Experiments In Vivo

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So here we are, two years after the scientific community was told which rock to look under, still arguing about whether two or three scientists can reproduce their work or not. In the meantime, a promising avenue of treatment, antiretrovirals, has been shut down like a prohibition, for the flimsiest of reasons. Too dangerous (compared to what?). Too expensive (for whom?). AIDS patients need their drugs (since they have a serious illness). How can we treat it if we don’t know the precise agent we are treating? The way doctors treat people every day. Best guess. I actually think we have a better model than the rheumatologists are using to prescribe incredibly toxic drugs for patients with autoimmune diseases.

AIDS patients have to be treated forever, but we don’t have any idea if that is true for us or not. Just think how much we’d know now if part of the money that was spent trying to find a virus that doesn’t exist in nature could have been spent on very simple clinical trials of safe, existing drugs. It is becoming clear that at least some are concerned about lab contamination by viruses that are very good at infecting human cells in vitro. See Zhang and Sfanos on the side bar. It’s about time somebody worried. Whatever works, and fear is a good motivator. It worked for HIV.

Here are a few excellent papers that have helped me to refine my working model, though I don’t like it that it is going towards greater complexity, since I like grand unifying theories. But the level of complexity of the problem is intersecting with the state of the art. Cutting edge sequencing and analytics are required.

I still think it’s simple retroviruses at the bottom of it, and maybe not just gammas. Simple retroviruses go for the germ line and become endogenous. Multiple assaults. Most end as ineffective sequences, with deletions, tamed by restriction factors that give an individual’s offspring an evolutionary edge. ERV’s can be defective and still cause disease. They can even become symbionts:

Defective sequences can be reconstituted by new incoming. It is not as simple as one sequence or one virus, or even five strains of one virus. Lots of viruses and pieces of viruses. Lots and lots of exposures, if it came from vaccines, grown in all kinds of cells, murine and avian, administered parenterally to most of the human race for decades, and subject to recombination. There were clearly waves when people got sick, but those may have been recombination events, when some necessary piece was supplied to reconstitute something that was there already. Or maybe there were waves of helper viruses that went out and turned on what was there. Or particular environmental toxins that activated one from an earlier invasion (from the Weiss paper above: “..we were able to show that treatment of normal chicken cells with a variety of activating agents such as ionizing radiation or carcinogens stimulated release of virus..”).

This was probably part of the problem too; endless selective breeding of sick mice that produce retroviruses that they are resistant to, but the cells of other species may not be, hence putting lab workers at risk, especially those working directly with tissue culture and xenografts. The Mouse Trap: The dangers of using one lab animal to study every disease. Engber.
The younger women I am seeing, and who have written to me, often have symptoms consistent with PCOS (polycystic ovary syndrome). The few I have tested in my practice, have laboratory evidence of LH insensitivity, LH/FSH ratio greater than 2 in a menstruating woman with normal FSH. LH insensitivity interferes with the egg being released from the developing follicular cyst, so the corpus luteum doesn’t form properly, progesterone isn’t made normally, and estrogen dominance, with all its problems, ensues. The condition is also characterized by high androgens and a dysmetabolic syndrome causing central body fat distribution. Does progesterone deficiency favor the virus? Physiologic replacement is a powerful therapeutic option for women so affected. PCOS is a very common cause of reduced fertility, so if germline retroviral infection is involved, it isn’t a very good strategy for a virus that is not spread horizontally. However from an evolutionary perspective, if the virus succeeds in most of its hosts, the few that become infertile and are a dead end, are just part of the evolutionary process. Remember that only a very small percentage of HTLV patients ever get sick and genetic factors are probably key.
Env proteins are strongly implicated in the neuropathogenicity of MLV’s, and also recognized in the evolving retroviral model of RRMS (relapsing remitting multiple sclerosis).

Could antiretroviral drugs be effective in multiple sclerosis? A case report. Maruszak: This is a letter to the editor behind a paywall, but documents the resolution of significant neurologic impairments, including bladder and bowel incontinence, in an MS patient after being treated with HAART for HIV infection. The patient developed MS and was infected with HIV in ’85. He was treated with HAART in ’96, improved rapidly with resolution of many MS symptoms, including fatigue, within two years. It happened in the late ’90’s and it was just published… It is the only paper I could find where anyone has documented an effect of arv’s on MS, despite the fact a retrovirus has been suspected for over a decade. How’s that for blinders! What is it about this particular class of drugs that has everybody so spooked? Is it because AIDS patients have to take them forever? It may not be the case here. The best anecdote I’ve heard was 16, only sick for 8 months, responded quickly, stopped treatment after 6 months and has stayed well, as far as I know. And even if the drugs are for good, they are very clean drugs. HIV infected people have gotten very good research into their disease.

The literature suggests that the search for a sensitive enough reverse transcriptase assay was abandoned for HIV, as specific testing became highly sensitive. However, if you were looking for generic replication competent retroviruses that you could monitor, a clinically useful RT assay would seem to be indispensable. RT assays have been used in the lab since the late ’60’s, but seem to have been abandoned more recently, except for research purposes involving monitoring of retroviral vectors. Maybe one of the scientists reading can explain why this test isn’t clinically available? Why wouldn’t it be useful for MS, for example, given the suggestions of the papers above concerning that disease? Maybe some money to be made here, for any diagnostic test patent seekers who might be reading.

Ali remains on Viread/Isentress and continues to be surprised by greater than expected resilience, e.g. rapidly recovering from having her wisdom teeth extracted. I came off Isentress a couple of months ago and didn’t notice much of anything. It didn’t seem a good idea to stay on monotherapy and someone already committed to the experiment needs to give a protease inhibitor a try; therefore, I started Lexiva two weeks ago.

There was a recent paper showing that amprenavir inhibits XMRV in vitro (Li/Wlodawer on the side bar), but also, there are several clues in the literature that suggest that it might inhibit MLV proteases more broadly. HIV treatment wasn’t truly effective until PI’s were added. The first time I tried Lexiva, as a fourth drug then, still using an HIV model of HAART, it had the unexpected effect of CNS activation and it is doing that again. I describe it as “turning up the volume”, a perceptual shift. I am more reactive, but that is dying down now. It doesn’t do this with AIDS patients and I have no explanation, other than it moves the disease in some way, since I don’t see how it is an adverse effect of the drug. The other arv’s shook things up for me for a while too, but that felt like an inflammatory flare of usual symptoms. Physically, I think I feel a bit better, stronger in the last few days, but it could well be the swing of the pendulum. I will stay the course and report.

Here is a letter that I received a few days ago:

Dr. Deckoff-Jones,
I’m writing to you in the hope that by sharing a little of my medical history I can help. If XMRV is totally out of the picture it must in my case be a related retro-virus. I think if there were a place to pool ME/CFS patient information there might be something made obvious through comparative analysis.
I started on AZT about a year and a half ago On 3/6/10, my health seemed to gradually improve, by december I developed pain on the inside of both legs so at the end of december I stopped taking AZT. I declined rapidly and by the first of February I was worse than before I started on AZT. A few days into February I started taking Viread and Isentress and felt even worse for the next 10 days to two weeks (which I had read to expect this) I actually kept busy just to take my mind off how bad I felt.
Gradually I started to feel better and by the end of May of this year I thought I was well on my way to a normal existence. I think it was July and September I declined. Today I am definitely better than when I started but still far from my goal. I don’t want to stop taking anti-retrovirals.
I’m wondering if I would have done better if I had included Emtricitabine and if I should start now. I will discuss it with my doctor. If a yet unknown retrovirus is the culprit, it’s anybody’s guess as to which drugs are most effective.
I think the best course of action would be to find the cohort who have responded to the three above mentioned drugs and divide them into groups to see how they respond to other (additional) anti-retrovirals.
I think everyone affected would be perfectly okay with finding the treatment before finding the cause. Even if it’s a small subset of patients, we will have chipped away a little at this stumbling block we call ME/CFS.
I have had this for 18 and 1/2 years and I’m about to turn 64. So like everyone else I want answers now.

Sick patients trying to figure it out on their own, the ultimate failure of an ineffectual system. Scientists not only don’t talk to patients or doctors, they don’t even talk to each other, since somebody might steal their ideas. All closeted, each guy alone in a lab looking at a little piece of the elephant, writing in notebooks with pens?!! No copies? It seems even more dysfunctional than our broken medical system, that a dispute between a scientist and their employer can result in the hopes of an entire patient community being dashed on the shoals of intellectual property law and the criminal justice system.

I would like to thank Dr. Lipkin for being the voice of reason in an insane situation. He is positioned to help us. I hope he stays interested in our plight. We have very few friends, but maybe one new one who has the wherewithall to crack the case.

I maintain a confidential elist for patients taking antiretrovirals. Anyone reading who is taking arv’s and who would like to be signed up, please contact me: jdeckoffjones@gmail.com

Today’s song: If Not Now
by Tracy Chapman
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210 thoughts on “Experiments In Vivo”

  2. >"None of those negative papers have found the PMRVs. Where did they come from?"

    Occam's razor – maybe the reason no one else found them is that they really don't exist?

  3. >anon @ 4:46

    I agree with you, sort of. The disease labeled CFS will eventually be broken into more than one disease. Certainly Lyme will be one. Will toxic mold be a category? Mycoplasma probably is not a cause but a cofactor, just as it is in AIDS.

    But I have to say again that amouse retrovirus that has crossed species makes perfect sense as the main underlying cause and we must continue to remind ech other that Alter and Lo's finding and Mikovits' antibodies cannot be ruled out at this time unless we want to be worse than stupid.

  4. >"There is analytical validation – for simplicity I will call this in vitro.
    There is clinical validation – for simplicity I will call this in vivo.

    If an assay can detect a spiked sample it is analytically validated.
    If an assay can detect a positive clinical samples it is clinically validated."

    If there was ever a statement by this individual who screamed: "I have no idea what I'm talking about" this would be it.

    You are making things up as you go along and your statements have no basis in reality.

  6. >I think the shot at Dr. Snyderman was very unfair and not called for.

    Also, I'm not sure who is supposed to be scared?

    Lots of good points, including by Paula. I also would like the cause — and treatment — for CFS to be found in my lifetime, actually soon, so I can enjoy some of my remaining years on the planet.

    I, for one, am waiting for Dr. Lipkin's test results to come out. He has the technological means to do extensive searches for viruses, and he is looking for a possible viral link to CFS.

    Meanwhile, lots of other researchers are finding biomarkers. There are thousands, according to Dr. Komaroff.

    And I wish everyone good holidays and the hopes that the new year will bring some answers for us.

  7. >"Occam's razor – maybe the reason no one else found them is that they really don't exist?"

    Mikovits and Ruscetti found PMRVs separately. Alter and Lo also found PMRVs. Hanson is finding PMRVs.

    Everyone knows this.

  8. >http://www.oie.int/fileadmin/Home/eng/Health_standards/tahm/1.1.05._VALID_PCR.pdf

    "The availability of standard samples is crucial for a successful assay validation. Unfortunately this is often the most problematic issue to solve when planning a validation project. It is not sufficient to use only cultivated agents or spiked samples; true samples from the field may have very different characteristics than these laboratory-generated samples. "

  9. >"I think the shot at Dr. Snyderman was very unfair and not called for.

    Also, I'm not sure who is supposed to be scared?"

    Who shot at Snyderman? The scared comment is about the immaculate contamination fanatics.

  10. >"I, for one, am waiting for Dr. Lipkin's test results to come out. He has the technological means to do extensive searches for viruses, and he is looking for a possible viral link to CFS."

    There is no evidence Lipkin is looking for PMRVs and he is not testing anything for the multi lab study. Do you realise you are suggesting that one person only has to screen people for everything and then we can move on. Really? How many times has EBV and HHV6 been ruled out? Lipkin is not a god like figure who only has to touch a person to find the cause. He has no background I this field.

    People are still waiting for NIH assurance that the lab given to Mikovits and Ruscetti was never used for mice or 22rv1 or vp62. If any of those were present it would destroy otherwise valid results. They should not have to work in environmental conditions they have not used before.

  11. >Here is the New York Times article on the Science retraction.

    Dr. Mikovits is continuing to do the study in Maryland. She is quoted in the article as saying that if XMRV is not found, that it's wrong.

    And Ian Lipkin is quoted as saying that the Science retraction was premature.

    Here is the link to the Times article:
    http://www.nytimes.com/2011/12/23/health/research/science-journal-retracts-chronic-fatigue-syndrome-paper.html?_r=1&hpw

    I'm not saying Dr. Lipkin is the be-all and end-all on a possible viral cause of CFS. However, he is hanging in there and seems quite determined to keep looking and investigating, and appears to be quite fair.

    That is good enough for me.

    Meanwhile, I hope that researchers everywhere will find a cause and treatment soon. And hope that more will do research here and in many other countries. The more the better, and the more countering with scientific evidence to the Darth Vaders CFS-deniers in Britain, here and elsewhere, the better.

  12. >Lipkin can therefore get the NIH to put all details of the study on the NIH website in the interests of transparency. If he cares about patients that is the least he can do.

    We don't need to see it was messed up by having any lab use assays set to vp62, or not clinically validated to pMRVs. We don't need to discover contact controls were used.

  13. >“The fact that we didn’t find XMRV doesn’t bother me because we already knew that retroviruses tend to be variable. They mutate a lot, basically. This is true of HIV and HCV [hepatitis C virus]. It’s not one virus. It’s a family of viruses.”
    Harvey Alter, 'The FDA/NIH/Harvard “XMRV” study: The same thing only different' (CFS Central, 23 August 2010)

  14. >"We presented a paper at the Cold Spring Harbor RNA tumor virus meeting in May showing that patients reported in Lombardi [the Science paper] contained both X [XMRV] and P [polytropic MLV] variants as well as at least one other family member,"
    Dr. Judy Mikovits, 'THE FDA/NIH/HARVARD “XMRV” STUDY: THE SAME THING, ONLY DIFFERENT' (CFS Central, 23 August 2010)

  15. >Anonymous at 6:10pm:

    Your argument makes absolutely no sense at all. If a retrovirus was proven to be a cause of CFS/ME, the 'corporations' would make millions, if not billions churning out a variety of new, specific antiretroviral drugs to treat the infections.

    Oy vey!

  17. >@Anon 1:25

    Many many more corporations would find themselves without work due to their tests and treatments being rendered obsolete.

    Most investors also have their funds in all of these industries and an upset like this would affect them and the economy in general.

  19. >Why is the Lipkin multi lab study not definitive and why does research have to continue.

    A study without scientifically objective entry criteria cannot be definitive.

    Without PET SPECT and NMRI spectroscopy there is no way of telling whether they have a neuroimmune disease or not.

    MRV positive people have the cytokine/chemokine profile of activated microglia, other patients daignosed with CFS don't.

  20. >The retraction of Lombardi et al by Science is not the end of the story. Negative studies looking at only XMRV are not relevant. Because XMRV is gone, Dr. Coffin and other scientists cannot go beyond their data as they have done and say that HGRVs do not cause CFS and by extension other human disorders. I counsel these scientists to not exclude other evidence which I have to believe they are fully aware of and will repeat below.

    As a physician I am used to looking for as much evidence, from as many aspects as possible before excluding a diagnosis. This includes clinical evidence; after all we are not just test tubes. For example, the classic laboratory tests for B12 deficiency can be negative and yet the patient can respond to B12 administration. In this latter case the penalty for dismissing the diagnosis prematurely would be brain and spinal cord damage for the patient. As physicians, we know that there are indeed false positive lab findings but also, and just as importantly, false negative results. The textbook picture exists only in the textbook.

    The first chapter of our story was written 30 years ago from three independent laboratories, including Robert Gallo’s at the NIH. Lest the scientists forget this, the studies proved the association of MLRVs and human disease.

    The second chapter is mine. As you know, I tested positive in Dr. Mikovits laboratory for antibodies to MLRVs. As you know, both my leukemia and my CFS have responded to ARVs. If I had listened to Dr. Coffin’s advice to not take ARVs, I would have lost at least 18 months of life. Dr. Coffin and Science have seen my results. The only comment Dr. Coffin made was that it had to represent “selective toxicity” which as an Oncologist with 40 years’ experience, I can confidently exclude. Bruce Albert of Science never commented but relies heavily on Dr. Coffin’s judgment. I presented my data at a peer-reviewed Hematological Malignancy conference at MD Anderson Cancer Institute in 2010 and it was well received. including by the physician that is considered the premier researcher in my leukemia, Dr. Kanti Rai. I am just one patient, but I am a typical patient and I am told the association of HIV and AIDS was initially made with data from only a few patients.

    So where does that leave us? Research will continue. We still have some scientists with enough courage and wisdom not to abandon the quest. There is a virus, or viruses and these will be found. This story will never end, despite Dr. Coffin and Science. The viruses are likely to be involved in many more disease processes and the world will be a better, or at least healthier place, when they are tamed.

    Michael Snyderman, MD

  21. >Well said, Dr Snyderman.
    A reasonable person might expect that the discovery that ARVs can restore some longterm ME and cancer sufferers to relative health would be enthusiastically welcomed by a medical and research community that purports to exist to heal and relieve the suffering of disease.

    The exact mode of action of a drug on a disease is often not known, but that does not prevent a drug from being employed to help patients, as the disease process itself is usually also imperfectly understood. This happens all the time in medicine.

    So why the hysteria over the apparent effectiveness of ARVs in some CFS patients?

    One would hope that the opportunity to research a new therapeutic approach could be seized, not rejected.
    Can this refusal be rational or sane?

  22. >"There is a virus, or viruses and these will be found. This story will never end, despite Dr. Coffin and Science."

    You see, this is the kind of bullshit that lot of uneducated people post about on this blog. I'm surprised that someone of a physician status would state the same thing.

    It is pretty clear that Coffin and Science is against XMRV being the etiology behind CFS/ME. That's it. Nowhere did Coffin or the journal publicly state that a virus, ANY VIRUS, is not behind CFS/ME. Quite the opposite actually. I've heard Coffin (I've had dinner with him) on many occasions state that he wishes the causative agent be found be it a virus. He has indicated sympathy towards patients and their plight.

    What he has not given sympathy to, and rightly so, is XMRV or "HGRV" as causing CFS/ME.

    No scientist would because THERE IS NO PROOF. Not yet. Not even Lo/Alter proves it.

    And please. Don't give me any of this clinically validated nonsense. Absolutely makes no sense.

  23. >@Anon 12:45

    There was nothing xenotropic in Mikovits and Ruscetti findings. What about this do you not understand?

    We don't need sympathetic comments, we need scientists.

    Clinical validation is a must or anyone can make claims that tests can detect anything and they can make money off sick people.

    Now I already hear the nonsense about having to prove the virus exists. But think of it this way. You are not trying to find a man made variant that is free floating. People didn't expect HIV to be a laboratory artefact free floating in blood. Other labs used the same positives to clinically validate. So you are going to have to check the previous positive samples using the same assays. Then and only then do you begin to alter an assay. This is science.

    What do you think a lab is optimising to when it uses a clinical positive? They can sequence the finding and show what it is easily enough. So what do you think they are optimising too?

  24. >"Clinical validation is a must "

    This is getting so old nobody believes you anymore.

    "There was nothing xenotropic in Mikovits and Ruscetti findings."

    *cough* a xenoMLV lab contaminant that came from a mouse *cough*

    "What do you think a lab is optimising to when it uses a clinical positive?"

    Do you realize this sentence makes NO SENSE??? Stop pretending you are educated in this. It is clear to everyone that you are pretty ignorant when it comes to the literature and science in general.

  25. >Sorry guys, I agree (partially) with Tony Mach. As a 'severely ill' CFS patient I was led to believe (no, no one coerced me but you know what I mean) that Ampligen ($$) MIGHT help me-based on some very loose studies. I was one of those stupid patients who jumped on the Ampligen bandwagon and what I saw 'behind the scenes' was enough to make a scientist puke.

    Data that was 'manipulated' so that patients who didn't qualify to be in the study in the first place were put in there, many of them not only high-functioning but also having some serious mental health issues which were NEVER ever addressed. (yes, i know CFS can cause psych problems but I truly doubt these people had CFS in the first place).

    I could go on and on but I won't. Did some patients feel their quality of life improved? YES!! Maybe anti-virals have immunomodulatory effects! Maybe they increase blood flow to the brain and other parts of our bodies…We don't know why. Only a very very small number of severely ill CFS patients responded to this extremely expensive drug which was once touted to be the 'cure' for CFS.

    I'm not quite sure retrovirals are necessarily the way to go though many of us became sick after a 'flu-like' illness.

    My confused brain doesn't quite know what point I'm trying to make. Would I try ARV's right now? No I would not. There isn't enough data to convince me. I was too traumatized by my experience with Ampligen.

    Do I hope there will be more studies? YES! But I know many of us have suffered and suffered 'waiting' for Godot and it may never happen so people like JDJ who herself was a 'guinea pig' put themselves out there and pave the way for the rest of us.

    I continue to read this blog when able, kudos to all of you who see both sides of the argument. And certainly kudos to JDJ for all her hard work.

  27. >"*cough* a xenoMLV lab contaminant that came from a mouse *cough*

    Mikovits and Ruscetti only sequenced the gag region on the viruses in people with ME. That is polytropic.

  28. >"My confused brain doesn't quite know what point I'm trying to make."

    Mark, that explains why you are not following what the evidence shows.

  29. >"My confused brain doesn't quite know what point I'm trying to make. Would I try ARV's right now? No I would not. There isn't enough data to convince me. I was too traumatized by my experience with Ampligen.

    Do I hope there will be more studies? YES! But I know many of us have suffered and suffered 'waiting' for Godot and it may never happen so people like JDJ who herself was a 'guinea pig' put themselves out there and pave the way for the rest of us."

    First of all Mark, I think you made your point quite clear and eloquent. And yes, the unethical motives behind the test, the money that patients spent, and the unfortunate action of taking ARVs when the data was lacking was enough to make a scientist puke. Myself included.

    As yes there will be more studies. In contrast to many doomsday posters, conspiracy theorists, and JDJ's lack of faith in research, studies on CFS will continue. Definitely will not end with the Lipkin study, even though chances are he will not find anything of significance concerning retroviruses.

    However, what you and other CFS patients must realize, is that science and research wil continue on CFS. Perhaps other viruses besides retros. But one positive thing is clear – this whole XMRV debacle shone a light on CFS and more research will funneled into this disease. This I know for a fact.

  30. >"Mark, that explains why you are not following what the evidence shows."

    You are an asshole for that comment.

  31. >http://www.ann-clinmicrob.com/content/7/1/18

    Conclusion
    We show that current methods for real-time PCR assay design have unacceptably low sensitivities for most clinical applications. Additionally, as new sequence data becomes available, old assays must be reassessed and redesigned. A standard protocol for both generating and assessing the quality of these assays is therefore of great value. Real-time PCR has the capacity to greatly improve clinical diagnostics. The improved assay design and evaluation methods presented herein will expedite adoption of this technique in the clinical lab.

  32. >"the unfortunate action of taking ARVs when the data was lacking was enough to make a scientist puke. Myself included."

    Do you as an unproven retrovirologist feel this way about people with HIV, when the world wasn't ready to accept that virus or the use of ARVs?

  33. >"Conclusion
    Current real-time PCR assay design approaches produce signatures with sensitivities generally too low for clinical use. We suggest that a rigorous approach involving false positive and false negative analysis should be the standard by which an initial assessment of signature quality is made. Signatures must also regularly be reassessed as sequence data becomes available. For targets with wide nucleotide diversity, it becomes necessary to develop a set of signatures, for which we suggest a minimal set clustering approach that may also include signatures with degenerate/inosine bases."

  34. >Prospective Clinical Evaluation of the Accuracy of 16S rRNA Real-Time PCR Assay for the Diagnosis of Melioidosis

    Narisara Chantratita,
    Vanaporn Wuthiekanun,
    Direk Limmathurotsakul,
    Aunchalee Thanwisai,
    Wasun Chantratita,
    Nicholas P. J. Day and
    Sharon J. Peacock*
    + Author Affiliations

    Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Pathology, Faculty of Medicine (Ramathibodi Hospital), Mahidol University, Bangkok, Thailand; Center for Clinical Vaccinology and Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
    Reprint requests: Sharon Peacock, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand. Tel: +66 2 354 9172, Fax: +66 2 354 9169, E-mail: sharon@tropmedres.ac.
     
    Next Section
    Abstract

    The accuracy of a Burkholderia pseudomallei 16s rRNA real-time PCR assay was evaluated against culture for the diagnosis of melioidosis in Thailand. A total of 846 samples were obtained from 383 patients with suspected melioidosis. One or more specimens were PCR positive for 47 of 77 patients with culture-proven melioidosis (sensitivity 61.0%, 95% CI: 49.2–72.0%). PCR was negative for all 306 patients who were culture negative for B. pseudomallei (specificity 100%, 95% CI: 98.8–100%). Diagnostic sensitivity of PCR was 22.7% for patients who were culture positive for blood only, compared with 79.4% for patients who were culture positive for samples other than blood. The median (interquartile range) B. pseudomallei colony count in blood for 44 of 77 patients with positive blood cultures was 2.4 CFU/ml (0.2–13.5 CFU/ml); this may explain the low sensitivity of PCR for this specimen. The PCR assay described here is not sufficiently sensitive to replace culture in our clinical setting

  35. >Can't folks argue points without the insults to each other and arrogant remarks? And directed at people with CFS is really a cheap shot and totally insensitive.

    People are sick and are admitting some of the symptoms here, which is fine. No one should be criticized for that, which is hard in itself.

    One point that I wanted to report in is that today on my CFS list-serve, someone wrote in that a woman with CFS was denied coverage in her state Empire BC-BS for her illness and had to have "CBT first." (and that is the police of the national BC-BS). It seemed to her and to the CFS sufferer who posted it that this is the first time an insurance company in the U.S. did this. This is rather alarming.

    This is why someone better find a cause or more biomarkers quickly, before this practice spreads and more CFS sufferers are denied coverage for our illness.

  36. >@Anonymous

    I won't start (another) yes-no battle, but these references do not support your position at all. Assays are being validated all the time, but you cannot demand that assays are validated when you are trying to validate a finding itself (i.e. check if the (/a) virus is really present in samples).

    In fact, show me ONE SINGLE EXAMPLE of assay validation (in the context that you are demanding) being part of an actual validation attempt of a scientific (finding instead of an already accepted finding), and I will gladly donate $100 to the Mikovits legal defense fund.

    Come on. You can do it. The fact that you are spamming (false) references on this blog proves that you are really trying to back up your claims with references.

    You won't find any, because it's not a logical way to validate findings (unless you like circular logic).

  37. >Anon 12:45 PM:

    You have to look at the Ottawa conference. Mikovits presentation was why a HGRV causes CFS and Coffins' was why HGRVs do not cause CFS.

    Vague utterances about a virus that is not this and not that and sympathy do not help us. We depend on scientists to think outside the box and do something valuable. I don't see you at all interested in doing that.

    What do you mean "clinically validated nonsense" – perhaps you mean that clinical data such as leukemia counts and cytokines improving with ARVs is nonsense? Is this how you deal with data that goes against your beliefs? If you put your energy into constructive research rather than rage and foul language we might make some progress. We would welcome that!

    Michael Snyderman, MD

  38. >Thank you, Dr. Snyderman for clearing up these issues.

    I find that people rigidly arguing points about research, some of whom are not ill, but want to score points in being "right," do not help people with CFS — which is the whole point of research in the first place, to find out the cause to find treatments that work.

    And as I said, use the energy that's misdirected at bloggers here to constructively help us to find the cause(s) and treatment(s) to help people with CFS.

    Best wishes to Dr. Snyderman and Dr. Deckoff-Jones and others for a good holiday and a new year, where hopefully, CFS research will make strides to help those of us with this horrendous disease.

    And a correction to my post above: It should say that a state Blue Cross/Blue Shield policy required a person with CFS to get Cognitive Behavior Therapy for 10 weeks before it would approve her to go to Dr. Enlander's medical center for treatment. And it was said that this is a national Blue Cross/Blue Shield policy!

    I hope that this does not become a policy with governmental health insurance programs or tens of thousands of CFS sufferers will have a hard time.

  39. >I believe the US is now attempting to do what the UK (minus Scotland) has done with this disease. They will only use a fatigue criteria and call it CFS. They will attach this to ME. Placing them both at G93.3. They will then be unable to ever confirm a bio marker or finding and will when the WHO update comes around again have everything moved to the mental health classification. They will do this to prevent the retrovirus being discovered.

  41. >Yes, and I know that the French sent Gallo some of their samples.

    However, THAT DOES NOT MEAN that Gallo calibrated his assays to those "known positives" or used those "known positives" IN ANY OTHER WAY as part of his experimental design.

    If it were, it would be described in the paper and you could quote the relevant part from the paper. You can't, which is why you come up with a mixture of actual circumstance and your "logic" to make it appear as something did happen or something like this is normal science.

    It isn't.

  42. >"the fact that the virus Gallo grew in his lab and used as the basis for the AIDS blood test – a virus he called HTLV-IIIB – was identical to a virus known as LAV that originated from the Paris-based Pasteur Institute. This coincidence, wrote Crewdson, was the result of either "an accident or a theft."
    http://www.sciencemag.org/content/254/5034/944.extract

    "However, subsequent nucleic acid sequence analyses proved Gallo's virus from 1984 to be the same as the virus discovered by Luc Montagnier in 1983. Since Montagnier had sent his virus to Gallo in 1983, it appeared that Gallo had rediscovered Montagnier's virus. "
    http://www.virusmyth.com/aids/hiv/pdhunting.htm

    Gallo explains in this letter.
    Gallo's virus sequence
    MARVIN S. REITZ, JR, HOWARD Z. STREICHER & ROBERT C. GALLO
    http://www.nature.com/nature/journal/v351/n6325/pdf/351358a0.pdf

  43. >"If it were, it would be described in the paper and you could quote the relevant part from the paper"

    Gallo at the time incorrectly said HIV was HTLV type virus.

    The CDC left out of their first HGRV/CFS paper that they had retested 20 positive WPI samples and could not find the virus or contamination. That is evidence that the assays they used do not work.

  44. >http://ajcp.ascpjournals.org/content/124/5/722.full.pdf

    "Increased sensitivity of HC2 compared with PCR was surprising, given the theoretical advantages of PCR-based methods for analytic sensitivity. Smaller amounts of material used in PCR could have limited its sensitivity, but our results demonstrate the importance of optimization and standardization of PCR-based assays for clinical applications."

    You cannot discover a virus without clinical diagnosis. If you only look at spiked samples you can never find a wild type virus. If you have never detected the wild-type virus an assay has not been shown to work. It does not show a virus is not present.

  45. >You can see that clinical positives are routinely used to confirm the discovery of a virus here. This was how they tried to confirm the existence of HTLV.

    "In 1975, Gallo and Robert E. Gallagher announced that they had discovered a human leukemia virus, but other laboratories were unable to replicate their results. Scientists to whom they had sent samples for independent confirmation had found two different retroviruses not from humans, but from animals. The samples had been contaminated by viruses from a monkey or a chimp."

    "Almost a year before Gallo announced his findings, Montagnier at the Pasteur Institute had identified a virus he called LAV, though he was not able to prove that it caused AIDS. The two laboratories were cooperating with each other in the race to find the cause of AIDS and several samples of this virus had been sent to Gallo at the National Cancer Institute."

    http://www.enotes.com/robert-c-gallo-reference/robert-c-gallo

  46. >Mikovits sent samples to Van Kuppeveld and Blomberg too. Nobody's disputing that scientists sent out some of their (supposed) positive samples to other scientists and nobody is arguing that this is bad science.

    What is disturbing is that you have apparently searched all over the internet for support of your ridiculous claims, have (naturally) apparently found nothing to back them up, but are using somewhat related papers and news stories instead.

    So please keep your worthless links coming. Pleae warn me when you have actually found something that contradicts my assertions regarding this.

  47. >"It does not show a virus is not present."

    So unless and until all these other studies and assays show that some kind of virus is not present, you will continue to claim that there is one? Oh yes, that makes a lot of sense.

  48. >Van Kuppevled didn't use the clinical positives to validate. They used VP62/22Rv1.

    Blomberg was sent positive controls for gag sequences and he tested those controls with VP-62 int specific primers! Blomberg then used mouse erv sequences as postive controls for env and gag sequences!

    Blomberg also only declared G3 patients negative. A total of 53 patients. However, where are the results for Group G2 that contained 59 members.

    RRM they used clinical positives to validate the first two human retroviruses. Stop complaining about your problem with this. What do you intend to do to now help?

  49. >"So unless and until all these other studies and assays show that some kind of virus is not present, you will continue to claim that there is one? Oh yes, that makes a lot of sense."

    Do you really think that any researcher can get a PCR assay off the shelf and it merely works? The way to answer the questions you have is to continue investigating. You look for why there may be discrepant results. Two positive studies finding PMRVs and a number failing to find a synthetic virus called VP62/XMRV is not hard to understand. If they had simply followed the scientific method they could have saved patients and the public time and money. Not that much has been set aside to study this yet. Talk about trying to avoid the inevitable. A scientist knows that the minute you change one variable you cannot predict what the results will be. So you start with replication first. Speaks for itself that those producing negative studies refuse to do that. You and no one else can assume a virus is not present when the assay can be at fault. You do not throw out data.

    Really you hate that quotes speak much louder then any anonymous person here. They cut through those lies very easily. I think people are sick of hearing this now and they can see who is lying to them.

    It has always been the method by which new viruses have been discovered and confirmed. Discovering a virus is infecting people is a clinical diagnosis. Finding that you can spike a sample with a man made virus is not going to find a virus infecting people.

    Sadly I don't think you realise that you are also loosing your future because they are not acting like scientists.

  50. >@Anon 9:28AM

    Why do you and others continue to regurgitate these silly excuses over and over again? What part of "full retraction" do you not understand? Except for Mikovits of course, and perhaps Ruscetti to a lesser degree, every other scientist involved in the Science paper study wanted a full retraction. Every one of these people knows vastly more about science, viruses, PCR, the scientific method, and the actual study itself than you do now, or can ever dream of knowing. They are experts, you are not. They have all made it clear that the study was flawed and want it thrown out. Poor quality control, important information omitted, discrepancies in treatment of patient vs. control samples, etc. Basically garbage. And that is being generous in my opinion.

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