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

 

great article cort!

(cort my personal messages are stick, could you sort this out for me, thanku!)

 

Another very interesting and readable piece, Cort - thanks.

One point on my hobby horse:

Some of the CDC samples also came from people meeting the Empirical definition which increased prevalence rates dramatically and ushered in a new breed of CFS patient.

Not sure why you are saying that? Do you have inside information. The Switzer et al paper is presented in a way to suggest that they all satisfied the "empirical" definition.

We also know that the "empirical" definition was used for the Georgia and registry cohorts. There is a slight doubt about the Wichita cohort - was it taken between 1997-2000 (normal Fukuda definition) or 2003 (empirical definition) 2-day study. The two-day study is when they did lots and lots of testing and involved 43 patients (number mentioned in Switzer et al paper) so unless somebody has inside information, I think one should assume they all satisfy the "empirical" definition.

 

So the FDA found no XMRV in their own samples and none in the CDC ones either. But did the FDA find any evidence of MLVs in the CDC samples? that might tell us more.

This is an intriguing question.

One that may or may not be so good is - Is it possible that Lo/Alter weren't able to find XMRV because they missed it? Would be interested to know if the WPI has tested any of their samples and what the results were.

 

I looked briefly as I am trying to read all of this info, but I did not see what I was looking for.

Did any of the reports give the current status of the "ViroChip"?

It seems that with all of the differences, or apparent differences in the cohorts and various definitions that "Bio Markers" would be invaluable. One thought I had though was "Would the Bio Markers be different (or suspected to be) for various virus strains or would you look for a common marker and leave it at that?"

Having a hard time processing this science!

 

Initial analysis shows that the FDA test results are generally consistent with CDC, with no XMRV-positive results in the CFS samples CDC provided (34 samples were tested, 31 were negative, 3 were indeterminate).

So the FDA found no XMRV in their own samples and none in the CDC ones either. But did the FDA find any evidence of MLVs in the CDC samples? that might tell us more.

I asked Dr. Lo about the quote and this.

He said:

The primer sets we used for studying CDC samples were the same ones published in our paper. The primer sets should amplify both XMRV and MLV-related virus gene sequences we identified in our PNAS study.

Although several CDC samples are being further studied for sequencing confirmation, the samples provided by CDC clearly showed lower frequency of positivity and the virus titers or gene copy numbers were also lower than the CFS samples provided to us by Dr. Komaroff.

 

Great article, Cort. Thanks so much.:victory:

I'm going to keep asking this question until somebody answers it. Does the fact that they are polytropic MLVs mean that they can still be passed back and forth between mice and humans? If so, this could open up a big can of worms of how CFS got to be so prevalent--people working with lab mice, gene therapy, vaccines (an interesting paper about this at http://www.ecs.umass.edu/~mettu/ece597m/papers/Leung/sdarticle-1.pdf Or even wild mice. Has there been any research into MLVs in actual mice that might be relevant to us?

 

Good breakdown of the results, Cort. My reading is really slow these days. Thank you!

For how long have we people with CFS/ME been pointing out the Georgia cohort selected by several CDC researchers was invalid? The absence of evidence of any retrovirus in their "patient" population has no bearing on the other findings by researchers using samples from people who actually have the disease. There is no need to discuss the CDC findings any more. They are irrelevant.

What I perceive is that we have a well defined disease in people who are "mouse gamma-retrovirus" positive. We have suspected for decades there were subgroups of this illness. I rejoice to think that up to 80% or so might be well defined by being virus positive, and there may be treatments in the drugstores for them.

These positive samples: I wonder if any of them were from sudden onset cases; are they the instances of US CFS that are more ME like? If the researchers were to try to characterize the types of patients who were positive, it might lead to sick people queuing up for a clinical test when available, yielding a lot more relevant cases to study.

We need horizontal studies as well as vertical.

 

Another very interesting and readable piece, Cort - thanks.

One point on my hobby horse:

Not sure why you are saying that? Do you have inside information. The Switzer et al paper is presented in a way to suggest that they all satisfied the "empirical" definition.

We also know that the "empirical" definition was used for the Georgia and registry cohorts. There is a slight doubt about the Wichita cohort - was it taken between 1997-2000 (normal Fukuda definition) or 2003 (empirical definition) 2-day study. The two-day study is when they did lots and lots of testing and involved 43 patients (number mentioned in Switzer et al paper) so unless somebody has inside information, I think one should assume they all satisfy the "empirical" definition.

Everything I got was from the paper. I think technically you are correct. The paper said 11 from Wichita and 22 from Georgia. The empirical definition (developed in 2005) was not in place during Wichita (2003?) so they chose those patients fitting the Fukuda criteria. The paper did say that they all meet the Empirical criteria but since the Fukuda criteria is more restrictive, the most salient fact for me is that that there were people that met the more restrictive Fukuda criteria; ie neither group, Fukuda or Empirical - picked up during random sampling - had XMRV according to the CDC.

Actually there is doubt regarding the Fukuda group as well. We know that a substantial # of that Wichita group meet the Fukuda criteria at one point but not when they were sampled later - so I don't know if we can say them met Fukuda....maybe we should just say they were the 'CDC's (peculiar?) CFS' patients...

 

Great article, Cort. Thanks so much.:victory:

I'm going to keep asking this question until somebody answers it. Does the fact that they are polytropic MLVs mean that they can still be passed back and forth between mice and humans? If so, this could open up a big can of worms of how CFS got to be so prevalent--people working with lab mice, gene therapy, vaccines (an interesting paper about this at http://www.ecs.umass.edu/~mettu/ece597m/papers/Leung/sdarticle-1.pdf Or even wild mice. Has there been any research into MLVs in actual mice that might be relevant to us?

My recognition is that several people have said it didn't come from lab mice and they seem to have pooh poohed the wild mice idea altho I don't know why. However I have heard that they are looking at populations of wild mice to see if it is present. If they are polytropic they certainly can infect both mice and humans.

 

Treatment

Thanks for the post Cort.

I think the important thing is definitely the positive result, any treatment protocol may well be the same for all these virus as they are related and the most suitable anti-virus drugs will probably work on all of them.

Simon Lawrence

 

On "Alter/Lo Day +2" i have two remaining burning questions

1. why did alter/lo name their variants CFS1, CFS2, CFS3, and then say that there is not a direct link between these retroviruses and CFS?

2. are any of these newly discovered (alter/lo discovered) retroviruses the one Elaine DeFreitas found?

(and i like all the mito questions others had!!)

(and daffodil, you are emailing with Dr. Lo????)

 

I asked Dr. Lo about the quote and this.He said:

Well, you can't beat from the horses mouth! But did he really say this?

Although several CDC samples are being further studied for sequencing confirmation, the samples provided by CDC clearly showed lower frequency of positivity

Doesn't that mean they found some positivity in the CDC samples? And if so, isn't that very important?
The fact that "several CDC samples are being further studied for sequencing confirmation" suggests that they have found positives, otherwise they would have nothing to sequence.

Given the CDC's use of empirical criteria, you might expect to find some positives but at a lower level than found by Lo - which seems to fit with what Dr Lo is saying.

Can you stop me before I get carried away with excitement?
Thanks

 

Posted elsewhere but confounding enough to repost here (with a few additions)!
................................

How confusing that the:

'RV' in 'HGRV' = retrovirus

whereas

'RV' in 'XMRV' = related virus

And then we have 'MLV's', as well as 'MLV related viruses'! - which are all retroviruses (RV's)?

In addition 'XMRV' is a 'MLV-related virus', but an 'MLV related-virus' does not even have to be in the same part of the 'family tree' as an 'XMRV'! It can be a 'P-MLV', 'X-MLV' or even an 'E-MLV' (and one other which I've forgotten)!

Maybe 'retrovirus' could be indicated by the capitals 'RV', whereas
'related virus' (which is actually a retrovirus too in this instance) could have a small 'r' & a large 'R' = 'rRV'.

And after the September conference I'm sure we will have a few more to add.

Wasn't it just easier to use 'M.E.'?!

I bet even future top researchers are going to have trouble remembering all this!

 

Andrea Whittemore Unfortunately their is much misinformation in this and Mr . Johnson should have contacted the Whittemore Peterson Institute for his facts . I believe the WPI will be commenting on this shortly .
3 hours ago

Found on XMRV Global Action Facebook 5 posts down
http://www.facebook.com/pages/XMRV-Global-Action/216740433250

 

Another very interesting and readable piece, Cort - thanks.

One point on my hobby horse:

Not sure why you are saying that? Do you have inside information. The Switzer et al paper is presented in a way to suggest that they all satisfied the "empirical" definition.

We also know that the "empirical" definition was used for the Georgia and registry cohorts. There is a slight doubt about the Wichita cohort - was it taken between 1997-2000 (normal Fukuda definition) or 2003 (empirical definition) 2-day study. The two-day study is when they did lots and lots of testing and involved 43 patients (number mentioned in Switzer et al paper) so unless somebody has inside information, I think one should assume they all satisfy the "empirical" definition.

Everything I got was from the paper. I think technically you are correct. The paper said 11 from Wichita and 22 from Georgia. The empirical definition (developed in 2005) was not in place during Wichita (2003?) so they chose those patients fitting the Fukuda criteria.

No, that's not correct.
Remember it takes a while for things to be published.
The patients were seen in 2003.
The paper on them is what started the "empiric" definition:
http://www.biomedcentral.com/1741-7015/3/19

The paper did say that they all meet the Empirical criteria but since the Fukuda criteria is more restrictive, the most salient fact for me is that that there were people that met the more restrictive Fukuda criteria; ie neither group, Fukuda or Empirical - picked up during random sampling - had XMRV according to the CDC.

I think you're getting confused. The CDC say that the empiric criteria are just an operationalised version of the Fukuda criteria. That's why they say the prevalence is now 2.54%. That's what they say in all the papers using the empiric criteria - they don't say they're using a different set of criteria.

Actually there is doubt regarding the Fukuda group as well. We know that a substantial # of that Wichita group meet the Fukuda criteria at one point but not when they were sampled later - so I don't know if we can say them met Fukuda....maybe we should just say they were the 'CDC's (peculiar?) CFS' patients...

That is partly my point. Although the people who were diagnosed as CFS (empiric) in http://www.biomedcentral.com/1741-7015/3/19 may never have satisfied the ordinary Fukuda definition in 1997-2000 as they also brought in ISF, CFS MDDm (i.e. hadn't been given the diagnosis of CFS because they previously had melancholic major depressive disorder). The paper at http://www.biomedcentral.com/1741-7015/3/19 doesn't make things as clear as it should.

Unless we know that the blood was taken from them between 1997 and 2000, rather than 2003 (when they did all the testing), we should assume that they all are just "empiric" criteria patients.

 

Well, you can't beat from the horses mouth! But did he really say this?

Doesn't that mean they found some positivity in the CDC samples? And if so, isn't that very important?
The fact that "several CDC samples are being further studied for sequencing confirmation" suggests that they have found positives, otherwise they would have nothing to sequence.

Given the CDC's use of empirical criteria, you might expect to find some positives but at a lower level than found by Lo - which seems to fit with what Dr Lo is saying.

Can you stop me before I get carried away with excitement?
Thanks

Cort's piece talks about the CDC providing more samples.

On the FDA website http://www.fda.gov/BiologicsBloodVaccines/SafetyAvailability/ucm223232.htm and the first line of the piece to me, they talk about no positives. So the only way this makes sense to me is that:
- on the patients from the Switzer et al paper, they found none.
- the CDC provided more samples from somewhere and they found a few positives, but a low percentage, from them.

Actually, an alternative explanation might be that these positives are from other patients from the Switzer study as 34 isn't all the patients.

I think it's easiest just to go with the public statement that is out there:

Additionally, the CDC laboratory provided 82 samples from their published negative study to FDA, who tested the samples blindly. Initial analysis shows that the FDA test results are generally consistent with CDC, with no XMRV-positive results in the CFS samples CDC provided (34 samples were tested, 31 were negative, 3 were indeterminate).

and that XMRV means MLVs as confirmed in the first line of the e-mail to me.

 

...
2. are any of these newly discovered (alter/lo discovered) retroviruses the one Elaine DeFreitas found?...

I can't answer other questions, but I think I can say the sequences DeFreitas found were considerably different. There was more than one kind of virus in the TEM micrographs, and one of them was a C-type virus with a diameter of 70 nm. This could hardly be anything except a retrovirus. Questions about exactly what it was and where it came from were never answered.

It is important to distinguish the kind of science taking place here. She was in the position of a marine biologist trawling for organisms in the unknown deep sea. She found things in a region which others told her was important for disease. She was an explorer who was not prepared for for ruthless attacks from those horrified by the clinical/political/financial implications of finding anything. She had convinced Hilary Koprowski she had something, and he was far from the most gullible researcher around. He even staked his job on her results, and lost when funding evaporated.

I'll make another analogy, with paleontologist Charles Wolcott and the Burgess Shale fossils. These came from a period which had been completely unknown before. Virtually every identification he made has been overturned, sometimes repeatedly. He still gets credit for bringing these to the attention of other paleontologists, and doing his best to describe what he thought he had found.

At the time she did her work, the biology behind CFS was a complete mystery, less known than the far side of the Moon. She was held to standards which were years ahead of the state of research in this area. If Robert Gallo had been subjected to these at a similar stage, HIV research might have been set back by years.

 

I have just started to read this, and well there is quiet a bit wrong with it. Mainly facts. I dont have time to point them out right now, but can I suggest that anyone reading this goes and looks at the facts.

 

A quote from the PNAS paper to start correcting this misinformation:

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

http://www.pnas.org/content/early/2010/08/16/1006901107.full.pdf

 

The Lombardi (WPI), Groom, McClure and Switzer (CDC) papers all looked for ‘gag’ sequences identified by primer #’s 419F/1154R.

Where have you got this from?

The gag sequence they identified, however, is not specific to XMRV - it is a marker for a range of murine leukemia retroviruses of which XMRV is one.

this is what the PNAS paper says:

"Nevertheless, the heterogeneity in gag gene sequences that we observed suggests that geographic differences in different MLV-related viruses may be considerable and could affect both the sensitivity and the specificity of molecular amplification using standard primer sets" Lo et al.

As in multiple not one.