XMRV Update: The science

Also, the people over at JDJ's blag still don't get that you see unspecific ERV activities when you treat PBMC with IL-2, PHA and 5-Azacytidine.

*Hint*

XMRV. The Generalissimo Franco of viruses. (Yes, I'm old. Ish.)

A few areas you may need to read up on

That is what Silverman has said. That he made VP62 in 2006. This is not the same virus as VP42, or the polytropic found in those with ME/CFS.

What about the sequences that are 1 to 2 % different to VP62? LOL where are they coming from?

"We already knew that XMRV was the result of a recombination event between two mouse endogenous retroviruses, called 'Pre-XMRV-1' and 'Pre-XMRV-2."
Do we? Could you at least try and provide some evidence?

MLVs can get around all kinds of defenses against retroviruses, like epigenetics, tetherin, Trim5, APOBEC, etc.

"The title of this article is kinda a spoiler... but none of the 43 animal workers had any signs of XMRV infection." Those were animal workers not lab techs reported to be positive. So any old sausage can make a test can they? How do you tend to know if your test works?

@Abbie, Great summary of recent papers...XMRV, like Generalissimo Franco, is still dead as a door nail!
@ smil, try learning some molecular biology, chemistry, bioinformatics, statistics, and then read the papers...your word salad doesn't deserve a rational response, since you seem to be completely unable to comprehend the evidence despite all effort. Just a few hints:
Silverman didn't make VP62; he cloned what he believed was a virus that was in his prostate tumors. Vp42 is not identical to Vp62, but it's close enough...it's the same virus.
Regarding evidence that xmrv was generated from Prexmrv1 and Prexmrv2, read the first two papers Abbie listed above.
Sequences that are 1-2% different from VP62? Where? Not Judy's, surely? They could be other endogenous MLVs that got cloned from mouse DNA contamination.
MLvs can get around host defenses? Nope. Not XMRV.
Lab techs reported to be positive. Now you are just making shit up.
Don't expect me to respond to further idiotic posts...I don't have time.

VP62 is a lab artifact from three patients with extra filler made in 2006.

VP42 is a full length clone from patient VP42. It is a different strain to VP62. Do you know anything about strains TCC?

"Regarding evidence that xmrv was generated from Prexmrv1 and Prexmrv2, read the first two papers Abbie listed above."

What evidence are you wanting looked at? Prexmrv2 is not present before or after contamination of the cells for xenografting of 22rv1 and no mouse used for 22rv1 has been found to have contained prexmrv2.

The 2% is from all sequences. Fisher covered this well in 2010. You have to alter the assay to detect other strains and alter the compartment you are screening.

The infected lab techs were reported at CROI. Perhaps you would like to know who you are accusing of lying before opening thy mouth?

Thanks Abbie.

It's handy to have all this in one place and to refresh one's failing memory cell. I think the attention has now focused on XMRV as a novel retrovirus (of the 'it can't infect humans and cause disease') variety; and I am still trying to follow those developments despite the suggestion in those two papers not having held up to replication and/or being found deficient.

XMRV is an interest nothing more than that for me at least, but it and retroviral 'theories' continue to be a 'fascination' for a handful on the forums I do frequent as a patient with 'ME'.

And let's face it a retroviral association with my condition (or perhaps a sub-set of patients with my condition) cannot be ruled out in the future; so it has been an interesting learning experience if nothing else, and has served to break some of the tedium. Your input (and that of others) has been very helpful in helping me navigate the science.

Personally, I wish those 'scientists' etc. who continue to support any notion of XMRV/MLVs being associated with my condition would just publish a bloody paper on it and until they do, shut the hell up or at least knock the speculation on the head.

But as they don't or won't and although there is I think a definite change in wind direction following the retractions - perhaps even before they happened - from many more patients on the internet; a small handful of 'folk' still hold onto the notion that... well you know...

Re: Paprotka et al.

Now you know I ain't no scientist but here's something addressed to Mr Tuller (also not a scientist) in relation to the above from someone who might think he's a scientist and for all I know could be making some semi-coherent observations.

Though if Mr Tuller is anything like me (as a non-scientist) he will duly file under 'can't be arsed to even read this email' or forward it to someone who might ;)

http://www.mecfsforums.com/index.php/topic,11360.0/topicseen.html 9 February 2012

Not related to the overall science of XMRV, but further questions about the state of science behind the Whittemore Peterson Institute (Lombardi et al) that kicked off the hype of an infective RV transmissable in blood:

http://cfsuntied.com/blog2/2012/02/08/the-wpi-loses-uk-study-blood-samp… deals with sample handling in a follow up to the Science mag article - WPI doesn't even seem to have been able to track its donated samples, you know those ones full of active retrovirus !

And for anyone who's missed it - the (soon to be a day time TV mini series starring Greg Evigan in the Harvey Whittemore role) WPI saga gets ever more bizzare:

http://cfsmirror.blogspot.com/2012/01/good-science-cant-happen-in-bad.h…

@ #5
Reported at CROI? Do you have a name or abstract number? It is easy to verify.
Am I supposed to be impressed with your handle? I don't care who you are....your ignorance is fully revealed by your nonsensical statements above.

Abbie - Just to warn you, there will be a new manuscript submitted in April ......on the first day of April........that will blow all that negative data away entitled: "High prevalence of XMRV in Nevada female inmates. A causal link of XMRV to Criminal behaviors." I think she'll mount her appeal with this seminal piece of science. Hey, they have to come up with a substitute for the Twinky defense since that company is in bankruptcy.

re #3 + #5; I know the square root of fuck all about science. Not my trade.
But being a dreadful old vagrant has given me a passing familiarity with dialects.
âSo any old sausage ...
If I'd a gun to my head, I'd guess old-fashioned (as in, so-o-o last century) English, possibly even a Welshy strain thereof ...
âPerhaps you would like to know who you are accusing ...â
I feel fairly confident that if you have owt to do with it, it'll stay your own little secret.
Well done. Have a biscuit.

Sorry to play devil's woo advocate, but the XMRV crazies will come up with these arguments and I think it is better to preempt.

"XMRV is from the lab, not nature."

Woo argument: So it was created earlier in the lab. Eighties. Fifties. Thirties. Whatever.

"XMRV isnt infecting humans. Like, at all. Anywhere."

Woo argument: But XMRV can infect human cell lines!!!!1!!ELEVEN!! You are in the pockets of big harma!!!!

"XMRV doesnt even want anything to do with primates. Certainly not humans."

Woo argument: But human cell lines!

(As a personal question: Why does APOBEC and all the other stuff not hinder XMRV replication in cell lines? I know that cell lines are missing all the shiny parts of the immune system, like leukocytes, that a real human being has to offer, but isn't APOBEC present in cells, and shouldn't it be present in cell lines as well?)

@Smil,5

"That is what Silverman has said. That he made VP62 in 2006. This is not the same virus as VP42, or the polytropic found in those with ME/CFS."

1. Silverman made VP62 plasmid from patient samples in the Urisman et al. 2006 study. He made it available to Mikovits in March 2008.

2. Funny enough, VP62 was the only thing that was the only thing reported by Mikovits/VPI. No other virus sequences were reported by WPI:

http://2.bp.blogspot.com/-pQNQs8VaUX4/TyADukbquhI/AAAAAAAAAFk/sShjvWYYA…

http://1.bp.blogspot.com/-SYkzL01lHUo/TyADvVmeYtI/AAAAAAAAAFo/jPtGGbPNF…

This was presented by Daniel Peterson on the CFSAC October 2009 meeting:
http://videocast.nih.gov/summary.asp?live=7908
http://www.hhs.gov/advcomcfs/meetings/agendas/cfsac091029_agenda.html
http://www.hhs.gov/advcomcfs/meetings/presentations/xmrv_cfs.html

All sequences published by the WPI are VP62:
http://www.ncbi.nlm.nih.gov/nuccore?term=Whittemore%20AND%20Peterson
http://www.ncbi.nlm.nih.gov/nuccore?term=Mikovits
http://www.ncbi.nlm.nih.gov/nuccore?term=Khaiboullina

Run BLAST for yourself.

@IVI:
Greg Evigan as Harvey Whittemore? Day time TV?

Nah!

I want a proper blockbuster! John Woo as director. Robert de Niro as Harvey Whittemore. Danny Aiello as Albert Seeno. Christopher Lloyd as Doc Mikovits. Tom Sizemore as Vincent Lombardi. John Tormey as Francis Ruscetti. Now, that'll be some work of fiction I would paid for to watch â unlike the fictional works we have seen so far from these actors.

@Tony,
Good question about APOBEC proteins and cell lines. Cell lines are basically abnormal cells because they are typically cancer cells and have adapted for growth, often indefinitely, on a plastic Petri dish under artificial conditions. Some cell lines have shut off expression of their APOBEC genes while some still express them. It is a total genetic crapshoot. For example, human T cell line CEM expresses APOBEC and inhibits XMRV, while prostate cancer cell lines LNCaP and 22Rv1 don't express APOBECs and don't inhibit XMRV.

@Tony,
Good question about APOBEC proteins and cell lines. Cell lines are basically abnormal cells because they are typically cancer cells and have adapted for growth, often indefinitely, on a plastic Petri dish under artificial conditions. Some cell lines have shut off expression of their APOBEC genes while some still express them. It is a total genetic crapshoot. For example, human T cell line CEM expresses APOBEC and inhibits XMRV, while prostate cancer cell lines LNCaP and 22Rv1 don't express APOBECs and don't inhibit XMRV.

Ha! Everyone knows that retroviruses are transmitted by having sex.

Find the people who are having sex with mice and you will find the mouse-human-link to cases of XMRV!

@ #16,
You mean unprotected sex, of course. I always insist my mouse wear a condom.

@17, that's very mice of you.

Science of XMRV? What kind of backwater blog is this? Don't you know that the XMRV-WPI issue has moved from the lab to the courtroom and now the highest political offices in the country? Politicians are now running from Whittemore, dumping the campaign contributions he and others made. This scandal is spreading faster than the MEV-1 virus in Contagion.

http://www.rgj.com/article/20120210/NEWS/302100029/Senate-Majority-Lead…

Maybe it will come full circle and the mice will disown the Whittemores too.

@ TCC
Ok, that makes very much sense.

I have one question regarding the Lombardi et al. 2009 timeline.

AFAIK, some/most/all of the serology was done at Ruscetti's lab. Was there serology work done at WPI before Ruscetti got involved?

Who (WPI?), when and how (by which method) found the first "evidence" for XMRV in CFS? When did Ruscetti's lab got involved? Does anybody know if WPI did have XMRV positive results *before* Ruscetti's lab got involved? Is there a timeline somewhere like "WPI reported evidence by method A in XX/XXXX, then turned to Ruscetti for method B in YY/YYYY and to Silverman for method C in ZZ/ZZZZ"? Surely Dr. Mikovits did brag about this somewhere in her own humble way. This must be somewhere, but if I have seen it somewhere in the ocean of material available, alas, I forgot it againâ¦

@Tony
The virus isolation work was done by Ruscetti..the infamous Fig 2c western was done by the Ruscetti lab as well...I believe the serology was done by Ruscetti alone but I'm not sure whether some of it also done by Judy at WPI.
Beyond this, I don't know but I would guess Judy had the PCR data first. It would be interesting to know the sequence of events....ultimately, though, aren't they both equally guilty?

BLAST for yourself.

Shame on you, Tony! You know that Smil/Gerwyn doesn't know how to use BLAST...and why would one need to? After all, it's much easier to simply make claims based on ignorance than to actually take the time to learn stuff.

@smil,#5
Hey smil/Gerwin...I'm waiting for that CROI abstract number to check up on your claim that lab worker are infected with MLVS.

@TCC
"...ultimately, though, aren't they both equally guilty?"

In the end yes. But I want to understand how this unfolded. I am having a hard time imagining a "I fake the PCR, can you fake the serology?" talk. One side faking the PCR, then the other side feels the pressure to either get positive serology or make something up, for fame and glory â after all, how often can you participate in finding a human retrovirus? History is not going to ask much questions, if the serology was fudged a bit. So Dr. R was tricked into believing in the PCR results by Dr. M? That would explain Dr. M throwing out the PCR by now, but her still believing in the serology. "Yes, the PCR was wrong, but Dr. R found it too!"

Dr. M and logic are not best friends, but that would explain the most.

BTW, I found an article claiming that Dr. M was the first person to isolate HIV in salvia. With the events of the last two years, I wonder how solid this finding is. And if Alter/Lo type of replication studies were done.

.
.
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@Poodle Stomper
First of all, it needs to verifiably clear for everybody checking in this thread that whatever the smil/gerwyn/v99 sockpuppets say, it is wrong. Verifiably wrong. I have little hope for whoever is behind this handle, but for every smil you have dozens who just read this thread â they need to be shown what the evidence say.

And secondly, I find the "Christopher Hitchens strategy" the best by now: Show the inconsistencies in their scripture. Show were they are lying bastards. They say the contamination was Silverman's fault? Tough luck, the WPI reported VP62 in August 2011 â without Silverman's involvement. They make claims that are not verifiable? Quote with sources showing what their saints have done. Nothing pisses disciples more off, than when they find out that their high priests are lying to them.

Oh, come to think of it, Brian Deer does something similar: he quotes the heck out of Wakefield. Not that I am going to reach the level of proficiency like Deer or Hitchensâ¦

So show were they are wrong, everytime, with citations. They don't care about the work others do, but they adhere to their scripture â and this scripture is riddled with inconsistencies.

And with regards to trying to understand BLAST and VP62, I have written something, that I hope might be helpful:

Let's say hypothetical, that Alice has a fragment of a handwritten book, only a few pages. These pages look like from medieval times, but Alice doesn't know how old the pages are, and is not sure exactly from which book they came from.

So Alice makes a copy of the few pages she has and gives these copies to Bob. Bob has a large database with copies of the content of all handwritten books he could get. If anybody can find out more about the book, then it is Bob.

And Bob looks into his database and the closest match he finds are handwritten Bibles from some 13th century monastery in northern Italy. Bob finds that the copies from Alice have a few spelling differences from the copy that is in Bob's database. But Alice copies share all the peculiar spellings that only these 13th Bibles from that northern Italy monastery have.

So Bob is pretty certain that the handwritten pages Alice has were directly transcribed of these 13th century Bibles from that northern Italy monastery. They may have been made later, they may have been made in another place, but it is a direct copy of that Bible, alright.

Yet, Alice says that these pages are not from a Bible, but actually from the Talmud! So Bob asks for some pages that show that these pages came from the Talmud. Alice declines to provide pages that could show that these pages came from the Talmud, but keeps on insisting these pages came from a Talmud copy.

Now, what would you find more closer to reality? Alice's claim that these pages came from the Talmud? Or Bob's analysis that show the relation exactly one sort of Bibles?

(With thanks to Dan Dennett's book "Darwin Dangerous Idea" for giving me the idea â a book, albeit a bit longish, I can only highly recommend for anybody trying to understand some of the basic concepts of evolution)

@TCC

At CROI, after the presentations about XMRV, there was a panel discussion. During that discussion, one scientist (Mike Busch) expressed some concern about lab workers sometimes testing positive.

It's at 53:09 from the following video:

http://app2.capitalreach.com/esp1204/servlet/tc?c=10164&cn=retro&s=2044…

[Please note that I am merely passing on information and that I feel that this is really grasping at straws]

@24 Tony Mach:
â.. whatever the smil/gerwyn/v99 sockpuppets say, it is wrong. Verifiably wrong.â
As a bit of a completist, I'd add âSmynnâ to the flypaper of Gerwyn Morris sound-alikes.
How many more I still have to spot to get my Big Chief I-Spy feather - well I simply dread to think.

@ Tony

The PCR identification of XMRV would have to come before serology; to look for XMRV in patient blood, you need to know which antibody to use; they decided to use anti-SFFV antibody mainly because they knew they were looking for XMRV, and thought the anti-SFFV antibody might detect XMRV. 

@ RRM

Thanks.  Yes, Iâm aware of the discussion that lab workers âmight be infectedâ with XMRV.  This is quite a bit different from Smilâs claim that âinfected lab techs were reported at CROIâ.

By analogy, Smil would claim that âMoon colonies inhabited by humans were reported in Floridaâ.  But Newt Gingrich only said âWe should go to the Moon and build human coloniesâ.        

 As an aside, looking for XMRV prevalence in moon colonists could be an excellent subject for a grant proposal  ;)

Response to Comments on "Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome"
Mikovits and Ruscetti
Science 328, 825-d (2010); DOI: 10.1126/science.1184548

"Investigators at NCI received 100 samples from individuals without knowing their health status; furthermore, the samples were sent to NCI directly without passing through the WPI laboratory space."

What ever went wrong with the results at Ruscetti's lab, they can't blame the WPI - or else this sentence would be a lie.

"The WPI has examined all 218 control and 101 patient samples by both PCR and serological methods for the presence of XMRV nucleic acid and antibodies. In addition, NCI used plasma from all 100 samples they received in infection experiments with LNCaP cells."

And this makes it look like the WPI did most of the serology. Plus, this can be read as both PCR and serology were done for all samples by the WPI. But serology was not done for all samples!

(I have no idea why I would think that, but I get the feeling they intentionally obfuscate things.)

BTW, from the same comment:

"Unpublished comments made during a medical conference (7) exploring hypothetical connections with immune system defects, viral reactivation, and malignancies should not be used to judge the merits of the science in the published paper."

The XMRV cult of Mikovits came into existence only through her unpublished comments. The whole cult lives by unpublished comments like the one with the supposed "infected lab worker". Take away all unpublished comments, and the thing collapses faster than you can say soufflé. What chutzpah to distance herself from her own comments.

RRM, you are thinking of Mike Basham at CROI. He was concerned about finding his lab assistants positive for the retroviruses.

TCC, why do you think VP42 and VP62 are the same virus and not different strains?

(As a personal question: Why does APOBEC and all the other stuff not hinder XMRV replication in cell lines? I know that cell lines are missing all the shiny parts of the immune system, like leukocytes, that a real human being has to offer, but isn't APOBEC present in cells, and shouldn't it be present in cell lines as well?)

APOBEC doesn't restrict MLVs. Are you sure you have done your research? Perhaps these will assist.
|
Downregulation of APOBEC3G by xenotropic murine leukemia-virus related virus (XMRV) in prostate cancer cells
http://www.virologyj.com/content/8/1/531

The Glycosylated Gag Protein of a Murine Leukemia Virus Inhibits the Antiretroviral Function of APOBEC3
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950561/

Species-Specific Restriction of Apobec3-Mediated Hypermutation
http://saturn.med.nyu.edu/research/mp/littmanlab/pubupdate/18032489.pdf

"APOBEC doesn't restrict MLVs." In cancer cells or cell lines.

You forgot to add in cancer cells or cell lines.

See here it says IN CANCER CELLS:

Downregulation of APOBEC3G by xenotropic murine leukemia-virus related virus (XMRV) in prostate cancer cells
http://www.virologyj.com/content/8/1/531

.

See here it says IN CELL LINES:

gGag is critical for infection of in vitro cell lines in the presence of APOBEC3.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950561/

.

See here it says IN CELL LINES:

Three cell lines were used: 293T cells, NIH 3T3 cells, and GHOST-X4 (a human osteosarcoma-derived cell line with a GFP expression cassette under the control of the HIV long terminal repeat).
http://saturn.med.nyu.edu/research/mp/littmanlab/pubupdate/18032489.pdf

.

Let me repeat, just for maximum impact:

In cancer cells or cell lines.

.

One more time for maximum impact:

IN CANCER CELLS OR CELL LINES.

.

You know what I'll say?

IN

CANCER

CELLS

OR

CELL

LINES.

.

One more time, for good measure:

I N

C A N C E R

C E L L S

O R

C E L L

L I N E S.

Got it?

And what did I ask? I wanted to know: Why APOBEC is not able to restrict XMRV in cell lines. That was the question I asked. With the added bonus that cell lines are at large derived from cancer cells. So what point exactly did you want to make?

@Butter#31
"APOBEC doesn't restrict MLVs."
IT seems you are not grasping some basic concepts, including some key points made in the abstracts of two of the three references you linked to. The main point is that mouse APOBEC3 protein doesn't restrict some MLVs, indicating that some MLVs evolved to overcome this host defense so that they could replicate in mice. You make this statement to suggest that human ABOBECs don't restrict XMRV, which is in correct as several studies have shown that human APOBECs potently restrict XMRV.
The Virology journal paper is a really weak study. See comment below from Dusty Miller, which pretty much destroys this paper and it's conclusions. The title is "Conclusions not supported by data.

http://www.virologyj.com/content/8/1/531/comments#712698

Oh, and VP62 and VP42 are the same virus.

http://www.virologyj.com/content/8/1/531/comments#712698

I think you have skipped some information in your rush to fit research to your desired outcomes. In vitro and in vivo are not on a par. The studies you have posted here are based on an unnatural isolate.

"In contrast, hypermutated HTLV-1 genomes were not identified in peripheral blood mononuclear cell DNA from ten patients with non-malignant HTLV-1 infection. Thus, although HTLV-1 DNA can indeed be edited by at least four APOBEC3 cytidine deaminases in vitro, they are conspicuously absent in vivo."

http://vir.sgmjournals.org/content/86/9/2489

MuLVs research has already shown these viruses integrated into B cells to evade APOBEC. APOBEC has no affect on these cells. To propagate MuLVs use clonal expansion.

VP62 and VP42 are different strains that are over 20 nucleotides different. Urisman describes them as viruses.

"Here we report that 40% (eight of 20) of all tumors homozygous for the R462Q allele harbored the genome of a distinct gammaretrovirus closely related to xenotropic murine leukemia viruses (MuLVs)."

APOBEC also mutates HIV, but we don't then deduce that HIV would not result in disease.

http://www.sciencemag.org/content/305/5684/645.abstract

"They looked at blood donors from the Reno/Tahoe area (heh/heh) for antibodies capable of neutralizing XMRV. 6.5% could, kinda-ish, but when that sera was further investigated, none of the neutralization was XMRV specific, nor was there any evidence of XMRV genome."

This HIV study did not look for XMRV antibodies in patients as the pseudotype virus contain the genome of another virus. The proteins and will not be of XMRV (VP62), but another virus. There is also no evidence and no reason to think that VP62 would produce an immune response in macaque's or mice. It would be appropriate to return to the research and use an appropriate assay.

@room
APOBEC activity causes hypermutaton and inactivation of XMRV in pigtail macaques...that's in an animal and therefore is in Vivo.
Unnatural isolate? That assumes there are other isolates in humans, for which there is no evidence.
APOBEC mutates HIV on rare occasions when HIV fails to block it with it's own defense mechanisms. without this defense, HIV wouldn't cause any disease.

I can't be bothered to try to make sense of the rest of gibberish you wrote. It's clear that you have little understanding of what you are writing.

@TCC

That is in pigtail macaques. What about humans?
APOBEC causes HIV hypermutation in humans and MLVs are able to avoid APOBEC. It's not an arguement.
Unnatural isolation does not assume the viruses are in humans. The evidence from multiple assays does that. VP62 was an artifact from three patients, unlike the other isolates.