Retrovirology Publishes Five Papers on XMRV and Contamination

[richvank]

Hi, all.

I think it's important to note that these papers are concerned only with PCR testing. DNA contamination can impact PCR testing, but it cannot explain either the ability to culture viruses, which means that there were whole virions in the samples, or to detect antibodies, showing that the immune system had responded to a viral infection in the host.

Judy Mikovits has emphasized many times that using only the PCR technique is not sufficient for conclusively identifying the presence of these retroviruses. It's a powerful method, but it has its limitations, and sensitivity to contamination is one of them.

Best regards,

Rich

 

[eric_s]

Do we know when Ila Singh's work will be published?

Unfortunately, i think this is not known. Should have been published already. Like so much, it takes longer and longer. But i think she will want to make sure she has not been working for a year or more on something that's not really a human virus. So one more group that will be working to find out what's the truth. I don't think she will just say "Oh, yes, i've been wasting my time and your money for the last year or two. Sorry, i'm not very smart, you know...".

 

[oceanblue]

However this still doesn't explain why so many controls were not positive for MLVs as if they were handled the same then nearly all would be MLV positive - if the contamination theory is valid. If the controls were handled differently, we need to know that because it violates the concept of a control. If this is contamination, it is due to repeated failings, by multiple experts, at different labs, on multiple occasions, to hold to the expected standard of care with controls. I find this very unlikely at this point.

As I understand it, Robert Weiss - arch-XMRV sceptic - argues that generally patient samples are handled more than negative controls that are often just water. The sample might be handled multiple times in collection, in storage, in retrieval (I think the WPI samples were frozen and drawn some time ago). And this is his explanation for why patient samples could end up with a higher positive rate than controls if contamination is the real cause. I think he's also saying that such different handling of samples and controls is quite common place, not just in the case of XMRV testing.

 

[Esther12]

As I understand it, Robert Weiss - arch-XMRV sceptic - argues that generally patient samples are handled more than negative controls that are often just water. The sample might be handled multiple times in collection, in storage, in retrieval (I think the WPI samples were frozen and drawn some time ago). And this is his explanation for why patient samples could end up with a higher positive rate than controls if contamination is the real cause. I think he's also saying that such different handling of samples and controls is quite common place, not just in the case of XMRV testing.

This is why it's a bit of a shame that the new WPI UK study also collected control samples in a different way to patient samples.

 

[Jemal]

I don't think she will just say "Oh, yes, i've been wasting my time and your money for the last year or two. Sorry, i'm not very smart, you know...".

ROFL. No, I guess she won't.

Anyway, it's all so frustrating. It's like watching a very slow boxing match, where parties are exchanging blows for more than a year now, and neither side seems to get the advantage.

 

[Jemal]

So this news is doing rather well it seems:

http://www.cbc.ca/technology/story/2010/12/20/chronic-fatigue-xmrv-contamination.html
http://www.msnbc.msn.com/id/40751132/ns/health-health_care/

 

[eric_s]

And i also don't see how an endogenous mouse retrovirus could infect monkeys. Or could it?

But i'm no scientist and don't really understand these things, so i think it does not make a lot of sense for me to speculate.

 

[Jemal]

This is also pretty relevant again, 12 arguments why XMRV is not a contaminant:

http://www.hetalternatief.org/XMRV 2010 747.htm
(scroll down a bit for the English text)

Yes, it's an older list, but still relevant.

 

[eric_s]

So this news is doing rather well it seems:

http://www.cbc.ca/technology/story/2010/12/20/chronic-fatigue-xmrv-contamination.html
http://www.msnbc.msn.com/id/40751132/ns/health-health_care/

I don't think it's correct to say that "researchers have found that samples were contaminated in the original [Lombardi et al., published in Science] study" as they say in the article the first link leads to. They have not looked at those samples, have they? So how can they say that?

 

[aruschima]

If indeed it was to turn out that the contamination theory is true, then i see a danger that interest would decrease. Then it would be up to us, to make sure things continue to go forward. We can do it, if we get everybody with ME/CFS onboard, worldwide. I believe we can do much more than we have done up to now.

I believe the whole issue of advocacy has not been to well handled by us; to much focused on validating XMRV, instead of focusing to validate the disease itself. Of course you can argue that by proving XMRV is real, you will eventually prove the disease is real, but this alone is a risky move when there is so much at stake. And association with a disease and a virus includes a lot more than just finding a possible pathogen. Pathology has to be proven, and this is a whole other chapter.
I believe one does not exclude the other though and the XMRV finding are of course the reason we experience such a change in attention, we should use it wisely though.

I do agree, we can do a lot more than we did and a lot more has to be done. I suggest though to do this now, because now the whole issue is still very hot topic, but we have to shift the focus on to validating the disease, independent of the outcome of XMRV/MVL related research. ( As the Spanish Liga is doing. I still awaiting impatiently the promised ASSAM publication)

I was arguing this topic for a long time now with people involved in campaigns and hoped just for the best. Obviously hoping is not enough, all this publication in the news of contamination shows how wrong things can go. There is so much politics involved here, so much at stake ......

 

[oceanblue]

This paper by Robinson et al is interesting in that it finds evidence for murine DNA contamination for samples that is NOT picked up by testing for mitochondrial murine DNA, as used by Lo/Alter (though they looked at a different mtDNA probe).


Mouse DNA contamination in human tissue tested for XMRV

BACKGROUND
We used a PCR-based approach to study the prevalence of genetic sequences related to a
gammaretrovirus, xenotropic murine leukemia virus-related virus, XMRV, in human
prostate cancer. This virus has been identified in the US in prostate cancer patients and in
those with chronic fatigue syndrome. However, with the exception of two patients in
Germany, XMRV has not been identified in prostate cancer tissue in Europe. Most
putative associations of new or old human retroviruses with diseases have turned out to
be due to contamination. We have looked for XMRV sequences in DNA extracted from
formalin-fixed paraffin- embedded prostate tissues. To control for contamination, PCR
assays to detect either mouse mitochondrial DNA (mtDNA) or intracisternal A particle
(IAP) long terminal repeat DNA were run on all samples, owing to their very high copy
number in mouse cells.
RESULTS
In general agreement with the US prevalence, XMRV-like sequences were found in 4.8%
of prostate cancers. However, these were also positive, as were 21.5% of XMRVnegative
cases, for IAP sequences, and many, but not all were positive for mtDNA
sequences.
CONCLUSIONS
These results show that contamination with mouse DNA is widespread and detectable by
the highly sensitive IAP assay, but not always with less sensitive assays, such as murine
mtDNA PCR. This study highlights the ubiquitous presence of mouse DNA in laboratory
specimens and offers a means of rigorous validation for future studies of murine
retroviruses in human disease.

 

[Cort]

Hi, all.

I think it's important to note that these papers are concerned only with PCR testing. DNA contamination can impact PCR testing, but it cannot explain either the ability to culture viruses, which means that there were whole virions in the samples, or to detect antibodies, showing that the immune system had responded to a viral infection in the host.

Judy Mikovits has emphasized many times that using only the PCR technique is not sufficient for conclusively identifying the presence of these retroviruses. It's a powerful method, but it has its limitations, and sensitivity to contamination is one of them.

Best regards,

Rich

Kozak's paper showed that endogenous retroviruses in laboratory mice can produce XMRV - which then could be cultured. See - of Mice and Men - it's all in there.

Antibodies can pick up a cross-reaction to other viruses; if the WPI's antibody results are similar to the NCI's as was reported at BWG meeting (did Dr. Mikovits actually say that?)- then the WPI's antibody test is not in very good shape. Note that the WPI was the only lab not to report antibody findings to the BWG and it was always the last lab -sometimes by quite a margin - to report any findings. That may be due to their working on other things but that did not inspire confidence.

Yes, Dr. Mikovits has said PCR is not sufficient or is not the best method but that was the most important method they used in the Science paper. It was the nested PCR looking for the gag sequence with the nt deletion that was the main finding in the Science paper. We have all gotten sidetracked by the culturing argument but the WPI and the Cleveland Clinic found XMRV in about 70% of CFS patients using simple PCR.

The bottom line is that PCR was good enough then and there's no reason in the world that it should not be good enough now. They laid their line down in the sand with nested PCR without culturing.....So even if culturing is better - researchers should still readily be able to find it in patients - and if they can't then someone needs to figure out how the WPI's PCR testing procedures are different from the other labs.

 

[Cort]

As I understand it, Robert Weiss - arch-XMRV sceptic - argues that generally patient samples are handled more than negative controls that are often just water. The sample might be handled multiple times in collection, in storage, in retrieval (I think the WPI samples were frozen and drawn some time ago). And this is his explanation for why patient samples could end up with a higher positive rate than controls if contamination is the real cause. I think he's also saying that such different handling of samples and controls is quite common place, not just in the case of XMRV testing.

That is an interesting point that I had not thought of before because one thing we do know is that while some of those samples came up positive immediately Dr. Mikovits did say that they had to test others repeatedly before they came up positive - so they were handled more. We also know - it was reported both by Dr. Singh and at the BWG meeting - that nested PCR, which is what they used, is more prone to contamination because the procedure is done twice and at some point in the procedure the tubes are opened up or something like that.

Critics did point out that the WPI only tested the healthy control samples once while they tested some of the patient samples several times. This could have introduced bias in at least two ways; a) they searched harder for XMRV in the patient population and b) they, as was reported above, exposed the samples more.

I don't think (a) matters because no one has shown markedly higher levels of XMRV in the controls than the WPI did but b might.

 

[free at last]

I believe the whole issue of advocacy has not been to well handled by us; to much focused on validating XMRV, instead of focusing to validate the disease itself. Of course you can argue that by proving XMRV is real, you will eventually prove the disease is real, but this alone is a risky move when there is so much at stake. And association with a disease and a virus includes a lot more than just finding a possible pathogen. Pathology has to be proven, and this is a whole other chapter.
I believe one does not exclude the other though and the XMRV finding are of course the reason we experience such a change in attention, we should use it wisely though.

I do agree, we can do a lot more than we did and a lot more has to be done. I suggest though to do this now, because now the whole issue is still very hot topic, but we have to shift the focus on to validating the disease, independent of the outcome of XMRV/MVL related research. ( As the Spanish Liga is doing. I still awaiting impatiently the promised ASSAM publication)

I was arguing this topic for a long time now with people involved in campaigns and hoped just for the best. Obviously hoping is not enough.

I think you are correct, but when something comes along as exciting persuasive and just seems to fit so well as a retro virus causing in full, or in part ME/CFS then its not surprising that most want to run with it. If xmrv falls, despite what Dr Alter said the damage will be incalculable.After such a long debate with both sides saying they are correct, if the negatives win, i feel we will not only go back to times of past, but worse than that, a lot will look at the disease as the one that wasted so much of researchers times, and wasted money that could have been spent elswhere,

I know since xmrv has been in the picture the patients have had many important doctors and researchers start to take the illness seriously.But those will fall somewhat to the side with the avalanch of the negatives and psychitrists who will be somewhat vindicated.

If the truth is not xmrv.I cant even imagine the damage scorn that is going to be coming, the likes of Dr Alter will not be enough to stop those loud mouths from continuing to destroy the belief that ME/CFS is a real disease. look at the media news already, A statement by Dr alter or Judy. will not get as much coverage, because im afraid the power of saying finding a real cause for ME/CFS generated a huge splash.well, now the media will want another huge splash, and if prominent scientists stand up and shout XMRV IS CONTAMINTATION then im afraid the media will have its scoop,

a balanced veiwpoint, will often not be necessary for the media, the scoop will do thank you very much, and its happening already.

I just hope to god they are wrong about contamination.Because untill a study 100% proves it, the damage will already be done and even persuasive studys to the contary may not be enough to undo the percieved veiw, by the public, the media, some goverments, and some researchers ( though i know not all ) and treatements may still be coming, though maybe this may yet again slow that down though i hope not.

I want to inspire everyone to not let this get us, But its getting to me so i cant lie. I will certainly be waiting for a comment by judy and Dr Alter and others, and i trust there word ( well def judy ) likely Alter too, so of course what im fed by the media and negative uk scientists, i will not necessarily 100% agree with. But the point is, they are clever, are they not releasing all this in one oh so clever go,

there playing a game as well as science.And the game im afraid is stacked with them, because of the history and uncertainty of the illness made worse by the likes of wessley, even now hes still in some way damaging us, just by the damage hes already laid down with hes theorys.

well its happening all over again, we need some proof, some conclusive studys proving xmrv is real and infecting CFS paitients, and we need them now. Of course but only if it IS the truth, which i have always believed. but those negativeists, have a way of getting to people. and yep there getting to me now damm. Judy where are you. if shes wrong i forgive her though, at least she tried sod the rest of the doubters

 

[Wildcat]

The BBC interviewed Professor Tim Peto for the BBC Report on the “contamination” studies published in Retrovirology Journal today
http://www.bbc.co.uk/news/health-12041687

Prof Tim Peto told the BBC: “It now seems really very, very unlikely that XMRV is linked to chronic fatigue syndrome”

Professor Tim Peto, consultant in infectious diseases at the University of Oxford, said the original paper in Science came as a great surprise to experts.

What great timing for a high profile piece by the BBC to have one of the PACE Trial Management team (Professor Tim Peto) announcing that "it now seems very very unlikely that XMRV is associated with Chronic Fatigue Syndrome".

Especially as the PACE Trials are due to be published some time after Christmas - how jolly good for White Sharpe and Chalder to get publicity for scuppering ideas of an infectious cause for ME.

Prof Tim Peto was involved in the CBT/GET PACE Trials as a Centre Leader Leader (the local PACE Research team) at the John Radcliffe Hospital Oxford

Professor Tim Peto is on the [PACE] Trial Management Group (TMG)

http://www.biomedcentral.com/1471-2377/7/6

Trial Management Group (TMG)

The Trial Management Group (TMG) will be responsible for the day-to-day running and management of the trial. It is composed of:

• The three principal investigators

1. Professor PD White, Professor of Psychological Medicine, Centre for Psychiatry, Wolfson Institute of Preventive Medicine, Bart's and the London, Queen Mary School of Medicine and Dentistry, Department of Psychological Medicine, St Bartholomew's Hospital, London, EC1A 7BE.

2. Professor MC Sharpe, Professor of Psychological Medicine and Symptoms Research, School of Molecular and Clinical Medicine, Symptoms Research Group, Royal Edinburgh Hospital, Edinburgh, EH10 5HF.

3. Professor T Chalder, Professor of Cognitive Behavioural Psychotherapy Academic Department of Psychological Medicine, Guy's, King's and St Thomas' School of Medicine, Weston Education Centre, Cutcombe Road, London SE5 9RJ

• All centre leaders and co-leaders
1. Dr D Wilks
2. Professor S Wessely
3. Dr M Murphy
4. Dr BJ Angus
5. Professor T Peto
6. Dr E Feldman
7. Dr G Murphy
8. Hazel O'Dowd
.

 

[Cort]

Unfortunately, i think this is not known. Should have been published already. Like so much, it takes longer and longer. But i think she will want to make sure she has not been working for a year or more on something that's not really a human virus. So one more group that will be working to find out what's the truth. I don't think she will just say "Oh, yes, i've been wasting my time and your money for the last year or two. Sorry, i'm not very smart, you know...".

I'll tell you one thing - its not going to make her route to publication any easier.....Hue is suggesting the XMRV itself - whether it is present in the prostate or the blood is a chimera; if I understand what he is saying I believe he thinks that XMRV came from the 22Rv1 cell line used in laboratories and that that cell line picked XMRV when it was passed through mice.

Basically an endogenous retrovirus produced XMRV which then jumped into this prostate cancer cell - which then contaminated laboratories and ended up in blood samples. I think that is his thesis; its not an easy paper to read....

 

[Cort]

I don't think it's correct to say that "researchers have found that samples were contaminated in the original [Lombardi et al., published in Science] study" as they say in the article the first link leads to. They have not looked at those samples, have they? So how can they say that?

No they can't. Hue, though, I think is proposing that every instance of XMRV is a contaminant. If you've found it - you've found a contaminant. He did a phylogenetic analysis to figure out, statistically speaking, where XMRV is most likely to have come from. His paper stated that the results in every case (3000 runs) suggest that genetically speaking, XMRV was most likely to have come from a laboratory cell line - not a mouse.

This happened way before the Science paper came out. If I'm reading Hue right he's suggesting that the problem was not the Science paper but the fact that XMRV wasn't caught the first time around. Of course it was the Science paper that drew attention to the virus and started researchers like Hue digging into it. XMRV itself had never been that closely examined before.

 

[Esther12]

re advocacy: I think we've done alright even if XMRV doesn't work out. Most of the big organisations have stayed calm about things, and tried to use XMRV to get attention for CFS generally, rather than insisting that XMRV must be the key. We could always do better, but that's life.

 

[Cort]

If XMRV does not work out I really think more positive will have been done than negative. It really put CFS on the map once again....

Bear in mind that all we have gotten those far is the contamination side of the story; we haven't the WPI's reaction or Dr. Singhs or Dr. Alter's reaction. The pMLV studies really are separate from XMRV - they are not necessarily effected by Hue's paper. (He didn't test them)...

I still wonder about XMRV integration into human DNA....even if it was a contaminant - if its integrated into human DNA - its still a virus that has infected a human cell....it's still there....isn't it? Was XMRV integration into human cells proved in the Science paper?

 

[eric_s]

I believe the whole issue of advocacy has not been to well handled by us; to much focused on validating XMRV, instead of focusing to validate the disease itself. Of course you can argue that by proving XMRV is real, you will eventually prove the disease is real, but this alone is a risky move when there is so much at stake. And association with a disease and a virus includes a lot more than just finding a possible pathogen. Pathology has to be proven, and this is a whole other chapter.
I believe one does not exclude the other though and the XMRV finding are of course the reason we experience such a change in attention, we should use it wisely though.

I do agree, we can do a lot more than we did and a lot more has to be done. I suggest though to do this now, because now the whole issue is still very hot topic, but we have to shift the focus on to validating the disease, independent of the outcome of XMRV/MVL related research. ( As the Spanish Liga is doing. I still awaiting impatiently the promised ASSAM publication)

I was arguing this topic for a long time now with people involved in campaigns and hoped just for the best. Obviously hoping is not enough, all this publication in the news of contamination shows how wrong things can go. There is so much politics involved here, so much at stake ......

Yes, but what better way to validate a disease than finding a virus that causes it...

I'm waiting for the Spanish group to report too.





I think only research can help us get what we want and this is in the end a treatment. In order to get a treatment you need to know the disease mechanism (unless you just stumble across something that works, even though you don't know why).

What gets you successful research?
Money that goes to the right places (where they do the best research). The more money, the faster and better the results, i guess. (And i actually don't like money a lot, but what can you do...:Green hat

How do you get money?
You raise it from patients or the public or you get your country to spend it.
To do that (all of those 3), i believe that it's essential to have everybody with ME/CFS contribute. With their own donation and also with their presence for demonstrations, lobbying, awareness/fundraising campaigns etc. Only if the public and governments, members of parliament, judges, etc. are really aware of the situation will they do what's needed and what we deserve.
Everybody with ME/CFS must get that message. This can only happen if there is some channel of communication that reaches all the PWCs. I think only ME/CFS organisations can be that channel. So there needs to be cooperation between those organisations and they need to be able to reach "everybody" who has ME/CFS. I think that they can best do that, reach people and get them to act, if more or less everybody is a member of an organisation and all those organisation are in touch with each other.
How to make people aware of the existence of ME/CFS organisations and the need to join them? Probably best would be through doctors and then of course through the internet, ads in papers, tv, etc. I think if we can achieve this, a high degree of organisation, and then do the right things (raise money, fund the right work, lobby), we can get where we want to.

Now what's a bit difficult is that the situation at the moment is quite uncertain.
If XMRV is validated, probably we will get much more support. But with the current knowledge it's not possible to remove a retrovirus from the body, so there would still be a lot of work to be done. Even in this case it won't hurt to use our potential to achieve progress faster.
And if XMRV was proven to not be of importance for ME/CFS we would have to continue the search for the cause.
So i think no matter what happens, what we have to do is the same.

Now that was a lot of talk and that alone won't really help us :mask: But i think this is what should happen. Me, i never wanted to join the organisation here in my country, but XMRV has changed things for me, and so i think i have to look for an organisation to join and then i will try to pursue that plan. Unless someone presents a better one. Suggestions are much welcome