Article: Four Viruses! Alter Paper Confirms Retroviral Findings in CFS

You can view the page at http://www.forums.aboutmecfs.org/content.php?213-Four-Viruses-The-Alter-XMRV-Paper-Arrives

 

http://www.retrovirology.com/content/7/1/57/comments This is the link to Gerwyn's rebuttal

 

Here are some important quotes for everyone:

Although we find evidence of a broader group of MLV-related viruses, rather than just XMRV, in patients with CFS and healthy blood donors, our results clearly support the central argument by Lombardi et al. Lo et al.

Indeed, it is possible that the PCR primers used in various studies may have different sensitivity in detecting the diverse group of MLV-related virus gag gene sequences that we found in the clinical samples. The 5′ gag leader sequence of previously described XMRVs represents the most divergent segment of the XMRV genome in comparison with the genomes of the other MLVs (4). In particular, there is evidently a unique 15-nt deletion in the 5′ gag leader region in all of the XMRVs previously iden- tified in patients with prostate cancer and CFS (3, 4). To detect XMRVs in human samples with better sensitivity and specificity, some studies used a PCR primer spanning this unique deletion as the XMRV-specific primer (6). However, none of the viral gag gene sequences amplified from the blood samples of CFS patients and blood donors in our study has this particular deletion (Fig. S1). As a consequence, such primers might have been in- sensitive in detecting the MLV-related gag gene sequences that we have identified. Lo et al.

In sum, none of the four studies that have failed to confirm the PCR evidence reported by Lombardi et al. (3), nor our own study, has attempted to fully replicate that study. Lo et al.

we suspect that the association will be lower in CFS cases identified through com- munity-based surveys, Lo et al.

and this

Dr Alter: "Does raise questions because there isn't consensus in different CFS populations. Many things still have to be looked at. It does at least confirm the findings of Whittemore Peterson. I think one wants to go back to their studies because they have had more time and more they have done extensive work... so its not just finding isolated viral sequences. But they have found gag, env sequences. They have been able to transmit this to an animal model (the macaque). They have seen antibody in the macaque and they have seen ab in pts and they have seen the viral particles. So this study is more advanced than ours. But with them having done the groundwork, I think our study is highly confirmatory of their work and we are in the process of trying to culture virus from our patients and to find antibodies. We have already shown that some of our pts also have envelope sequences, and preliminary work appears that there is antibody present as well but this has not been confirmed. But there are many things that need to be done, many more CFS populations that need to be tested. (More) numbers of blood donors that need to be tested. Other diseases that need to be tested. More culture work. More robust assays."

Dr Lo. "No, actually this group of virus that we call polytropic MLV this is actually more characteristic for the retrovirus infection instead of a single viral gene. They very quickly can evolve and have multiple different kind of a sequence found. In fact what we found is that actually gave us good confidence that this cannot be a laboratory artifact or PCR contamination product because the sequences they are so varied from one patient to another."

Dr Alter. "My thought came back. Since their original publication the WPI and NCI groups have now found that they too are finding greater variability among their patients, so it is not just XMRV even in the original cohort of patients."

Dr McCluskey: "One thing that hasn't been mentioned so far is that this virus at least in our hands is present in a variable titre which increases the difficulty of detection so that may be also complicating or adding to the variability among the labs."

Dr Lo: "I would also add on this. I think most of the irregularity or the different findings. Many probably due to a very low copy or viral gene copy in the blood and that is a main concern for a consistent finding and using different kind of assay systems."

Dr Lo: In a way it was a little bit surprise when the WPI's first publication in Science and they show it as a single kind of kind of a sequence. That is unusual for retrovirus, but now they are also stating they do see the variation of the sequence and also appear to be more closely related to polytropic related MLV's.

 

The other factor the FDA response cited was differences in sample preparation. Since that's all they stated they stated its difficult to know what they were referring to. The Alter/Lo group found that testing plasma cut their positive rates in half compared to whole blood. The CDC used plasma - but so did the WPI in the original Science paper - and they, of course, had results similar to the Alter/Lo study. The FDA response did not, interestingly, suggest that they believed other problems with methodology played a role. However, the Alter/Lo paper in PNAS discussed primer problems which may be similar to those Dr. Mikovits referred to in her video.

It will be as others have said, that they did not use a known human sample to calibrate to. That they were carefully looking, but perhaps in the wrong place.

 

Almost everything in those quotes is in my 'nonsense' paper as you put it. To show how difficult this is in the paper they refer to geographic prevalence of the virus, primers and patient cohort heterogeneity and then Dr. Lo talks about how rare the virus is. All those elements (except for geographic prevalence) are present in my article.

 

Science has an article up on the latest findings. I thought everyone might take heart from the last sentence of the last paragraph:

Subtle differences in sample collection and handling, or in the way tests are performed, could also have led the four labs to miss the virus. But CDCs Monroe says hes confident that his lab can identify XMRV correctly. As part of the NHLBI program, researchers at FDA, CDC, WPI, and other labs have all blindly tested a panel of samples, some of them spiked with different amounts of the virus; all of them performed well. Further exchange of samples and reagents is now under way. They should be able to clear this up by Christmas, says Kurth.

 

And there was I with link ready copied, and its been given twice already. Oy vay.

Just as an aside, and by the way, all the semantics of this science are in flux, being assigned as the discoveries progress. No XMRV, MLV, ME, XAND, NDS (or whatever it is) GERD etc is yet set in stone. A certain humility is appropriate.

Words only try to describe reality.

 

The nonsense was for the facts that were nonsense. As in, don't make sense, not factual, nothing more. You have been changing your article, so it's not a case of saying they are there. The quotes are not aimed at you, they are information for everyone else who doesn't want to read the paper, but likes to at least interpret things for themselves.

 

That's true Jace. They have a long way to go to position everything. Lots of renaming and classifying to come

 

Is there something to reconcile?

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Question: Lauren Niergard: Associated Press "Does finding that its polytropic actually suggest a looser correlation with CFS than finding of Xenotropic would have? It would seem to suggest more of a process of chance than a firm association."
<o></o>
Dr Lo. " Normally the PCR lab contamination you more or less anticipate that all the sequences will be the same..."
<o></o>
Lauren: "But what I was thinking of was not lab contamination, but rather you are finding essentially multiple different kinds of viruses withing the same family."
<o></o>
Dr Lo: "Right they are in the same family. They are compatible with the earlier finding of the XMRV. They are not identical, they are more diverse."
<o></o>
Lauren: "Is it usual that you would find an association with a single disease this kind of variety of viruses."
<o></o>
Dr Lo: "Yes, indeed, that is exactly what we would anticipate for retrovirus infection over time with the many different sequences there."

<o></o>Dr Alter: "Just on that last point, the retroviruses exist in big families of viruses. So Hep C is a very good example. Nobody is infected with one variant of HCV. It is a huge family of variants, HCV divided by genotypes and HIV divided by clades. And if you take any given patient the patient will have multiple variants in them. And different patients will have different variants in them. So it is very characteristic of these kind of RNA viruses...."

<o></o>Dr McCluskey... "Just reiterating Dr Alter<st1ersonname w:st="on">'</st1ersonname>s point. I think that is the essence of the characteristics of these retroviruses. That their polymerase is really faulty and creates lots of mutations. So you would never have just one single species - causes multiple species..."

<o></o>Lauren: "So this is basically then saying that there is a stronger association than you had before because of that variability."

<o></o>Dr Lo: "I think we can say we found this kind of variability and that is actually more consistent with the natural form of a retrovirus infections in this group of patients."

Hope this helps...<o></o>

 

I was just going to post that bit before from that same transcript:

Lauren: "It would seem to suggest more of a process of chance than a firm association."

Dr Lo. "No, actually this group of virus that we call polytropic MLV – this is actually more characteristic for the retrovirus infection instead of a single viral gene. They very quickly can evolve and have multiple different kind of a sequence found. In fact what we found is that actually gave us good confidence that this cannot be a laboratory artifact or PCR contamination product because the sequences they are so varied from one patient to another."

Lauren: "So that means it's probably not lab contamination?"

Dr Lo. "Right, exactly. Normally the PCR lab contamination you more or less anticipate that all the sequences will be the same."

Lauren: "But what I was thinking of was not lab contamination, but rather you are finding essentially multiple different kinds of viruses withing the same family."

Dr Lo: "Right they are in the same family. They are compatible with the earlier finding of the XMRV. They are not identical, they are more diverse."

 

The nonsense was for the facts that were nonsense. As in, don't make sense, not factual, nothing more. You have been changing your article, so it's not a case of saying they are there. The quotes are not aimed at you, they are information for everyone else who doesn't want to read the paper, but likes to at least interpret things for themselves.

Arrrrgghhh. Nothing in there was 'nonsense' I assure you. This *(79w2$)P)*()* is nonsense - it doesn't mean anything. Changing something does not mean what was there was there before was 'nonsense'.

I'm checking out of our lovely conversation, though. Hopefully I'll be back tonight with an addition to the paper that I think will be enlightening - it certainly was to me.

 

camas - Today

Science has an article up on the latest findings. I thought everyone might take heart from the last sentence of the last paragraph:

Subtle differences in sample collection and handling, or in the way tests are performed, could also have led the four labs to miss the virus. But CDC’s Monroe says he’s confident that his lab can identify XMRV correctly. As part of the NHLBI program, researchers at FDA, CDC, WPI, and other labs have all blindly tested a panel of samples, some of them “spiked” with different amounts of the virus; all of them performed well. Further exchange of samples and reagents is now under way. “They should be able to clear this up by Christmas,” says Kurth.

Even when the CDC is able to detect the virus in a panel of samples it is still possible that they have problems with collecting/storing/handling the samples before the actual testing. Especially when they used plasma. It could be critical to immediately centrifuge whole blood to get the plasma, because the longer the blood is stored before centrifugation, the more time antibodies in the blood have to form complexes with the virions and those antibodies can make those virion adhere to cells in the blood (macrophages express Fc-receptors that bind antibodies etc.) and the more time virions will have to attach to blood cells with their surface proteins as they do when they infect new cells. This would cause most if not all virions to end up at the bottem of the centrifugation tubes after centrifugation and this pellet is not tested for virus when they use the plasma.
This is just my thinking about this matter, i do not claim it is correct, only an hypothesis.
About myself: I'm a CFS patient for 6 years, not able to study 90% of that time and only able to progress towards my degree in biomedical sciences at a very slow pace. But i won't give up and the current science does give me hope, although i would rather have something else than a retrovirus, it is certainly better than being labeled as a psychiatric patient!

 

Arrrrgghhh. Nothing in there was 'nonsense' I assure you. This *(79w2$)P)*()* is nonsense - it doesn't mean anything. Changing something does not mean what was there was there before was 'nonsense'.

I'm checking out of our lovely conversation, though. Hopefully I'll be back tonight with an addition to the paper that I think will be enlightening - it certainly was to me.

Facts that are incorrect are. If you changed facts, it means you were using the incorrect facts previously. The point is when is it factually correct, as soon as it is posted, 10mins, 20mins, 2 days?

You should have asked for information before posting, most people will only read it once, and never know that you changed something.

I'll be back tonight with an addition to the paper that I think will be enlightening - it certainly was to me.

Well, tonight is now for me.

All this is about is facts. Lets not start spreading false information around the world like those who began the lie about the WPI cohort.

 

Even when the CDC is able to detect the virus in a panel of samples it is still possible that they have problems with collecting/storing/handling the samples before the actual testing. Especially when they used plasma. It could be critical to immediately centrifuge whole blood to get the plasma, because the longer the blood is stored before centrifugation, the more time antibodies in the blood have to form complexes with the virions and those antibodies can make those virion adhere to cells in the blood (macrophages express Fc-receptors that bind antibodies etc.) and the more time virions will have to attach to blood cells with their surface proteins as they do when they infect new cells. This would cause most if not all virions to end up at the bottem of the centrifugation tubes after centrifugation and this pellet is not tested for virus when they use the plasma.
This is just my thinking about this matter, i do not claim it is correct, only an hypothesis.
About myself: I'm a CFS patient for 6 years, not able to study 90% of that time and only able to progress towards my degree in biomedical sciences at a very slow pace. But i won't give up and the current science does give me hope, although i would rather have something else than a retrovirus, it is certainly better than being labeled as a psychiatric patient!

That's very true, all possibilities are still open, but some just got a bit weaker.

 

Cort, I have just noticed that you are again changing your posts after they have been up for quiet a while. There is no point in changing how the posts have gone, it is easy to spot. You did it the other day when you 'emphatically' stated that an infectious agent was not the cause of ME, and then altered the words to prevent the embarrassment when I posted multiple quotes of doctors saying that the cause is most likely an infectious agent. You are now attempting to make it look like I am not responding to some of your points or questions.

So here's one point I will answer, and then wont bother as you will continue to alter the timeline.
If I chose to write an article myself I would get my facts right. That's the easy bit. But why should I do something I have no interest in doing, because you are upset that you are putting out incorrect information. That is a child's game. I will continue to get my information from scientific papers.

 

Cort, you're doing a fantastic job here, both with your excellent original article and the way you're updating it as points emerge on the forum: seems to me like a very powerful approach.

I don't suppose I'm the only one here who thinks V99's personal attacks on you are way out of line. She makes some valid points - amidst the misunderstandings - but they are wrapped up in so much unnecessary bile that it makes the forum an unpleasant place to be for everyone else, let alone you.

I'd thought we were all on the same side?

 

...

I don't suppose I'm the only one here who thinks V99's personal attacks on you are way out of line. She makes some valid points - amidst the misunderstandings - but they are wrapped up in so much unnecessary bile that it makes the forum an unpleasant place to be for everyone else, let alone you.
....

Totally agree.

 

Totally agree.

And me. Please stop posting these aggressive attacks on Cort.

People come here to read his reporting, not your self-important posturing.

If you want to contribute to the debate, there's no reason why you can't do so in a respectful and objective manner.

 

I had neither the time nor energy to read every one of these numerous points V99 is trying to make with Cort. Clearly V99, you are a smart person and a superb apologist. But seriously, for me to write 1/10th of the amount of words you've posted in the past 24 hours alone would take more energy than I had in a month! Judging by your mental acuity, your command of the English language, and the requisite energy it takes to write 5000+ words in so short a time, you may be one of the "healthiest" people who participate in this forum.

Perhaps you would be willing to channel that energy into writing some of your own blogs, doing some original research, and keeping those of us who don't have your strength better informed?

 

Jeeeesh people seriously...
This stuff is super difficult, especially for the brainfogged ( like me). I apreciate all the hard work that Cort does and I love reading his articles. I am sure they are not perfect and contain some assumptions or errors that is unavoidable at this stage. Great if people can point these (assumptions/mistakes) out and improve the info out there. But the personal attacks against Cort, I find them very distressing. He is not the enemy, he is human, allowed to make mistakes and allowed to have unpopular opinions if he chooses to. I can't explain it well but this all makes me so sad.

Thanks, leaves, for saying exactly what I was thinking at this point in the thread.

Personal attacks are both unnecessary and distressing to many of us.