

 

[eric_s]

One more interesting thing, Ruth, is that basically all the labs i know of that could find these viruses or sequences first didn't find them and then got in contact with the WPI and after this they were able to find something. It happened like this with the Lo lab (FDA) too, if i remember correctly. I don't think this is beacuse they got contaminated material from the WPI, because they certainly checked for that. Now it would be interesting to know if these labs, prior to finding XMRV/MRV in clinical samples, were able to pick up the spiked positive controls. If they could find the DNA in these controls but not in clinical samples that would argue against that kind of controls, i think.

 

[Bob]

But the positive controls are extremely low copy number which means the PCR is very sensitive why would the Mikovits' lab PCR be more sensitive than say the Levy lab's PCR?

Well, this is the essential issue. We just don't know why Judy Mikovits can detect XMRV, and others can't. That's why many of us want to see the XMRV research continue, until we have definite answers.

But with a novel virus, and copy numbers at the limits of detection, it doesn't seem beyond possibility that the small changes in methodologies and techniques in each study might make all the difference between detecting and not detecting the virus. The number of variables are enormous.

Judy Mikovits has been refining her techniques for years now, and she is reportedly still detecting XMRV in CFS patients and healthy controls at different rates, which seems pretty significant to me.

I was just repeating Cort's comment, I assume he keeps up with the current research. What new genbank sequences are you talking about?

The WPI published some new sequences about 3 or 4 months ago. I haven't seen a peer reviewed analysis carried out on them yet. I don't know what information Cort is basing his comments on.

It comes down to method of replication. Generally retroviruses use their own reverse transcriptase for the first stage of infection of a host cell, this enzyme is error prone so sequences between patients and even from the same patient will vary considerably. If however the retrovirus has become endogenised into a Human cell line then replication will only be via the host error checking machinery. So high sequence variability is evidence of an infective, replicating virus. Low sequence variation is evidence of a contamination of lab reagents with the DNA from an endogenous retrovirus.

There are two other reasons why the sequence variation might be low in a human infection:
1. XMRV may be like HTLV, which has very low variation.
2. The route of infection may not be from person to person, but it may be from contaminated lab product to human, such as in vaccines.

 

[jace]

Well, this is the essential issue. We just don't know why Judy Mikovits can detect XMRV, and others can't. That's why many of us want to see the XMRV research continue, until we have definite answers.

The IMEA have a few pages explaining the technicalities of PCR and other assays:
How PCR can go wrong
Validating an assay
Multiple primers needed
PCR and HGRVs
Optimising a Western Blot

 

[currer]

Quote from Judy Mikovits reply to Science (the EEC)

...but good science is difficult and takes time...

 

[RedRuth]

Well, this is the essential issue. We just don't know why Judy Mikovits can detect XMRV, and others can't. That's why many of us want to see the XMRV research continue, until we have definite answers.

But with a novel virus, and copy numbers at the limits of detection, it doesn't seem beyond possibility that the small changes in methodologies and techniques in each study might make all the difference between detecting and not detecting the virus. The number of variables are enormous.

True, but Lo et al evidently did do some kind of qPCR in their PNAS paper,( it's in the supplementary) to test the sensitivity of their detection (threshold: 100 copies in 30 ng Human DNA). It's at least an order of magnitude less sensitive than Levy's method (threshold: 10 copies in 100ng Human DNA) It really is a shame that the Mikovits lab haven't determined how sensitive their method is.

There are two other reasons why the sequence variation might be low in a human infection:
1. XMRV may be like HTLV, which has very low variation.
2. The route of infection may not be from person to person, but it may be from contaminated lab product to human, such as in vaccines.

1. It's true that HTLV1 infects cells that then expand clonally (T cells I think) but there's no evidence that XMRV infects these cells but the real problem is with the phylogenetics. The sequences don't seem to fall into a nested hierarchy that would explain a slow evolving virus like HTLV (this is the conclusion of the Coffin paper that's the subject of another thread)

2. This is a possibility though it seems far fetched. I'm no epidemiologist but is there any link between vaccination and ME?

 

[Bob]

I'm no epidemiologist but is there any link between vaccination and ME?

Yes, there is a link, at least anecdotally. But I don't know if there has been any solid research on this.
Hep B vaccines have been associated with ME, and people have reported becoming ill on return from holidays, for which they received vaccinations beforehand.
Also, health workers are at high risk of getting ME, and they receive more vaccines than average.
Again, I don't know how much research has been carried out here.

Also, it could be possible that people carry XMRV for years before becomming ill with ME, in which case any link with vaccines would not be obvious.

 

[Mark]

This is a possibility though it seems far fetched. I'm no epidemiologist but is there any link between vaccination and ME?

I would say there is quite a lot of very circumstantial evidence to be found pointing in this direction when you look into the history, politics, pathophysiology and epidemiology from a generalist perspective. Pointers that I can think of...and yes I realise these are very circumstantial...the point is that this overall picture seems (to me) consistent, in the round, and explains many mysteries...

- Perhaps the most suspicious evidence: Best known/seminal outbreaks: 1934 Los Angeles, 1955 Royal Free Hospital, almost exclusively affecting health workers and not patients (were those health workers heavily or experimentally vaccinated???). Experimental polio vaccines were being trialled in those areas at those times. The disease profiles in those outbreaks were initially characterised as somewhat atypical forms of polio.

- I've come across several anecdotal patient accounts of their illness being provoked or seriously worsened soon after vaccination, though I certainly don't think there's any good evidence either way on this subject - a detailed survey would be very interesting.

- Parallels/connections with autism: Some commentators go so far as to claim - on the basis of pathophysiology (eg immune/IBS/cognitive impairment aspects) - that autism and ME are fundamentally the same condition, with autism striking the same neurological aspects at a different stage of development; and there are many accounts of parents with ME who have children with autism. Suspicion of autism/vaccination connection remains despite the alleged disproof of this theory; considerable overlap between the political opponents of these theories.

- Recent Scandinavian 'narcolepsy' outbreak following H1N1 vaccination: children in at least 10 countries developed a novel neurological disease following H1N1 vaccination, which appears to only affect specific genetic groups; big pharma is now 'investigating' with big studies in the areas that weren't affected...this incident demonstrates that rare and new neurological conditions can be induced by vaccination, in localised outbreaks - possibly due to MLV-like contamination?

- Nature of ME/CFS: Impaired neurological and immune function; often relapsing/remitting but I have never encountered a credible account of a complete cure, the condition is considered by most of those who have 'recovered' somewhat to be lifelong - as a risk of relapse, at least - all of which seems consistent with a persistent low-level retroviral infection (especially the peculiar immune impairment).

I realise that's all pretty sketchy, but in all of these areas, sadly it's the only evidence we have got - none of these questions have ever been properly investigated. To me, the contaminated vaccine theory, combined with the recent discoveries around MLV creation/contamination, and XMRV, presents a very credible narrative with the ability to answer a wide range of mysterious questions which are otherwise very hard to explain. The whole thing is a very complex picture, but the more you look into the details, the more the dots seem to join up and it makes sense. Doesn't mean it's right of course...but I find it quite compelling...I'm really not wedded to vaccine mediated infection as a theory, but it seems like one of the strongest hypotheses going...

 

[Bob]

I'm very disappointed with scientists who are basing their assumptions on something like phylogenetic trees. They are not "real" things and prove absolutely nothing.

Phylogenetic trees for anyone who hasn't been involved with them for XMRV, are mathematical models that supposedly show how different things (like viruses) could possibly related to one another.

They do not show how things do in reality relate to one another and they do not prove anything. They are just a way of comparing and guessing how data could possibly be related. Like all mathematical models they suffer from the old "garbage in, garbage out" and there are many different types, and different parameters that can be set up to determine the outcome. A lot of guessing.

Scientists will need to come up with real data based on actual things if they wish to prove that contamination of samples or equipment occurred. I for one, wish that they would either provide the proof or start looking at this problem with more open minds.

Even if they want to argue that phylogenetic trees are "proof" they are still stuck with other scientists who argue that this is in fact proof for the contaminated patients theory.

i.e. that the lack of genetic diversity is because of a common vector

(start)
Once a virus is endogenised, it is forced to follow the evolutionary rate of the host. Since XMRV is integrated in cell-lines the virus evolution is restricted to the host's pace of evolution, and viral descendants have none or minimum sequence diversity. Thus, if a contaminated product, previously cultured in cell-lines, is administered to people then the infections would provide the evolutionary patterns reported by Hue and colleagues.4 If the immunological data reported by Lombardi and colleagues5 are correct, then we need to trace the common source of XMRV and not through human contact

The Lancet Infectious Diseases, Volume 11, Issue 4, Page 264, April 2011
(end)

The scientist arguing "contamination" cannot have it both ways. It seems that they lose credibility by not examining all possibilities.

You make very good points here ukxmrv...
Phylogenetic trees are helpful but cannot be used in isolation.
And if lab products are contaminated with XMRV, then surely this is a threat to the human population.
Surely it must be easy for vaccines to become contaminated if no one has been testing cultures, cell lines and xenografts for XMRV contamination up to now.

 

[Bob]

I would say there is quite a lot of very circumstantial evidence to be found pointing in this direction when you look into the history, politics, pathophysiology and epidemiology from a generalist perspective. Pointers that I can think of...and yes I realise these are very circumstantial...the point is that this overall picture seems (to me) consistent, in the round, and explains many mysteries...

- Perhaps the most suspicious evidence: Best known/seminal outbreaks: 1934 Los Angeles, 1955 Royal Free Hospital, almost exclusively affecting health workers and not patients (were those health workers heavily or experimentally vaccinated???). Experimental polio vaccines were being trialled in those areas at those times. The disease profiles in those outbreaks were initially characterised as somewhat atypical forms of polio.

- I've come across several anecdotal patient accounts of their illness being provoked or seriously worsened soon after vaccination, though I certainly don't think there's any good evidence either way on this subject - a detailed survey would be very interesting.

- Parallels/connections with autism: Some commentators go so far as to claim - on the basis of pathophysiology (eg immune/IBS/cognitive impairment aspects) - that autism and ME are fundamentally the same condition, with autism striking the same neurological aspects at a different stage of development; and there are many accounts of parents with ME who have children with autism. Suspicion of autism/vaccination connection remains despite the alleged disproof of this theory; considerable overlap between the political opponents of these theories.

- Recent Scandinavian 'narcolepsy' outbreak following H1N1 vaccination: children in at least 10 countries developed a novel neurological disease following H1N1 vaccination, which appears to only affect specific genetic groups; big pharma is now 'investigating' with big studies in the areas that weren't affected...this incident demonstrates that rare and new neurological conditions can be induced by vaccination, in localised outbreaks - possibly due to MLV-like contamination?

- Nature of ME/CFS: Impaired neurological and immune function; often relapsing/remitting but I have never encountered a credible account of a complete cure, the condition is considered by most of those who have 'recovered' somewhat to be lifelong - as a risk of relapse, at least - all of which seems consistent with a persistent low-level retroviral infection (especially the peculiar immune impairment).

I realise that's all pretty sketchy, but in all of these areas, sadly it's the only evidence we have got - none of these questions have ever been properly investigated. To me, the contaminated vaccine theory, combined with the recent discoveries around MLV creation/contamination, and XMRV, presents a very credible narrative with the ability to answer a wide range of mysterious questions which are otherwise very hard to explain. The whole thing is a very complex picture, but the more you look into the details, the more the dots seem to join up and it makes sense. Doesn't mean it's right of course...but I find it quite compelling...I'm really not wedded to vaccine mediated infection as a theory, but it seems like one of the strongest hypotheses going...

Interesting post Mark.
And a nice summary of the possibilities, thanku.

 

[RedRuth]

I'd have to disagree with that. Alot of money has been wasted on studies involving hundreds of thousands of children to show that there's no link between vaccines and autism, all started by a discredited piece of research. The money could have been spent better on finding the real cause of autism and possible treatments.

 

[leela]

"Discredited" is a word often used by the media when there is stirred-up controversy like this. Just watch "Under Our Skin" and the Burzynski movie, and you will see how and why skewed studies and smear campaigns that discredit doctors and theories are put together. (It's a horror show of negative propaganda and outright lying.)
Seeing those films, one can begin to see how this kind of organized harassment is not conspiracy theory it's bald-faced fact. There is a lot of in-fighting not just for protection, but for profit, which really began in earnest in 1980 when it was, against all logic, suddenly permissible to patent organisms.
This has skewed medical and scientific motivation in unimaginably nefarious ways. Though the films I mention are not about vaccines, I was very much enlightened by them regarding the process by which information is suppressed, skewed, and manipulated for interests other than public health, by the very agencies that are allegedly there to protect it. It really pisses me off!

 

[Bob]

I'd have to disagree with that. Alot of money has been wasted on studies involving hundreds of thousands of children to show that there's no link between vaccines and autism, all started by a discredited piece of research. The money could have been spent better on finding the real cause of autism and possible treatments.

Whatever the cause of autism, vaccines can cause neurological disorders in children, and the children have been compensated by the US government.
The US authorities have also started a new investigation into the link between autism and vaccines. (Sorry, I can't remember the details.)
Also, there seems to be a link between Gulf War Illness, and vaccines.

 

[markmc20001]

I totally agree money has been wasted on vaccine research RedRuth. I also agree that alot of money has has been wasted on all the CFS research by William Reeves, Simon Wessley, the pace trial, etc...

 

[RedRuth]

No medical procedures are without risk, that said I think you're referring to the Hannah Polling case. The child had a mitochondrial disorder (a point mutation in the gene for the 16S ribosomal RNA (T2387C)), a subset of which cause autism like symptoms. Children with these disorders often regress when they get encephalopathy from any kind of stress or fever. In this case the US government accepted the fever may have been caused by vaccine ( a common side effect), it could just as easily have been any common childhood infection. I don't know if you have children but fevers aren't exactly uncommon in young children. At worst vaccination can trigger an extremely rare underlying mitochondrial disorder but then again so could any childhood illness.

Anyway, that's the last thing I have to say about vaccinations.