Virology podcast on XMRV

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Not much news.

They pretty much just go over what we already know, but it' a fine summary of where we are and how little we still know.

http://www.virology.ws/
what was the bit about supermarket cereal testing positive for XMRV sequences (i.e it wasnt REALLY xmrv it was a false positive and a common contaminant showing up in the testing) i.e something was wrong with the testing method??!?!?! can anyone explain that bit? by coffin and rhind???
 

Esther12

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I thought that was just more about how the current testing for XMRV seems really prone to picking up contamination... that the cereal had been contaminated with mouse DNA somehow? I'm not really able to comment though - everything I know about viruses has been learnt in the last 12 months.
 

LJS

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The guest speaker Alan Rein did not comment on much other then what is concretely known, which of course if not much at this point. You could tell from his comments that he felt that the possibility of XMRV being real in the human population is little to none and that the positive XMRV papers were an honest mistake. Professor Racaniello, Alan Dove, and Rich Condit had some great back and forth discussion with Alan Rein and raised some very important points that should be taken seriously in the patient community and science community.

Here are some of the interesting points raised that I could technically understand and remember:
- Mouse DNA can be found in city drinking water and can contaminate samples and negative controls even with extreme reverse osmosis filtration. This is a huge problem since water is used in the manufacturing of everything. Water is used to clean lab equipment, used as the negative control in PCR, and probably used in the manufacturing process of much of the equipment and chemicals in labs.
- Mouse DNA is prevalent in so many products that it is extremely easy for mouse DNA to contaminate a human sample. While discussing how wide spread mouse DNA is they mentioned that Dr. Coffin tested multiple cereal brands and found some positive for XMRV.
- Finding antibodies to XMRV in CFS patients does not hold much weight against the contamination theory until it is replicated and solidly reproducible in multiple labs. This is how everything in science works; multiple independent labs have to be able to verify a result.

Overall I think this was a good balanced discussion and made it clear that possibility of contamination should be taken very seriously. 2011 should be an interesting year of research for XMRV.
 

CBS

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One of the more interesting points was when Dr. Rein was asked by Dr. Raceniello about Dr. Silverman's group having identified proviral integration sites in malignant human prostate cells (J of Virology and PLoS One). Dr. Rein said that these studies needed to be replicated but that if the results help up, it would be "a very definitive way of showing that you really have an infected cell. If you can show viral sequences linked to human sequences there's really no way the DNA mouse contamination will give you that result." This exchange began with about -39:25 left.

Dr. Rein suggested that Dr. Singh was focused on validating the existence of these integration sites.

To do the same in CFS patients would probably require the identification of XMRV/MLV tissue reservoirs.
 
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We can all agree on that we need a standard for assays and that we need labs to interchange reagents and samples. It was a interesting discussion but didn't bring up any new information. What I found rather disappointing was that Vincent found it necessary to bring up the letter which connects PWCs with MMR vaccine autism link folks. We have these non scientific videos on youtube and I also think that we have problems with people who don't understand the current scientific discussion and therefore make wrong, emotional simplifications. However there are also extremely intelligent people in the CFS community who share great interest in XMRV and make very good points on where some studies made mistakes and when wrong conclusions were drawn. In my eyes these people should be mentioned too, they deserve it!
 

Jemal

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- Mouse DNA is prevalent in so many products that it is extremely easy for mouse DNA to contaminate a human sample. While discussing how wide spread mouse DNA is they mentioned that Dr. Coffin tested multiple cereal brands and found some positive for XMRV.
Well, I have another theory. He thinks he is picking up a contaminant in cereals, but in fact it's his laboratory that's contaminated. The cereal is not infected with a virus... eh, a contaminant :D
 

FancyMyBlood

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The guest speaker Alan Rein did not comment on much other then what is concretely known, which of course if not much at this point. You could tell from his comments that he felt that the possibility of XMRV being real in the human population is little to none and that the positive XMRV papers were an honest mistake. Professor Racaniello, Alan Dove, and Rich Condit had some great back and forth discussion with Alan Rein and raised some very important points that should be taken seriously in the patient community and science community.

Here are some of the interesting points raised that I could technically understand and remember:
- Mouse DNA can be found in city drinking water and can contaminate samples and negative controls even with extreme reverse osmosis filtration. This is a huge problem since water is used in the manufacturing of everything. Water is used to clean lab equipment, used as the negative control in PCR, and probably used in the manufacturing process of much of the equipment and chemicals in labs.
- Mouse DNA is prevalent in so many products that it is extremely easy for mouse DNA to contaminate a human sample. While discussing how wide spread mouse DNA is they mentioned that Dr. Coffin tested multiple cereal brands and found some positive for XMRV.
- Finding antibodies to XMRV in CFS patients does not hold much weight against the contamination theory until it is replicated and solidly reproducible in multiple labs. This is how everything in science works; multiple independent labs have to be able to verify a result.

Overall I think this was a good balanced discussion and made it clear that possibility of contamination should be taken very seriously. 2011 should be an interesting year of research for XMRV.
If mouse DNA contamination is that 'common' there should be tons of studies describing this phenomenon in all sorts of virus studies. In other words, is this phenomenon also described in HIV/HHV-6/EBV etc. studies? If not why would this only hold for XMRV?

And even when there is mouse DNA contamination, how do you tell the XMRV is not from human blood but from that mouse DNA? Hypothetically, if these tubes are indeed contaminated with mouse DNA but the human blood is the real source of XMRV wouldn't it be to easy to say 'because the tube contains mouse DNA it has to be contaminated'?

Maybe these are stupid questions, but the more I read about these contamination studies the less I seem to understand.
 

FancyMyBlood

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Also, if we take a look at the commercial tests (VIPdx, RedLabs) and contamination is indeed a factor that plays a role in these (false) positives, than wouldn't you expect 100% to be (false) positive?
It seems the same test tubes and methodology are used afterall.

What kind of arguments are there to explain that not 100% of these tests are (false) positive?
 

Esther12

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I don't think that for contamination to be a problem you would expect 100% positives. The studies that did find they had a problem with contamination weren't getting 100% positives. If you just need one cell of mouse DNA to get a false positive, there's going to be a lot of room for randomness affecting results.

re: why mouse contamination wouldn't be a problem for EBV etc studies: Couldn't it just be that mouse DNA doesn't contain sequences which could be interpreted as EBV, but they do for XMRV?

ps: I'm just guessing with this, but find trying to answer other's questions is a good way of testing my own knowledge. Please feel free to correct me if I'm wrong.
 

FancyMyBlood

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I don't think that for contamination to be a problem you would expect 100% positives. The studies that did find they had a problem with contamination weren't getting 100% positives. If you just need one cell of mouse DNA to get a false positive, there's going to be a lot of room for randomness affecting results.
Wasn't that because they examined different isolates? In only two of them they found laboratory contaminants. I'd expect if you checked those two isolates 100 hundred times you'd find find 100 times laboratory contaminants.
Why wouldn't this hold for the Mikovits/Alter/commercial labs testing? I know it's speculated that the former two used differences in handling of the samples between patients and controls. While I really doubt this, this absolutely can't be true for the commercial lab testing because they have no idea who's a patient and who's not.

re:
why mouse contamination wouldn't be a problem for EBV etc studies: Couldn't it just be that mouse DNA doesn't contain sequences which could be interpreted as EBV, but they do for XMRV?
I understand, and XMRV is a mouse virus afterall. But since this virologist said mouse DNA contamination is so common they have to get that from somewhere, don't they? Where are those studies? (this is a rethorical question because I know they exist, but are they representative? In other words, did they use studies that examined the methodology/tubes used in common practice, like testing for EBV/HIV etc.)


ps: I'm just guessing with this, but find trying to answer other's questions is a good way of testing my own knowledge. Please feel free to correct me if I'm wrong.
Offcourse, since most of us gain the knowledge because of this terrible disease and not in a professional setting it's quite hard to understand all of this. These discussions make us all smarter, and heck we even outperform most virologist by our common knowledge. (for example Vincent Racaniello retracted his statement after this forum discussed these studies) :)
 

LJS

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If mouse DNA contamination is that 'common' there should be tons of studies describing this phenomenon in all sorts of virus studies. In other words, is this phenomenon also described in HIV/HHV-6/EBV etc. studies? If not why would this only hold for XMRV?

And even when there is mouse DNA contamination, how do you tell the XMRV is not from human blood but from that mouse DNA? Hypothetically, if these tubes are indeed contaminated with mouse DNA but the human blood is the real source of XMRV wouldn't it be to easy to say 'because the tube contains mouse DNA it has to be contaminated'?

Maybe these are stupid questions, but the more I read about these contamination studies the less I seem to understand.
No, testing for XMRV is such a huge problem because the DNA of XMRV is so similar to mouse XMRV and ERVs. Mouse DNA would have no effect and not cause false results on HIV/HHV-6/EBV etc studies. XMRV originated as a mouse retrovirus and is very similar to many mouse ERVs. HIV/HHV-6/EBV tests would not cross react with mouse DNA because they are completely different DNA. HHV-6 and EBVs are not retroviruses and are not going to cross react with mouse or human ERVs.

XMRV brings contamination issues in testing to a whole new level.
 

LJS

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I don't think that for contamination to be a problem you would expect 100% positives. The studies that did find they had a problem with contamination weren't getting 100% positives. If you just need one cell of mouse DNA to get a false positive, there's going to be a lot of room for randomness affecting results.
From what I understand (could be wrong) you will only get 100% positive with contamination only if it is a laboratory contaminate and if that laboratory contaminant got in contact with each sample or if your test is reacting with the wrong DNA (PCR test). The problem is mouse DNA is all over the place, in water etc. Some blood tubes have mouse DNA, some heprine has mouse DNA in it. My guess is it is all coming from the water used to make all these cemicals, but I could be way off, this is just a educated guess. Water is used to make saline, which is used in heprine and of coarse not all the water used will have mouse DNA so some will have traces of mouse DNA while others don't.
 

RivkaRivka

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The top scientist actually says, he thinks its possible there is no xmrv and the whole thing is a mistake! and there is no xmrv in the human population and he says if thats the case the less money we spend on it the better.

I don't think anyone understands how ill we are. if only they new!
This is the main thing I heard, too, after listening to the whole interview last night. UUUUUUUUUUGGGGGGGGGGHHHHHHH!
 

*GG*

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The top scientist actually says, he thinks its possible there is no xmrv and the whole thing is a mistake! and there is no xmrv in the human population and he says if thats the case the less money we spend on it the better.

I don't think anyone understands how ill we are. if only they new!
Who is this "top scientist"? Not going to waste my time to listen to 1 hour plus just to hear that, no thanks!

GG

PS What kind of researcher/top scientist doesn't want to spend money to figure things out? Doesn't sound like much of a scientist to me!
 

Cort

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The top scientist actually says, he thinks its possible there is no xmrv and the whole thing is a mistake! and there is no xmrv in the human population and he says if thats the case the less money we spend on it the better.

I don't think anyone understands how ill we are. if only they new!

I just listened to it and while I can understand that it could be misconstrued that way I heard him say something very different: that he is not in favor of large-scale human testing before there is a consensus assay to test for it - that is what would be a huge waste of money but he is absolutely in favor of multiple labs continuing to test for XMRV and spending $ to continue to search for the best assay - and his lab at the NCI will be one of those participating in that process.

(His lab, by the way, did not find XMRV in prostate cancer - that's where he is coming from)

My take is that he leans towards XMRV not working but he also said 'of course' it is possible that its infecting people - he is definitely leaving that option open... but there's no way to tell what's happening until more studies are done.

I would not portray the TWIV program as 'fun listening' given that it was about the Retrovirology papers but they did all agree that the press way over-reacted to the Retrovirology, and interestingly enough, that the low genetic variability was not necessarily a problem. That's important because that is an argument that others are using against XMRV.

They all agreed that more study was necessary - and, of course, those studies are being done.
 

Crappy

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My understanding of this topic is below average for this forum.

I can’t help but wonder about the expertise of all these esteemed scientists, they can’t take steps to personally ensure sterilization of components of this process??? If they can’t filter it out, how about just sterilizing all the components to the process except for the test sample? Heat causes disassociation of proteins and other molecules, so does chlorine, so does Ozone, UV radiation, etc…It would seem molecular biologists would know how to sterilize (render all compounds in the water and elsewhere neutral)? What am I missing? Clean equipment? Clean solutions? Nothing contaminated in the process but the compounds in the sample itself.

Riddle me this?

Perhaps my ignorance is showing.
 
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My understanding of this topic is below average for this forum.

I can’t help but wonder about the expertise of all these esteemed scientists, they can’t take steps to personally ensure sterilization of components of this process??? If they can’t filter it out, how about just sterilizing all the components to the process except for the test sample? Heat causes disassociation of proteins and other molecules, so does chlorine, so does Ozone, UV radiation, etc…It would seem molecular biologists would know how to sterilize (render all compounds in the water and elsewhere neutral)? What am I missing? Clean equipment? Clean solutions? Nothing contaminated in the process but the compounds in the sample itself.

Riddle me this?

Perhaps my ignorance is showing.
You, young sir or madam, are far too uppity, how dare you ask this question. The esteemed, 'brilliant' minds have better things to do than consider the issue of sterilization, especially when it's futile, with mouse DNA over-running the whole world...

Nah- not really. Perfectly sensible question. Unlikely to be answered or even considered as a problem to be addressed in this whole debacle. Wish I was wrong.
 

eric_s

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Why wouldn't this hold for the Mikovits/Alter/commercial labs testing? I know it's speculated that the former two used differences in handling of the samples between patients and controls. While I really doubt this, this absolutely can't be true for the commercial lab testing because they have no idea who's a patient and who's not.
Yes, and it would be very interesting to get the results of VIP Dx for a number of ME/CFS patients and healthy people. Unfortunately i'm not aware of any such percentages. I've thought months ago it would be interesting to send them 30 or so samples of cases and matched controls. This would more or less prove wheter something is really there or not. I then dropped that idea again, because i thought the Lo et al. study or some other study would settle the question. Maybe this should be done, because it might still be a long time until we get results from the Blood XMRV SRWG.