Negative XMRV CFS study with Ila Singh's name on it (University of Utah)

[shannah]

WPI on FB tonight:

"Lombardi et al has made a response but it will not be posted until submitted to the journal."

 

[ixchelkali]

i hear that one of the samples in this study was from the patient they got the image of the virus budding from....what does this mean? that patient had another virus?

Cranky alert: Yes, I'm feeling cranky, so this may come out sounding cranky, but I don't mean it personally, Daffodil:
I wish that when people say things like "I hear that" such-and-such, they would say WHERE they heard it, so I could form some opinion about the reliability of the source. Otherwise it's just rumor.

Maybe I can just ask nicely, can you please tell us where you heard that?

 

[alex3619]

When it comes to finding a virus in tissue samples, are we facing the same difficulties as we are with blood samples? Is there ever a contamination/reagent issue involved?

Hi Lisette, this is an important question. Copy numbers are so low in blood that extreme testing has to be used, which increases the risk of amplifying a contaminant.

In highly infected tissues, presuming we can find some (and I bet we are not much different from macaques in this) we have multiple options. We can stain the virus in tissues like Singh does, using antibody based stains. Alternatively we can use PCR but have it set up so it is much less sensitive - in particular we might not need nested PCR. This means we are much less likely to find low level contamination. I would prefer we use both, and compare them. Also, because of higher copy numbers, we have a better chance of isolating the virus for sequencing, or isolating viral proteins, or finding DNA integration sites.

Bye
Alex

 

[alex3619]

Reverse Transcriptase testing would be a very useful test. I wonder though whether this enzyme differs from one retrovirus to another, or rather, theres some generic marker to measure them Do you know this?

I am thinking about my stomach sample It was taken in Spain, in a sterile room not used for lab work, i.e, where they dont work with mouse They did not touch the samples directlythey put the samples into one sterile plastic vial and I sent it off to Redlabs in Brussels, where they performed a PCR (not sure which one). How easily could my samples have been contaminated in Redlabs, taking into account that they only performed the PCR? Alex, any insight here?

Hi Serg1942, if contamination is an issue, and we don't know it is but it must always be suspected and controlled for, then it could happen either in Spain or Redlabs. The sterile room could be contaminated on occasion, despite regular testing and sterilizing. I still think this is unlikely in most cases but the problem with contamination claims is that after you have checked and rechecked for contamination, you still can't be a hundred percent sure. That is why we have controls in scientific experiments, and the control data produced does not fit with contamination claims at all.

However you had a tissue biopsy - the risk of contamination being amplified should be much lower.

I am not sure about reverse transcriptase testing. Wasn't there someone at CROI who said they had a new test? I could be misremembering. In any case, the reverse transcriptase is a protein that can be sequenced. It is likely to be highly conserved, but not completely - any variation in amino acid sequences may indeed tell us something about the virus that produced it. This is a good question to put to an MLV retrovirologist, I don't know enough about it.

Without doing further research, two ways to test for it is to see if there is an activity by the reverse transcriptase in a specialized culture, or to use antibodies specific for it to bind to it. Or you can try to isolate it using its molecular weight or other characteristics. Antibodies might be a better way to isolate it though - once isolated you can often run an amino acid sequencer, and find out what it is made of, but this would require a minimum quantity and I do not know if enough reverse transcriptase would be present to do this.

So it should be easy enough to prove the presence of reverse transcriptase, but could be very hard to precisely identify which virus produced it - except it has to be a retrovirus from our current understanding.

Bye
Alex

 

[Jemal]

So lots of new information today. A statement by Ian Lipkin, a response from Judy Mikovits and an interview with Ila Singh at CFS Central.
I am so confused right now! So Ila Singh still believes in a connection between XMRV and prostate cancer, but not in XMRV and CFS. And she finds no XMRV in controls either, in her ME/CFS research. But I think 4% of the controls in her prostate cancer research had XMRV? Somehow this doesn't sound right.

I have the feeling this virus is very hard to find in the blood. In the prostate cancer study they were looking in tissues I think? Or also blood?

 

[lansbergen]

Cranky alert: Yes, I'm feeling cranky, so this may come out sounding cranky, but I don't mean it personally, Daffodil:
I wish that when people say things like "I hear that" such-and-such, they would say WHERE they heard it, so I could form some opinion about the reliability of the source. Otherwise it's just rumor.

Maybe I can just ask nicely, can you please tell us where you heard that?

It is posted on a forum on may 4.

 

[In Vitro Infidelium]

I think its a good point that this disorder is quite heterogeneous. If FM researchers believe there are 4 or 5 subtypes there think how many there must be in ME/CFS. One kind of red flag regarding XMRV was that it appeared to show up in about 90% of people with ME/CFS according to the WPI. That was rather alluring; it was nice to think that we all had the same thing - and it was certainly possible - maybe XMRV was the puppetmaster causing different symptoms in different people - but maybe in the end that was asking too much of one virus. Of course AIDS does do that - but HIV/AIDS was clearly infectious - they knew that almost from the get go and there's really no one tie that binds everyone with ME/CFS together like that.

The other striking difference between M.E/CFS and AIDS (which is the defining symptomology of HIV infection) is that there are very clear susceptibilities unprotected penetrative sex, sharing of unsterilised hypodermic needles and transfusion of inadequately screened blood products - which in turn produced very distinct patient groups gay men, sex workers and their clients, users of illicit intravenous drugs, users of prescription drugs and haemophiliacs. In contrast M.E/CFS has almost no identifiable patient groupings - age profiles produce some broad clustering patterns and very young children seem to be unaffected and no identifiable population level behavioural or environmental susceptibilities.

Its also clear with the AIDS pandemic that it had points of origin, the illness spread (and continues to spread) through populations in identifiable patterns. With M.E/CFS, if there is a single causative infective agency, then because there is no pattern of infection, it must be ubiquitously present within all human occupied territory, so either it is (or has been in the past ), highly infectious but with very low symptomology in most humans, or it is a very ancient but poorly infective agent, or it is present in some animal reservoir to which most humans are frequently exposed but which again is poorly infective in humans. Certainly one can hypothesise the nature of such an infective agent but the required characteristics raise numerous improbabilities.

The only logical approach to research prioritisation is to employ some level of probabilistic reasoning. Chasing down every potential infective agent that might be common to the global population of M.E/CFS diagnosed people seems an anti probabilistic approach because one is looking for such an unlikely organism ubiquitous, poorly infectious (in humans) or only exceptionally symptomatic. And this raises very real questions about why the WPI selected XMRV as being a likely single shot candidate that XMRV could (along with a million other organisms) hypothetically be causative of M.E/CFS is not an unreasonable contention, but to pursue the conception of XMRV being of significance in a massively high percentage of M.E/CFS cases, without any reference to epidemiological considerations, was a gross oversight.

At the point when the 67% figure was arrived at, the alarm bells should have rung and questions posed about what XMRV is and how it exists. Having a poorly infectious organism that has a moderate association with the peripheral cells of a cancer that only appears with notable frequency in men who are (in evolutionary terms) geriatric and which can be characterised as a developed world disease, is one thing, having that same organism cause profound disability in (almost) all age groups, both genders and on a global scale is quite another. There are an infinite number of research directions that could be followed and making a choice on which to follow on grounds of novelty is not a reasoned basis on which to choose where to put research funds. Its difficult not to see WPIs decision to connect XMRV with M.E/CFS as anything other than opportunistic (novel retrovirus, in blood like HIV etc) and not based on rigorously argued research choices.

Opportunism of course sometimes pays off, but making research choices based on the lottery of what turns up next will be unlikely to help us in the long term. Of course if the Lipkin and the BWG studies support the original WPI work then XMRV will need further investigation but causation in M.E/CFS still remains unestablished, with the epidemiological imponderables remaining unaddressed XMRV should not be the focus of anyones hopes for a M.E/CFS solution.

IVI

 

[eric_s]

I have the feeling this virus is very hard to find in the blood. In the prostate cancer study they were looking in tissues I think? Or also blood?

Yes, and more and more it looks as if human factors are playing an important role as well. Whereever they come from and for whatever reason.

I like Lipkin's statement (but as i've said, it will be the actions that matter). He reminds me a bit of Alter, both seem to not easily be impressed, make up their own minds, want to get to the bottom of things, say what they believe and are not distracted by new results and all the talk. I like that and have a lot of respect for it. And really hope they continue along that line.

If Ila Singh sticks to her prostate cancer results, now produces a 0/0 study and says the pc association is valid, the ME/CFS one not, then sorry, but unless i'm missing an important piece here, that seems to me as having little credibility and even insult our intelligence.
She is supported by OFFER, right? A Fibro/ME/CFS charity?! Will they tolerate this? What's going on?

We have ME/CFS, prostate cancer seems to be a very different disease for me, a layman. But if there is a connection, and Lombardi et al. and Lo et al. and other positive studies hint in that direction, then we should not let anyone separate us from them (prostate cancer).
And whoever does this at this moment, with the data that's around now, is suspect to me. I wish i would not have to say that, but that's the conclusion i have to reach. If i'm wrong, please show me.
I don't know the motives and to be honest i don't care, i'm not in a position to ever find out, so i might just as well leave that open. But i know it's wrong and as long as it's not supported by the data we MUST NOT LET IT HAPPEN.

We have heard Lipkin's statement. Also Alter's at the State of Knowledge Workshope and before that. As long as those 2 top notch researchers, who are not affected by ME/CFS themselves (so have less personal interest than ourselves) say these things, i don't see how ME/CFS CHARITIES like the CAA and also PR could hint in the direction that we should move on from XMRV.
How on earth can they do that? Sorry if i have to say this, i would very much prefer to work together with them, agree on things and be allies.

We will see who's right and it might turn out XMRV is not of importance, but i think it's irresponsible at this moment to try to influence people to give up on it, no matter the final outcome that we can't know at this point. At least i will not forget the actions of people and groups at this crucial point and i hope everybody else is watching closely now too.

 

[taniaaust1]

Im so greatful to Dr. Bateman and Dr. Singh and Lights for the time and care which got put into that study..
I dont see it as no progress either just cause it was negative. Any "good" study done no matter what the answer turns out to be is a step forward in putting the puzzle pieces together.

There is a clear difference between saying that XMRV is (very loosely paraphrased here) probably not related to CFS/ME and saying that there is no biological cause of CFS/ME. What if in a month or a year someone finds that something like 'ugly hairy butt virus' (trying to make y'all laugh) is the cause of CFS/ME? What if 'ugly hairy butt virus' is easy to cure? Will you be angry that XMRV is not the "it" you hoped for? Will you demand to be treated for XMRV?

I think like that too, thou not as creative as to think of something like ugly hairy butt virus

I dont know if Im happy or sad the XMRV isnt working out as I never liked the thought of our illness being caused by something which would be very hard to treat like a retrovirus. I keep hoping that next month or next year they will find it is caused by something simple.. say a deficiency of a just discovered trace mineral which affects our immune system and other systems in some way.

Wouldnt it go so great if ME/CFS was just a simple deficiency we didnt know about just now which could be found real soon and easily treated. Who knows what may be just around the corner. Quite possibly the XMRV stuff got new researchers and researchers in other fields too interested in us who will remain interested. I sure hope so.

We should be supportive of any sciencists who are tackling our controversial illness which can be putting their reputations on the lines and their careers and really trying their best to help us even if they sometimes get it wrong.

Is Singh wrong or Judy Mikovits? It really dont matter as it wont be too long before other studies come out which help us get to the TRUTH which will help us get that one step closer to the right path of whatever this is. Progess thou the answers are slow to come out, is taking place right now!

 

[ukxmrv]

IVI,

I lived through the early AIDS/HIV time and saw friends die of the disease so I can testify that no, it did not spread in an obvious pattern and some features of the virus in families meant that doctor found it really hard to reconcile an obvious pattern.

If you don't believe me have a read of "and the Band Played on".

Children and partners of IV drug users developed symptoms before the person initially infected. There were children dying of HIV/AIDs and doctors were not willing to admit and could not proof causality to the virus.

Then there were the people who had HIV through a blood transfusion and were left to suffer and die with no explanation and deliberately not told their virus status or suspicions.

As Dr Mikovits said "if this were HIV it would be 1983"

There may be an obvious pattern but we don't know what it is. In the UK we have many families with ME. No one has done the epidemiology of these families. We don't know what is happening with them. There may be something very slow or it may be a combination of factors. There could be clusters of different diseases all caused by one or two viri.

That's a disgrace. We don't even have the data to make meaningful comments on ME type disease in families.

 

[eric_s]

Im so greatful to Dr. Bateman and Dr. Singh and Lights for the time and care which got put into that study..
I dont see it as no progress either just cause it was negative. Any "good" study done no matter what the answer turns out to be is a step forward in putting the puzzle pieces together.



I think like that too, thou not as creative as to think of something like ugly hairy butt virus

I dont know if Im happy or sad the XMRV isnt working out as I never liked the thought of our illness being caused by something which would be very hard to treat like a retrovirus. I keep hoping that next month or next year they will find it is caused by something simple.. say a deficiency of a just discovered trace mineral which affects our immune system and other systems in some way.

Wouldnt it go so great if ME/CFS was just a simple deficiency we didnt know about just now which could be found real soon and easily treated. Who knows what may be just around the corner. Quite possibly the XMRV stuff got new researchers and researchers in other fields too interested in us who will remain interested. I sure hope so.

We should be supportive of any sciencists who are tackling our controversial illness which can be putting their reputations on the lines and their careers and really trying their best to help us even if they sometimes get it wrong.

Tania... your conclusion that XMRV is not working out would mean you're one step ahaed of Ian Lipkin

 

[Cort]

This sounds like a very good question and idea.

Is there any reason why this could not be done and might not work?

And or why not also examine tissue taken from the gut identified as X+ and do it, with that?

Both Peterson and the WPI have said that the virochip tests shows an abundance of pathogens in CFS. I keep expecting that data to get published but it hasn't been - maybe because they are working so hard on XMRV. I would guess that would be an interesting paper.

 

[currer]

Sadly, you are quite right ukxmrv. The thirty (fifty!) years of ignorance on ME/CFS is a disgrace. We know nothing about this devastating illness. A good opportunity for someone to make their name as a researcher.

 

[Cort]

This was not a replication study. Many variables were changed from the science paper. If you read both papers you will see that many variables involving the assays were changed.

Why would you find XMRV in prostate cancer and then change assays in this paper. Did she check against her own positives from her previous prostate paper to see if her new assays worked?

There still has not been an actual replication study including this paper. It's really frustrating that no one will do one including these well respected researchers.

I don't know if this was a true replication study but if it wasn't it was darn close. Here is the from the paper:

PCR- On line 356 she says she used the PCR assay used in the first study to search for XMRV in the Utah patients. She repeated that statement at least twice more in the paper
Antibodies - I don't believe she replicated this test.
Culture - She worked with Dr. Ruscetti to used an improved culture test that lasted for 6 weeks. Later she noted the increased risk of contamination from using culture.

She also used the Lo/Alter version of the test and except for some sequences later determined to be due to contamination, failed to find the MLV sequences they had.

On line 421 she says "We also also analyzed the WPI samples using tests utilized in the two studies that found XMRV or XMRV-like viruses in CFS, a PCR assay for gag sequences both in single round (12) and nested formats and a test for viral growth in cultured cells (12)"

On lines 436/438 she repeats those statements - stating we used the gag assays and culture tests used in the original study....

#11 refers to the Lo/Alter study and #12 refers to the WPI study.

Now if you're asking if she used exactly the same reagents, test tubes, etc. I imagine she did not - my guess and its only a guess that in the history of pathogen research few if any studies have gone to that lengths, probably because they are not thought to matter. We do, however, have two replication studies on the way - the BWG and Lipkin studies. Lipkin said, his results would be in by the end of the year, by the way.

 

[Cort]

If anyone would like to read about, what I think is, a slightly more hopeful XMRV study (but not an entirely positive study), then one has just been published by Switzer of the CDC, which seems to have slipped quietly under the radar...

It's not an ME/CFS study, and he doesn't find very much XMRV... But he does find it in three prostate cancer patients... And they are new strains of XMRV... On first reading, it seems like a significant study to me, especially because it is from the CDC...

Here's the relevant forum thread:
http://phoenixrising.me/forums/showthread.php?11415-Switzer-now-finds-(some)-XMRV-in-Prostate-Cancer

That is more a bit more hopeful for XMRV in the prostate. It also shows, though,....that the CDC tests can pick up previously unidentified strains of XMRV - which is what Dr. Mikovits has been saying it can't do. Their ability to find XMRV in other disorders (as well as in their laboratory personnel) actually makes their findings of zero XMRV in CFS stronger. Its good for prostate cancer XMRV; bad for CFS XMRV.

 

[currer]

Cort, I did not interpret the Switzer CDC study in this way.

Its' implications are that all the previous contamination theories for XMRV in ME/CFS are incorrect.

The virus they found is very variable - they sequenced all they found. So XMRV cannot come from the 22rv1 cell ine or be a lab artifact or lab contamination.
Doesn't that make you sit back a bit?
It clearly shows that they believe they have isolated a highly variable replicating wild virus, and this is in line with what JM has always been saying.
There is a thread about this - it is worth reading.

 

[Cort]

Cort, I did not interpret the Switzer CDC study in this way.

Its' implications are that all the previous contamination theories for XMRV in ME/CFS are incorrect.

The virus they found is very variable - they sequenced all they found. So XMRV cannot come from the 22rv1 cell ine or be a lab artifact or lab contamination.
Doesn't that make you sit back a bit?
It clearly shows that they believe they have isolated a highly variable replicating wild virus, and this is in line with what JM has always been saying.
There is a thread about this - it is worth reading.

That's a good point - that the increased variability could suggest XMRV is not a lab creation - yes that would make one sit back a bit

In fact he says

Also, the finding of a viral strain in three prostate cancer patients that is distinct from the XMRV seen in previous studies is significant and demonstrates a broader viral diversity [7], [9], [14], [16]. This would be an expected result consistent with virus evolution during spread and persistence.

For the first time we have genetic evidence of the type of viral evolution expected during infection in humans. That's big! - at least for prostate cancer - although its muted by the low levels of the virus found and Switzer's expectation (but not proof) that XMRV probably does not contribute to it.

Still it does suggest that XMRV has entered humans rather than just contaminating samples. A crack in the dike? We shall see! It soiunds like the research will continue.

 

[Bob]

That is more a bit more hopeful for XMRV in the prostate. It also shows, though,....that the CDC tests can pick up previously unidentified strains of XMRV - which is what Dr. Mikovits has been saying it can't do. Their ability to find XMRV in other disorders (as well as in their laboratory personnel) actually makes their findings of zero XMRV in CFS stronger. Its good for prostate cancer XMRV; bad for CFS XMRV.

Cort, I did not interpret the Switzer CDC study in this way.

Its' implications are that all the previous contamination theories for XMRV in ME/CFS are incorrect.

The virus they found is very variable - they sequenced all they found. So XMRV cannot come from the 22rv1 cell ine or be a lab artifact or lab contamination.
Doesn't that make you sit back a bit?
It clearly shows that they believe they have isolated a highly variable replicating wild virus, and this is in line with what JM has always been saying.
There is a thread about this - it is worth reading.

I know I'm being a bit pedantic, but would it be OK if we have this discussion on the appropriate thread, so that the discussion about it doesn't get lost in this long thread?
http://phoenixrising.me/forums/showthread.php?11415-Switzer-now-finds-(some)-XMRV-in-Prostate-Cancer

 

[free at last]

That is more a bit more hopeful for XMRV in the prostate. It also shows, though,....that the CDC tests can pick up previously unidentified strains of XMRV - which is what Dr. Mikovits has been saying it can't do. Their ability to find XMRV in other disorders (as well as in their laboratory personnel) actually makes their findings of zero XMRV in CFS stronger. Its good for prostate cancer XMRV; bad for CFS XMRV.

Thats a fair point. but the argument can be turned on its head a little can it not ? 1.9% is a tiny detection. especially if more are infact infected. but the CDC detections are only JUST picking up some positives. How do we know its not the detections that are weak, rather than the amounts of infected patients. Would be my question.

One could argue out of this cohort the WPI would get many more positive detections. Proving judy right. Having said all this, its just a observation. im rattled by the sing study for sure. and confused too, about the lack of the 4% background detections, she should have got, her explanation, of im not really sure, but different types of samples might explain it, seems a bit weak to me.

The CDC Admitting they belive xmrv is indeed infecting people, is very very big news. they might like to split hairs by saying ok its only cancer paitients here. But really that makes little sense on so many levels, not least of which, i thought they belived it was all contamination from a cell line, and was just a lab creation. seems we are being told different things almost monthly by different groups, which is it, contamination, and a lab creation. or a virus really infecting humans ?????

And i note, hold on, these are not lab workers either ? very strange mr coffin. I do not belive a retro virus will only target cancer groups, that seems like complete rubbish to me. how can it only target cancer patients. infact theres more chance it would only attack ME/CFS groups with the altered weakened, immune systems many of them have. No way.

If its prostate cancer groups. sorry it must also be in healthy controls, and other groups with weakened immune systems. I dont know whats going on here. but all the arguments im seeing lately, Just seem plain absurd.

A desperate attempt to explain the fact that they can not find xmrv in CFS groups, can not find XMRV in cancer groups. but then out of knowwhere. hold on woops. we just found a small amount of patients infected ????

If the CDC are confident on this finding, that in no way is contamination to blame. Then just maybe this finding might actually turn out to be more important than the 0/0 Sing study.

why? well because once again. its suggesting all is not what it seems in this sorry saga. and something. ( we do not yet know what ) is going horribly wrong in the detection, and detection rates, of this virus in people.

regardless of the disease they are studying. That is just completely irrelevant. As a virus will infect all that it can. not just prostate cancer patients.

As usual. nothing really makes any sense does it. Just when im about to say ok, hold on, maybe, this virus actually isnt infecting humans. along comes the CDC, ( A group i would least expect to learn this shattering news from ) saying erm ACTUALLY FOLKS IT IS. CFS. PROSTATE CANCER. just splitting hairs now illogically too it would seem.? Or is it. i guess they would all be happier if cancer patients had this virus. but not the CFS patients, not suggesting any bias of course. but likely true. sorry it just is

 

[Cort]

It's yet another of XMRV's many twists and turns...and how funny that the CDC's HIV lab is finding it - which should give some of us more confidence in that lab ...they also reported that XMRV might be transiently showing up in their lab workers - if they find it they appear to be reporting it..