XMRV not found in Fibromyalgia Patients in Spain

[currer]

Hi,
I understand that this thread is discussing the minutiae of PCR so my comment will go off at a tangent, but I really feel that we should have more faith in the WPI and in people like Alter, Ruschetti and Mikovits.

From long experience in the ME world I have noticed that IT IS ALWAYS THE BEST PEOPLE who are prepared to listen to us and to try to help us. It is easy to judge with the collective voice but it takes an independence of mind to look at the patient in front of you and ask yourself some fundamental questions.
This makes for a better scientist. It might sound odd but there are moral and ethical issues here and those who try to help us are better people - I have seen this time and time again.

What I mean is that those who have believed us and accepted our story that we are ill, and have not made the easy judgement, and the safe one, will always be better scientists and will have the commitment to find the cause of our illness. What has this spanish guy ever done for us? Why should we be influenced by him when we have better, more committed scientists on our side? Has he ever thought much about ME/CFS? What does he care about our illness?
Negative studies will always be easier to do where the science is new. To really think and look for an answer takes care and understanding and commitment. This is what leads to good science, science that will look with understanding for the right answer, which means to look at the patient, not just at what goes on in the lab.
I stick with the WPI.

 

[MNC]

Since I am from Spain I want to add that I am starting to notice how more and more doctors are accepting CFS as a real illness, but not our authorities and those guys who come out with these predictable negative studies that we all know who they are.

For instance, today I was visiting an internist and a neurologist for different "symptoms" (blurred vision, nistagmus, abnormal eye movement (as said by eye doctor and optician) asleep right leg with loss of strength, cramps in legs, trembling in fingers, left arm and chest pain, swollen abdomen with pain, gas, nausea, diarrhea, lungs, sinus throat and nose pain and inflammation, low body temperature, orthostatic intolerance, dizziness, vertigo, cognitive inability, short memory loss... etc, etc,etc).

And they are now going to the other side. They soon will stop the conversation saying "CFS". Meaning waste of time to discuss all the symptoms because it's just CFS, and that they know it, that lots of us tell the same symptoms and stories and they can do nothing about it.

Last friday I was visiting an allergy doctor and said the same. He said: "Years ago we all thought this was emotional somatization because it was all middle aged women that we called them neurotic or anxious or depressed. Now we see it so often and not only women but also men and young people that we certainly have to admit that there must be something going on and perhaps CFS and fibromyalgia are very real not-emotional diseases". I was telling him my reactions to dental anesthesias, foods, chemicals, etc, and he was looking like... this cannot be somatization, another one with this disorder and I don't know what on earth it can be other than CFS-MCS-FM.

And the list goes on and on. Every doctor I see is more and more saying "you have CFS". Like we have passed from complete denial to a more genralized acceptance but also not wanting you to be their patients and sending you to someone else. They even have difficulties to put it by written in a medical report that could help me to prove my illness. But something is something and I can notice this change in the medical community.

So maybe we are closer to an acceptance from the authorities one day that could lead to getting public funds for research. I have never "hated" doctors for this. I was always feeling in their shoes and what I would do or say if I was in their situation. In fact I still prefer traditional doctors to alternative doctors who are very costly and promise a lot, say that they do believe in CFS but ultimately you won't improve either after spending a lot and hearing many false hopes and dubious unproved medical theories. AT least all my doctors are for free here, either by our social security service or through my private medical insurance that works pretty well and allow me to take endless expensive tests fast without any objection or rejection.

I just hope this keeps spreading and we could advance a little if more and more doctors are losing the fear to admit and recognize CFS.

 

[asleep]

The WPI was able to detect "wild-type" XMRV using an unvalidated PCR assay.

I've already addressed this twice, but I'll humor you a third time. First, I want to clarify terminology:

For an assay to be "validated," it must be shown to be able to detect XMRV from a known positive clinical sample (i.e. wild-type virus in clinical conditions). This is important given the nascent state of XMRV science (unknown clinical sequence variability, unknown PCR complexities). It is not sufficient to "validate" an assay against a VP62 synthetic-clone-based positive sample because this bypasses too many potentially confounding variables.

Validating an assay can be thought of as using a positive clinical control.

Now, as I've said before, a positive control is only necessary for negative findings in order to show that you are not producing false negatives. In the case of the WPI, their positive findings don't require a positive clinical control. They only needed a negative control to rule out false positives (which I believe they did more than adequately at the time).

So, in essence, it is nonsensical to say their assay is "unvalidated." Their assay was de facto "validated" by virtue of its ability to find wild-type virus in clinical samples.

The Huber-laboratory was able to detect wild-type XMRV and (wild-type?) MLV-like sequences using, by your metric, an unvalidated assay.

Firstly, they used two different assays. You are correct that both of their assays were "unvalidated." They were calibrated against a VP62-based sample and therefore never shown to be capable of detecting virus in a true clinical sample. The key difference from the WPI study is that their "unvalidated" assays never actually found wild-type virus in their clinical samples.

In essence, I don't understand how you come to the conclusion that they were able to detect wild-type XMRV. Their pol assay detected nothing. Their much-less-stringent gag assay did detect a variety of sequences, but all were shown to likely be due to contamination:

"Overall, our data are consistent with the conclusion that the positive results obtained with the XMRV gag PCR assay are due to variable contamination of the human samples with mouse DNA, most likely in laboratory reagents."

Unlike the WPI's case, detection of mouse contamination does not provide de facto validation of their ability to detect wild-type XMRV. If the contamination is factored out of their findings, there is no indication that they found anything at all.

So, in summary, you have over-characterized their study by asserting that they did in fact find wild-type virus when they did no such thing.

So what gives?

Who is the honest scientist?

What gives is that, as I've shown, your apparent contradiction is not a contradiction at all.

As for who is an honest scientist, I have seen nothing to date that would make me question to honesty of the WPI. Nor do I see anything particularly dishonest about the Huber study, though they do make a few suspect statements in their paper. The dishonesty lies in how the Huber study (and it's Retrovirology companions) have been represented in the press and by certain individuals and groups.

 

[asleep]

Hi,
I understand that this thread is discussing the minutiae of PCR so my comment will go off at a tangent, but I really feel that we should have more faith in the WPI and in people like Alter, Ruschetti and Mikovits.

From long experience in the ME world I have noticed that IT IS ALWAYS THE BEST PEOPLE who are prepared to listen to us and to try to help us. It is easy to judge with the collective voice but it takes an independence of mind to look at the patient in front of you and ask yourself some fundamental questions.
This makes for a better scientist. It might sound odd but there are moral and ethical issues here and those who try to help us are better people - I have seen this time and time again.

What I mean is that those who have believed us and accepted our story that we are ill, and have not made the easy judgement, and the safe one, will always be better scientists and will have the commitment to find the cause of our illness. What has this spanish guy ever done for us? Why should we be influenced by him when we have better, more committed scientists on our side? Has he ever thought much about ME/CFS? What does he care about our illness?
Negative studies will always be easier to do where the science is new. To really think and look for an answer takes care and understanding and commitment. This is what leads to good science, science that will look with understanding for the right answer, which means to look at the patient, not just at what goes on in the lab.
I stick with the WPI.

Very well said, currer!

I will reiterate two points I made before:

1. After 16 months, no one has yet attempted a genuine replication of methods shown to be capable of finding XMRV in clinical samples.
2. Despite this severe shortcoming from would-be dis-provers, there exists what increasingly feels like a concerted campaign to sell the illusion that these negative studies have merit in aggregate. They don't.

We are witnessing a political attempt to bury the WPI's quality work (which is underfunded and apparently black-balled from further publication) under a mountainous glut of scientifically flaccid studies.

Until the WPI's findings are given a fair scientific hearing, we must be extremely vigilant in demanding absolute scientific rigor and not falling prey to anything less.

 

[jspotila]

I've already addressed this twice, but I'll humor you a third time. First, I want to clarify terminology:

For an assay to be "validated," it must be shown to be able to detect XMRV from a known positive clinical sample (i.e. wild-type virus in clinical conditions).

Since we are clarifying terminology, "wild-type" virus does not mean what I thought it did when I first heard the phrase. I assumed "wild-type virus" meant virus out in the wild, meaning clinical samples. That is NOT what it means.

"Wild type" virus means an original virus (often laboratory-adapted) from which mutants are selected and which is used as the basis for comparison. The correct phrase for what you are talking about - virus isolated from clinical patients - is called "field isolate" or "clinical isolate."

A validated assay is one that consistently provides test results that identify samples as positive or negative. The difficulty of doing this is highlighted by the Blood Working Group results. WPI provided four XMRV positives, identified as positive by WPI by at least 2 of 3 methods (PCR, serology, culture). Even of these four known positives, WPI did not consistently get positive results in the BWG.* What that says to me is that creation of a validated assay for XMRV is proving to be a challenge.

*Phase 2a, WPI found all known positives to be negative in the whole blood assay. Nested PCR on plasma produced 3/4 negatives for samples not held before processing; 4/4 positive for samples held 2 days before processing, and 3/3 (one not tested) for samples held 4 days before processing.

Phase 2b (same 4 known people but blood collected a different day and testing done blinded), WPI found all known positives to be negative by nested PCR on plasma (samples held 0 days or 2 days). Nested PCR on PBMC found 1/4 positive in samples not held before processing, and 2/4 positive in samples held 2 days.

 

[Mithriel]

The WPIs methods work because they consistently detect virus and the commercial test offered also works. These tests are not being used by the Blood Working Group simply because donated blood must be tested using a method that is fast and cheap as well as reliable. This group is not working on ME or CFS, they are looking for a way to protect the blood supply, worthy, but not of major relevance to us.

A fast, cheap test will help us if it can be used in a diagnostic lab, but much of the research we desperately need could be getting done now if labs would use the WPI method. (I particularly want to know if my children are at risk if I hug them and if my husband is going to get ill.) There is much that could be getting done for us now if research teams would use the method that works.

Diagnostic virology labs use PCR routinely, BUT, it is not a simple process. It can take years to develop primers which detect every variation of a virus likely to be found and that only after finding which tissue has the most chance of success.

Some viruses have been studied for years but they can't get PCR to work.

It is not a test that has ever been used for even known viruses by simply picking up a simple primer and running a test. I am getting increasingly frustrated by all these 0/0 studies. If a team really wants to know if a particular population has HMRVs why don't they use a method that has been shown to work. Then if it is negative they will have shown something.

It is not scientific to continually repeat a method which does not give results. Biological systems continually confound notions that things "must be" so no matter how confident you are in your test method continually finding nothing should lead you to use the methods that have worked - especially when they are the sort of method necessary to detect MuLVs in other mammals.

(In the Huber study, the percentage of controls samples and patients samples infected was very similar so contamination was the likely answer.)

Mithriel