I tested Negative

kurt

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I keep telling everyone with CFS here they have Lyme and co-infections and its TREATABLE.

Oh well, I try.
I read a study a few years back that said 40% of PWC have Lyme, so it is not everyone with CFS. Also, Lyme is hard to treat if you have bad detox genetics, as most PWC have. Probably we need to get the CFS managed and our immune system working again before we are likely to make much of a dent in Lyme.

I don't think that this is question of validity. My first thought is that it is a question of sensitivity. The original 67% of the WPI CFS patients tested positive via PCR. Of the remaining 33 CFS patients that had negative PCR tests, the WPI was able to culture WXRV virus from the blood samples of 30 out of those 33.
True, that culture of the 30/33 was interesting, but the culture uses antibodies, which has some issues: 1) WPI used MuLV antibodies and according to one review of research, some MuLV antibodies cross-react with some HERV types, and PWC have high rates of activated HERV per the WPI May presentation and also per research at Tufts; 2) WPI did not publish their results of the antibody study for the control group, so we do not know whether that 30/33 is unique for CFS, or whether the MuLV antibody would have also found an antigen at that rate in the controls. They can cite the literature for standard control rates of positive on MuLV antibodies, but that does not validate their antibody test, they have to run controls in their lab using their reagents, the same test must be run on both the CFS samples and controls. Maybe WPI did that but it was not reported in their Science article.

Of course, that's also true. But if they're finding positive results for XMRV, my impression -- which may or may not be correct, to be fair -- is that that means the patient does have XMRV. We don't, of course, know that it means anything else at this point, in terms of causes to symptoms or anything else -- just that XMRV was present in the patient's sample.

Problem is, a negative result at this point can't easily be verified as being correct. It could be correct. It could not be correct. We just don't know, and that's regardless of whether XMRV itself is involved in the symptoms of CFS. That's a separate question, and I think you're absolutely right to remind people that we don't have data on anything but a correlation at this point, and one that still needs published replication studies at that.

I'd just caution people not to assume that current test results are absolutely correct on just the question of XMRV presence or absence, regardless of what we find XMRV to mean in the larger sense over time. Testing will change. Understanding of meaning of the results will change. It's very early to be making a whole lot of assumptions about any of it right now.
Yes, too early to be making assumptions.

Also, a negative result on a standard PCR is pretty strong. False positives are more common than false negatives for the type of PCR test that WPI used. I have heard that VIP is using one of the original prostate cancer tests, which I believe was standard PCR.

I doubt many people are operating under any assumptions at this point. More like trying to keep hope alive. I say, good on 'em. :)
We do need to keep hope alive. But hope should always be based on what is or can be reality. We do not yet know if XMRV is reality for CFS. So for me anyway my hope is that regardless of the outcome of the XMRV replications, more productive CFS research is in our future.
 

CBS

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True, that culture of the 30/33 was interesting, but the culture uses antibodies, which has some issues: 1) WPI used MuLV antibodies and according to one review of research, some MuLV antibodies cross-react with some HERV types, and PWC have high rates of activated HERV per the WPI May presentation and also per research at Tufts; 2) WPI did not publish their results of the antibody study for the control group, so we do not know whether that 30/33 is unique for CFS, or whether the MuLV antibody would have also found an antigen at that rate in the controls. They can cite the literature for standard control rates of positive on MuLV antibodies, but that does not validate their antibody test, they have to run controls in their lab using their reagents, the same test must be run on both the CFS samples and controls. Maybe WPI did that but it was not reported in their Science article.
Hi Kurt,

I don't know if you saw it, and I have forgotten the thread, but another question I posted earlier was; "Did the WPI go back and do what they would probably characterize as the more sensitive tests (XMRV cultures) on the controls?"

Good points to keep in mind.

Shane
 

Alesh

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In my opinion based on my personal experience with CFS, my illness is a kind of viral encephalitis. And as brain is the best place for a virus to hide against immune system, since brain lacks immune-competent cells, for me it is perfectly plausible that someone with XMRV encephalitis tests negative for the presence of XMRV in blood cells. What would be necessary is to test cerebrospinal fluid or eventually to perform a brain biopsy. The best strategy now is to survive to the point when more about XMRV is known. I contacted my distant fellow, who happens to be our national coordinator for testing of the prion diseases and he told me that he performed or supervised during his carrier more than 10000 brain autopsies but has never done an autopsy of a brain of a CFS patient. He also told me that if AIDS weren't lethal and thus autopsy impossible it would not be possible to identify HIV as a cause of AIDS. I think it is a striking fact-whatever that means-and we will know more in near future.
 
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He also told me that if AIDS weren't lethal and thus autopsy impossible it would not be possible to identify HIV as a cause of AIDS. I think it is a striking fact-whatever that means-and we will know more in near future.

Good post. And so true how difficult testing for in HIV was at first. Nancy said this in lecture: "When the first HIV blood test came out it wasnt any good either. You know, it went through stages and stages and stages before we got a really good one. "
 

kurt

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It's really never as simple as "accurate" vs. "not accurate", either.

False negatives and false positives don't always happen at the same rate -- in other words, for some tests, you can pretty much trust a positive, but you can't really trust a negative, or the other way 'round.

...

It's not as easy as "if they're saying it's a worthwhile test, it must be accurate", is all I'm saying. My impression is that you can pretty much trust a positive result, but that a negative isn't necessarily trustworthy at this time. They'll be working to increase the sensitivity over time.
Different PCR tests have different risks of false findings. The standard type of PCR has some risk of false positive, but low risk of false negative. So that means a negative finding is the strongest.

The replication studies will most likely be using the more current real-time PCR method, and the risks are reversed, more risk of false negative, but low risk of false positive.

There is some question about what test VIP is using right now, I believe though it is one of the original prostate cancer tests, which is a standard test. The Science article described a standard PCR, which means more risk of false positive than false negative.

As for the antibody and culture studies there is an extensive research literature from attempts to link retroviral infections to other illnesses, particularly auto-immune conditions. And that literature reveals a significant risk of false positive (cross-reactions) using an MuLV antibody due to its ability to react with HERV retroviruses, endogenous forms that are known to be present in PWC (per WPI as well as research at Tufts).

I keep telling everyone with CFS here they have Lyme and co-infections and its TREATABLE.

Oh well, I try.
One study showed 40% of PWC have Lyme, so it is not true for 'everyone' with CFS, but certainly for some of us. And not all cases of Lyme are easily treated, particularly with CFS, due to our intolerance of die-off. Also, Lyme bugs burrow in to our bones, really there is almost no way to eradicate that infection if it is long-standing, just have to find a way to manage it and try to keep it in remission. Besides, based on experience, I suspect Lyme can not be successfully treated in CFS until the underlying CFS pathologies are under control, due to the toxic nature of the flare-ups of the Lyme co-infections.

There is a lot of work to be done on this. I recently attended a lecture by Dr. Lucinda Bateman. She gave the same advice. Wait a few months to test; the cost will drop (a lot of other labs are owrking to develop standardized testing), insurance may cover it and we'll know more about what the result from each method of testing means. A reliable mechanism to measure the presence of XMRV is step number one and as hopeful as it seems, the science isn't quite ready to move beyond that first essential step.
Exactly. I would even say the science of XMRV in CFS is not even finished with the first essential step yet.
 

CBS

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Exactly. I would even say the science of XMRV in CFS is not even finished with the first essential step yet.
W. Churchill: "Now this is not the end. It is not even the beginning of the end. but it is, perhaps, the end of the beginning"

It may be even more accurate to say that we are at somewhere between the beginning and the middle of the beginning.
 
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Robin

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One study showed 40% of PWC have Lyme, so it is not true for 'everyone' with CFS, but certainly for some of us.
If Lyme tests are valueless after a certain point, I've always been confused at how Lyme literate doctors can arrive at a diagnosis of Lyme vs. CFS. Was the study based on lab work? If so, were the infected-but-testing-negative included?
 
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Of the remaining 33 CFS patients that had negative PCR tests, the WPI was able to culture WXRV virus from the blood samples of 30 out of those 33.

Shane
And that "extra test" the plasma culture test - that is not currently provided as part of public XMRV testing right, not by any lab?

Therefore, if I am understanding correctly, you have a 1 in 3 chance of a false (or a not yet) negative.
 
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...well I may not be understanding this right but the first tests that tested 67% positive - they are the tests offered currently?

If the plasma culture test, the one that scooped up the extra 30 showing evidence of infection (the one that has not been published yet) is not currently being offered as part of testing* then only 2/3 approx of positives are currently being detected. That's where I get 1 in 3 not currently being tested positive...but who may in fact test to be so with further testing.

*That's what I'm understanding from Nancy Klimas's talk. However that was a month ago and may be out of date. Also I'm not clear on which tests are in fact being offered as part of the general public testing, I asked in another thread, so don't take my word for it. I'm confused...I don't think you need to take much notice of my maths ;)
 
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I've been asking that all over...

...it's what I'm understanding from other things I've read and heard. But it may just be plain wrong.

Nancy Klimas says in her lecture "So, there are some issues here. That blood test only identified 67% so if I ordered a blood test on you right now and it was negative, what would happen to your soul? You know, and yet it might not really be negative, in fact it’s got a one chance in three of being wrong. The blood test that we don’t have yet that we will have very shortly, those tests are going to be improved on."
However...that lecture was last month, and things are moving on fast...
 

spit

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There is some question about what test VIP is using right now, I believe though it is one of the original prostate cancer tests, which is a standard test. The Science article described a standard PCR, which means more risk of false positive than false negative.
WPI used a nested PCR, I believe, which uses two sets of primers -- essentially, two PCR assays, the second acting on the product from the first -- to cut down on the chances of poor specificity of either primer leading to false positives. There was also some sequencing, but I'd have to reread with more brain power than I've got at the moment to figure out how many samples were sequenced, either gag or env or whole genome.

I'm not sure what VIP is doing, specifically.

Specificity and sensitivity in PCR always depend, so far as I'm aware, on the particular assay -- primers used, sequence targeted, etc.

Overall, we agree that the testing has a while before the results are really solid, and of course we don't know what to do with the results yet anyway.
 

Cort

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Dr. Bateman mirrored Dr. Klimas' suggestion regarding testing - she advised patients not to get to tested yet. Enough interest has been generated in the research community that it won't be long for a test that's been independently validated and standardized to appear. Right now you could falsely test negative or falsely test positive.

So many labs are working on this that we should pretty soon (6 months?) have a standardized test that insurance will hopefully cover.

I imagine the VIP dx test is a very good test and it will be accurate for many people - but not for everybody; that test will take some time to come out. IMReady could have XMRV with a slightly different sequence which the test simply didn't pick up. Someone just noted that XMRV envelope is quite variable genetically and the protein VIP dx tests for, I believe, is in the viral coat. (If I got all that right!)
 
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Dr. Bateman mirrored Dr. Klimas' suggestion regarding testing - she advised patients not to get to tested yet. Enough interest has been generated in the research community that it won't be long for a test that's been independently validated and standardized to appear. Right now you could falsely test negative or falsely test positive.

So many labs are working on this that we should pretty soon (6 months?) have a standardized test that insurance will hopefully cover.
The "Discussion on XMRV" Lucinda Bateman, M.D. clip I just watched (from December 2) http://www.offerutah.org/batemanxmrv.htm - she seems to suggest the same. (So encouraging to see another doctor so excited on our behalf. :D)

A standardised test sounds like a very good thing to look forward to.
 

spit

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anne likes red -- your analysis appears to me to be absolutely correct. WPI got positive results from their initial PCR testing in about 2/3 of the sample. Further testing gave much higher results. That would indicate that their initial PCR testing missed nearly 1/3 of the positive samples.

That's a very low sensitivity.

I will caution, though, that the higher results are still unpublished, so peer reviewers haven't had a chance to poke holes in them yet. That doesn't mean they're wrong, it just means they're shakier until they're reviewed. The incredibly strong unpublished correlation is one of the things I'd most like to see replicated, and soon -- you just don't typically see that kind of correlation without it meaning something, so it's essential to confirm it in published results.
 

kurt

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If Lyme tests are valueless after a certain point, I've always been confused at how Lyme literate doctors can arrive at a diagnosis of Lyme vs. CFS. Was the study based on lab work? If so, were the infected-but-testing-negative included?
There are very different clinical pictures for Lyme vs. CFS. CFS includes significant PEM (post-exertional malaise) and Lyme does not always have PEM. Some Lyme positives can still exercise, in fact for some PWL exercise helps them keep their Lyme under control. For real PWC the ability to exercise is like a memory from a prior life. There are some other differences, and certainly there are many similarities, and some of us have both so pretty hard to tell them apart.

And that "extra test" the plasma culture test - that is not currently provided as part of public XMRV testing right, not by any lab?

Therefore, if I am understanding correctly, you have a 1 in 3 chance of a false (or a not yet) negative.
This is under the assumption that the culture and WB antibody test are not also producing false positives, but as I tried to explain in an earlier post, that has not yet been validated. So right now it is hard to say if there are ANY false negatives in the testing. I suspect that VIP is unlikely to produce a false negative finding if they are still using a standard PCR and the reactive MuLV antibody. But a false positive is certainly possible.

Kurt (or anyone), do you know whether Cooperative Diagnostics is using the standard PCR test of the real-time PCR test?
They are using a real-time PCR design for their main commercial test.

I was told by CD that in their study (not yet reported) they ran both types of PCR, the WPI-style straight from the Science article, and their advanced RT PCR design.

@ anne - Thank you! That makes sense. I guess my only question remaining is the same as yours - are the 2 tests currently offered the ones that resulted in the 67%. Anyone?
CD used that standard PCR test only in their study, their commercial test is RT-PCR.

You would have to ask VIP what specific test they are using. I suspect VIP may have switched to the more accurate RT-PCR, just a hunch because WPI has said they want standardized testing and most other labs will be using RT-PCR.