Why did Alter not detect xmrv

[free at last]

Ok this feels like the wrong time to be discussing this,but after reading on the PA Advocate site that Frank Ruscetti Has detected xmrv in all the Alter samples, if the report is true something is clearly wrong with one of these researchers methods. Either Frank Ruscetti is getting false positives. Or Dr Alter is getting false negatives. How could either of them be getting that many false results ? If Dr Ruscetti is right, how the hell can Lo and Alter miss that many positives ?


Those who follow XMRV research closely know that two variants in the same virus family were found in humans in these two studies. Whether you call it XMRV or PMLV it is still a gamma retrovirus closely related to MLV propagating in humans. Dr. Harvey Alter himself stated that the Lo/Alter paper supports the Lombardi results and XMRV has been now found in all of Alters own samples (by Ruschetti)
http://cfspatientadvocate.blogspot.com/2010_12_01_archive.html

Im lost, Anyone understand whats happening here ?

 

[Valb626]

free, I'll try an answer, but am likely to be off, so I hope someone will correct whatever I say.

It turns out there are a ton of "pieces and parts" to a retrovirus. It appears that what you find depends on which pieces/parts you're looking at. (And other factors that have been endlessly discussed.)

It seems that they are all working together now and that all of them, WPI included, are expanding what they are able to look for and find. So, Ruscetti and WPI are finding PMLVs in the Lo/Alter samples and Lo/Alter are finding XMRV. They are probably finding other variants that nobody has reported yet, too!

There seem to be alot of variants/mutations of the mouse RVs, so it wouldn't be surprising to me if the ones that have been discussed to date are only the tip of the iceberg, and that we might be hearing about more. Maybe, in the end, we'll find out that having mouse RVs in humans is pretty common, but that there are only certain ones that are really nasty.

 

[lancelot]

Because there is not a standardized and universally accepted test for XMRV and MLV's yet. Everyone has their own unique "experimental" tests that may or may not pick up all XMRV and MLV variants.

 

[lancelot]

Ok this feels like the wrong time to be discussing this,but after reading on the PA Advocate site that Frank Ruscetti Has detected xmrv in all the Alter samples, if the report is true something is clearly wrong with one of these researchers methods. Either Frank Ruscetti is getting false positives. Or Dr Alter is getting false negatives. How could either of them be getting that many false results ? If Dr Ruscetti is right, how the hell can Lo and Alter miss that many positives ?

Im lost, Anyone understand whats happening here ?

If you have access to Lo/Alter's pre-hold original PNAS paper, they found XMRV as presented in alter's zagreb blood conference may 2010 slides.
here are two excerpts from his slides:

•XMRV and related MLVs are in the donor supply with an early prevalence estimate of 3% - 7%.

• We (FDA & NIH) have independently confirmed the Lombardi group findings

Why would dr alter say XMRV is in the blood supply on his slides, but not find XMRV in his post hold and "altered" PNAS paper?

"We(FDA & NIH) independently confirmed Lombardi group findings". What was the lombardi findings? It was XMRV not MLV's!

 

[free at last]

Hi valb,thanks for that. Lancelot too. Further thoughts hmm ok so Alter has indeed replicated the science study, so many things come to mind from that, 1 testing as of the science study time period [sometime after infact] was really unreliable.

2 that might explain the contradictory studies around the world more than anything else the BWG could hope to achieve with the small testing comparisons we have just witnessed.

3 How come no official statement from Dr Alter about this profound revelation, Especially with hes (Alters] speech to the BWG. In light of it now explaining those contradictory studies around the world, partculaly well, when the BWG was apparently trying so hard to. Yet the answer appears far simpler then ?

4 Alter apparently retested the samples, but again has made no mention of NOW detecting xmrv even though he apparently is. and never shared why he thinks he failed the first time.This still isnt making any sense to me.

5 Can we be sure when that leaked dutch report surfaced stateing that Alters lo study had replicated [confirmed] the wpi science study. That during the period the Alter paper was put on hold, after the CDC didnt find it. xmrv was left out of the equation, and we was given MLVs instead [Because MLVs showed up too]

The leak was never meant to happen.we learned something had been discovered, [Was led to belive it was xmrv by the words chosen] but then suddenly MLVs appear as a gift, But Dr Ruscetti finds xmrv in all of them, Now Dr Alter concurs and seems to have been shown how to by Dr Ruscetti. 6 One wonders why Alter and Lo were chosen when clearly they was not up to the job [ unless of course they were, and did detect xmrv ? ]
Just my thoughts wandering, i realize its pushing it, and probably way off base, but something always felt fishy about the paper being put on hold, and MLVs appearing instead.

 

[biophile]

• XMRV and related MLVs are in the donor supply with an early prevalence estimate of 3% - 7%.

• We (FDA & NIH) have independently confirmed the Lombardi group findings.

The intervention was unusual. This is what I think probably happened.

Lo/Alter's methods detected MLV's rather than XMRV, which were closely related enough to XMRV that these results "clearly support the central argument by Lombardi et al that MLV-related viruses are associated with CFS and are present in some blood donors" (XMRV being a MLV-related virus). Regarding the sentence in the slide, the "XMRV" + "3%" are from Lombardi et al and the "related MLV's" + "7%" are from Lo/Alter et al. These were combined because Alter believed they are the same issue. MLV's didn't suddenly appear after the intervention, they were there in the leaked slide.

I don't think Lo/Alter found XMRV and were then forced by the US government to lie in order to save the CDC from embarrassment. I mean, it's possible and I wouldn't really be surprised if that was true, but I think it's less likely. Perhaps it was Lo/Alter's insistence that their study provides confirmation of Lombardi et al (and therefore contradicted the CDC's findings) that prompted the DHHS to intervene. If no one thought detecting "related MLV's" would contradict the CDC's failure to detect XMRV, there probably wouldn't have been such an intervention. On the other hand, it may still have prompted an intervention for different political reasons.

 

[Otis]

free, I'll try an answer, but am likely to be off, so I hope someone will correct whatever I say.

It turns out there are a ton of "pieces and parts" to a retrovirus. It appears that what you find depends on which pieces/parts you're looking at. (And other factors that have been endlessly discussed.)

It seems that they are all working together now and that all of them, WPI included, are expanding what they are able to look for and find. So, Ruscetti and WPI are finding PMLVs in the Lo/Alter samples and Lo/Alter are finding XMRV. They are probably finding other variants that nobody has reported yet, too!

There seem to be alot of variants/mutations of the mouse RVs, so it wouldn't be surprising to me if the ones that have been discussed to date are only the tip of the iceberg, and that we might be hearing about more. Maybe, in the end, we'll find out that having mouse RVs in humans is pretty common, but that there are only certain ones that are really nasty.

Let me try to add a little to this. Most of what is known about human gamma retroviruses comes from studies if them in mice, which where these viruses originated. XMRV and the viruses found by Lo/Alter are both decended from MLVs but have distinct chacteristics.

XMRV is thus far the only *fully* sequenced human gamma retrovirus. It is also the only one thus far that has been isolated and shown to be able to replicate in human tissue. Once Lo/Alter are able to do isolate, fully sequence and prove the virus(es) they found can replicate in human tissue they will have shaken the still persistant Contamination Accusations.

It is believed that Lo/Alter found polytropic (gamma) retroviruses based on partial sequences made by Lo, although it will take full genetic sequences to accuratly categorize the virus(es) they found.

For the sake of brevity I'll use X to indicate xenotropic and P to denote polytropic.

It's not yet known the variety of gamma retroviruses that can infect humans.

XMRV is about 8100 nucleotide long. This sequece contains all the genetic material the virus needs. Due to that length, and because there is sure to be genetic diversity, lab assays look for one (or more) much smaller sequences.

The trick is to pick just the right sequence(s) or you'll get a negative result. If you choose to look at an area that changes from sample to sample you'll get a negative result unless you find another sample with the exact same genetic makeup (in the area you were looking). There are sequences shared across the X and P types such that if you're really good you can pluck out a result for either at which point additional sequencing is required to tell if you got X or P.

Ruscetti and Mikovits have said they've seen both P and X types although unfortunatly not in a published work. I belive the VIPDx antibody test is said to pick up antibodies to both X and P.

So to answer the original question, Lo picked up what appears to be a P variant and through additional testing Ruscetti has found X. This appears to mean than not only is it possible to have both variants, that some people do. It's almost certain that there is a "swarm" of gamma retroviruses that can infect humans and the real question now is how diverse is that range. In the end it may be considered "one virus" but that a given patient will have any number of individual sequences.

 

[August59]

Is this why Dr. Coffin keeps hammering at Dr. Alter about isolating the virus?

During the BWG meeting on the 14th there was a "tweet" that stated "Dr. Coffin was the reviewer that sent the Lo/Alter Paper back requesting more testing and further review thus resulting in the papers delay." This may be common knowledge, but I missed it somewhere.

 

[free at last]

Thank you Otis, That still doesnt explain Alters silence about xmrv in hes samples during retesting to the BWG now ? . Or why if he was uncertain how to detect x instead of just P, why he didnt ask Judy, or Frank early on, how to, so the paper in the morning reads NIH FINDS XMRV ? Like it or not the likes of Mclure and stoye made a big thing of ahh but its p not x, i think the original idea was to look for xmrv like groom and others was it not

 

[SOC]

Is it true that these "different" viruses that are being detected are no more different from each other than the different varients of, say, HIV or Hep-C? In other words, while they are scientifically (or cladistically?) different, they are effectively the same virus?

 

[free at last]

Is it true that these "different" viruses that are being detected are no more different from each other than the different varients of, say, HIV or Hep-C? In other words, while they are scientifically (or cladistically?) different, they are effectively the same virus?

Hi cfs Some dont seem to think so, as they are still staying Alter did not confirm the WPIs findings,rightly or wrongly they are saying it

 

[Cort]

That was a nice explanation Otis! - thanks

After talking to retrovirologist I think this is where the problem lies

Lo/Alter's methods detected MLV's rather than XMRV, which were closely related enough to XMRV that these results "clearly support the central argument by Lombardi et al that MLV-related viruses are associated with CFS and are present in some blood donors" (XMRV being a MLV-related virus).

Alter/Lo think they are closely enough related to XMRV for them to be put in the same category...Stoye and Coffin do not; we have the lumpers and the splitters. As Otis said, we'll only know when Lo/Alter more fully sequence what they found - which will, I assume, happen at some point in the not too distant future - and we'll know.

A journal is going to devote an entire issue to XMRV next year; hopefully Alter/Lo will have a paper in there describing exactly what they found.

 

[Cort]

free, I'll try an answer, but am likely to be off, so I hope someone will correct whatever I say.

It turns out there are a ton of "pieces and parts" to a retrovirus. It appears that what you find depends on which pieces/parts you're looking at. (And other factors that have been endlessly discussed.)

It seems that they are all working together now and that all of them, WPI included, are expanding what they are able to look for and find. So, Ruscetti and WPI are finding PMLVs in the Lo/Alter samples and Lo/Alter are finding XMRV. They are probably finding other variants that nobody has reported yet, too!

There seem to be alot of variants/mutations of the mouse RVs, so it wouldn't be surprising to me if the ones that have been discussed to date are only the tip of the iceberg, and that we might be hearing about more. Maybe, in the end, we'll find out that having mouse RVs in humans is pretty common, but that there are only certain ones that are really nasty.

This would be the best scenario I think! I hope this is it....These are the first gamma human retroviruses...so they can't be sure exactly which sequences to look for.....how would they know??? Viruses change when they get into humans - so who knows how they are going to change and exactly what to look for? Logically you've got to be kind of blind at the beginning, it would seem....

 

[Otis]

I won't speculate on Alter's silence other than to say it's possible that Ruscetti and/or Alter have has a paper in the works thereby making his reluctant to talk about it.

I don't recall, did Ruscetti mention finding XMRV at the BPAC meeting?

why if he was uncertain how to detect x instead of just P, why he didnt ask Judy, or Frank early on, how to, so the paper in the morning reads NIH FINDS XMRV?

He found what he found with his initial testing. It's quite plausible he felt that finding P was extending the pervious X work. He could have delayed publication to retest for XMRV using an entirely different protocol, but I believe he was/is very confident that finding a gamma retrovirus in CFS patients was confirmatory of the Science paper as he and Lo said at the Q&A held upon publication. FWIW, I agree, but your questions are valid ones.

Until he found P and we heard from the WPI that they had seen such variations too there wasn't any (public) discussion of it and it's possible he wasn't aware anyone else found P until his paper was at least as far as peer review. We don't know when the NCI/WPI first found P.

 

[SOC]

Hi cfs Some dont seem to think so, as they are still staying Alter did not confirm the WPIs findings,rightly or wrongly they are saying it

Yeah, well..... I'm thinking that there's always the nay-sayers and the deniers. And then there's those whose egos can't let them admit that they just plain missed it. I've decided to watch what the scientists are doing, not what all the political palaver is saying -- in so far as that's possible, of course.

All that said, I'm not SURE this "swarm" of viruses are all that much alike -- I'm working from my not-all-that-great memory.

 

[Otis]

Is this why Dr. Coffin keeps hammering at Dr. Alter about isolating the virus?

During the BWG meeting on the 14th there was a "tweet" that stated "Dr. Coffin was the reviewer that sent the Lo/Alter Paper back requesting more testing and further review thus resulting in the papers delay." This may be common knowledge, but I missed it somewhere.

Yes, I believe so.

I think the tweet came from Val's summary where she indicated that Lo (apparently frustrated with the Contamination Accusation) said something like "We did that contamination testing you (presumably Coffin) requested" leading Val (and the rest of us) to wonder if Coffin did play a part in the publication delay.

The only specific item I've seen regrading the additional testing requested came from a peer reviewer on the PNAS paper asking for proof the virus had integrated into human DNA. Alter was able to fight that off being too high of a standard, albeit a desirable goal.

 

[free at last]

I won't speculate on Alter's silence other than to say it's possible that Ruscetti and/or Alter have has a paper in the works thereby making his reluctant to talk about it.

I don't recall, did Ruscetti mention finding XMRV at the BPAC meeting?



He found what he found with his initial testing. It's quite plausible he felt that finding P was extending the pervious X work. He could have delayed publication to retest for XMRV using an entirely different protocol, but I believe he was/is very confident that finding a gamma retrovirus in CFS patients was confirmatory of the Science paper as he and Lo said at the Q&A held upon publication. FWIW, I agree, but your questions are valid ones.

Until he found P and we heard from the WPI that they had seen such variations too there wasn't any (public) discussion of it and it's possible he wasn't aware anyone else found P until his paper was at least as far as peer review. We don't know when the NCI/WPI first found P.

I can see your reasoning Otis and yes that does seem likely. The silence question is interesting though isnt it.

And a paper From Dr Alter on hes xmrv detections from hes samples would be most welcome wouldnt it.

whats interesting is the PA advocates words of all of Alters samples showing xmrv, so do we say those patients are infected wth two variants,or is the same virus being seen as x or p depending on the testing used, is that possible,i assume its not ? it cant be both at the same time can it,or can it ?

But as of now if culture detected xmrv in Alters samples, then yes, Alter / Lo have indeed confirmed the WPIs findings, Mclure is surely dead, then lipkin surely also will find it, if he uses culture for long enough for it to grow. And the patients are of similar cohorts Thank you everyone for helping me understand. Maybe im just too suspiciouse about the politics, people like Wessley make like that i think

 

[urbantravels]

Is it true that these "different" viruses that are being detected are no more different from each other than the different varients of, say, HIV or Hep-C? In other words, while they are scientifically (or cladistically?) different, they are effectively the same virus?

See what Ila Singh says about it here (in the full-text PDF)

http://www.mdpi.com/1999-4915/2/11/2404/

While each of these viruses, xenotropic, polytropic and modified-polytropic viruses (M-PMV), has been placed in distinct categories within the larger subgroup of murine leukemia viruses, it is important to note that they share considerable similarity with each other and utilize alleles of the same receptor for viral entry. The PMV and M-PMV share over 95% sequence identity, and the xenotropic viruses share over 90% identity with the PMV (derived from sequences within reference [12] and Genbank; [13,14]). Compared to this, an average pair of random isolates of HIV-1 in the U.S. are ~85-95% similar, depending on the region of the viral genome used for comparison [15,16]. Thus it is conceivable that PMV, M-PMV and XMRV may cause the same disease(s), if they cause disease at all.

 

[August59]

Yes, I believe so.

I think the tweet came from Val's summary where she indicated that Lo (apparently frustrated with the Contamination Accusation) said something like "We did that contamination testing you (presumably Coffin) requested" leading Val (and the rest of us) to wonder if Coffin did play a part in the publication delay.

The only specific item I've seen regrading the additional testing requested came from a peer reviewer on the PNAS paper asking for proof the virus had integrated into human DNA. Alter was able to fight that off being too high of a standard, albeit a desirable goal.

It was this tweet and I'm pretty sure H.B. is Heidi Bauer - H.B.:If I am not mistaken, Coffin was one of the reviewer who forced Alter and Lo back to the lab before their paper would be released.

 

[usedtobeperkytina]

Well

Well, I don't know about finding different ones in CFS patients.

But, there is a possibility that the differences are the different genetic/ evolutionary path. Might be geography? So different variants are different in different areas?

Of course, if one of you know why I am wrong, feel free to tell me why.

I did notice the study about the different variants (six was it?) in the new NIH study showing the viruses changed genetically but depending on species, immune system of the person / animal.

Also, I think it showed that quite a few of these variants can go into humans. Something about them combining sometimes?

I remember the study hypothesized that the prevalence of some diseases in certain geographical areas and less prevalence in other areas might be based on the changes in the evolution (of the virus and the hosts cells and immune system) in the different areas.

I am sorry if I can not be more specific. Mind not very clear tonight..

Tina