The novel human retrovirus XMRV has been associated with prostate cancer and chronic fatigue syndrome. The nucleotide sequence of XMRV isolated from humans indicates that the virus is nearly identical with XMRV produced from a human prostate tumor cell line called 22Rv1. This cell line was derived by passage of human prostate tumor tissue in nude mice. Sequence analyses reveal that the genomes of these mouse strains contain two different proviral DNAs related to XMRV. These viral genomes recombined to produce XMRV that has been isolated from humans.
XMRV was originally isolated from a human prostate cancer in 2006, and subsequently associated with ME/CFS. The human cell line 22Rv1, which was established from a human prostate tumor (CWR22), produces infectious XMRV. An important question is whether XMRV was present in the original prostate tumor, or was obtained by passage through nude mice. To answer this question, DNA from various passages of the prostate tumor in nude mice (called xenografts), and the mouse strains used to passage the tumor, were analyzed for the presence of XMRV proviral DNA.
Early-passage xenografts did not contain XMRV, but mouse cells found in them did contain two related proviruses called PreXMRV-1 and PreXMRV-2. The 3€™-3211 nucleotides of PreXMRV-1, and both LTRs, are identical to XMRV save for two nucleotide differences. The genomic 5€™-half of XMRV and PreXMRV-1 differs by 9-10%. PreXMRV-1 is defective for replication due to mutations in genes encoding the gag and pol proteins. PreXMRV-2 does not contain obvious mutations that would prevent the production of infectious viruses. The gag-pro-pol and a part of the env region of this viral genome is identical to that of XMRV save for two base differences; the LTRs and the remainder of the genome differ by 6-12% from XMRV.
Comparison of the sequences of PreXMRV-1 and PreXMRV-2 indicates that recombination between the two viral genomes led to the formation of XMRV. When the sequences of PreXMRV-1 and ˆ’2 are used to construct the recombinant XMRV, the resulting virus differs by only 4 nucleotides from the consensus XMRV sequence derived from all human isolates reported to date.
The nude mice used for passage of the original prostate tumor were likely the NU/NU and Hsd strains. Neither mouse strain contains XMRV proviral DNA, but both contain PreXMRV-1 and PreXMRV-2 proviral DNA.
These data demonstrate that XMRV was not present in the original CWR22 prostate tumor, but arose by recombination of PreXMRV-1 and PreXMRV-2 between 1993-1996. When the original prostate tumor was implanted into nude mice, some of the mice harbored both pre-XMRV-1 and ˆ’2 endogenous proviruses, which recombined to form XMRV. The authors believe that XMRV originating from the CRWR22 xenografts, the22Rv1 cell line, or other related cell lines has contaminated all human samples positive for the virus. In addition, they suggest that PCR assays for XMRV may actually detect PreXMRV-1 and ˆ’2 or other endogenous viral DNA from contaminating mouse DNA.
Another possibility to explain the origin of XMRV is that it arose in mice and can infect humans. If this is true, then XMRV would have to be present in the nude mice used to passage the CWR22 human prostate tumor. No evidence for an XMRV provirus was found in 12 different nude mouse strains, including two used to passage the CWR22 tumor. Furthermore, a screen of 89 inbred and wild mice failed to reveal the presence of proviral XMRV DNA. Hence the authors conclude:
€¦that XMRV arose from a recombination event between two endogenous MLVs that took place around 1993-1996 in a nude mouse carrying the CWR22 PC xenograft, and that all of the XMRV isolates reported to date are descended from this one event.
It is possible that XMRV produced during passage of CWR22 in nude mice subsequently infected humans. Because XMRV arose between 1993-1996, this scenario could not explain cases of prostate cancer and chronic fatigue syndrome that arose prior to that date.
How can these findings be reconciled with the published evidence that sera of ME/CFS patients from the 1980s contain antibodies to XMRV? Those antibodies were not shown to be directed specifically against XMRV, and therefore cannot be used to prove that XMRV circulated in humans prior to 1993-96. Furthermore, in the absence of clear isolation of an infectious virus, antibody tests alone have proven highly unreliable for identification of new viruses.
Where do these findings leave the hypothesis that XMRV is the etiologic agent of prostate cancer and ME/CFS? All published sequences of human XMRV isolates are clearly derived by recombination of PreXMRV-1 and ˆ’2. The finding of human XMRV isolates that are not derived from PreXMRV-1 and ˆ’2 would leave a role for XMRV in human disease. As of this writing, no such XMRV isolates have been reported in the scientific literature.
Update: A second paper has also been published in Science Express today entitled “No evidence of murine-like gammaretroviruses in CFS patients previously identified as XMRV-infected”. Editors of the journal Science have asked the authors to retract their 2009 paper linking XMRV infection with chronic fatigue syndrome. The authors have refused.
T. Paprotka, K. A. Delviks-Frankenberry, O. Cingoz, A. Martinez, H.-J. Kung, C.G. Tepper, W-S Hu, M. J. Fivash, J.M. Coffin, & V.K. Pathak (2011). Recombinant origin of the retrovirus XMRV. Science Express
Haven’t you got better things to read?
Is there another version of the Dunning-Kruger effect whereby smart people feel compelled to read dumb forums?I’ve got this DD, and this science is way over my head, but I choose to read this blog and similar impartial info over forums of that ilk.
I don’t appreciate true-believers perpetuating petty squabbles and blind faith in inappropriate forums. Â At this stage true-believers need to persuade the editors of Science of their superior skills or insight (or whatever it is that they have supreme confidence in), not the readers of this blog. Â Â Â Â
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Alan, this poster alleges that your wife believes ME/CFS to be a psycho-somatic disorder. I take it with a grain of salt, as I do most things alleged in blog comments. However, if she is, how shall I put it? under-informed about ME/CFS, I would encourage her to read about or talk with Dr David Bell, Dr Nancy Klimas, Dr Daniel Peterson, or one of the other undisputed experts in this disease. It appears that there are several separate subsets that are lumped together under one rather poor description. But at least one subset involves neuro-immune disregulation, and that is clearly the case with my own illness.
As an occasional listener to TWIV, I am always interested in what VR and other TWIV people have to say about this issue. (I almost wrote “TWIV guys”, but changed that because I know some virologists are female and you’ve had one or two on your show.)Â
Here are my concerns &/or questions:
1. If the results are due to tests picking up widespread contamination, why aren’t results always 100% positive?
2. If contamination is so widespread, how do you account for study results where no XMRV was found?
3. If WPI says they did not use the contaminated line, in a new laboratory, and have been testing weekly to guard against contamination, what else could they reasonably have done to prevent the alleged problem?
4. Regarding the subsequent study that didn’t show positive for the explicit variety of XMRV referred to in the Oct 2009 study, but did turn up more than one closely-related virus, shouldn’t subsequent studies be looking for those related viruses in the same way HIV testing looks for multiple HIV variants?
5. If the virus is difficult to find in blood, but easier to find in tissue biopsies, why aren’t researchers looking more at tissue biopsies? I don’t think it would be difficult to find volunteers.Â
6. Maybe this is too obvious an idea, but given all the controversy, shouldn’t there be at least *one* follow-on study that tries to duplicate WPI’s methods exactly, to see what happens? I got through on the phone once to Dr Mikovits, surely it wouldn’t be that difficult for a researcher to call up and ask to meet with her and/or some of the other researchers there to understand their methods better.Â
7. What do you make of the handful of ME/CFS patients whose condition has improved on anti-retrovirals?
You may have guessed that I have been paying close attention to this field because I am an ME/CFS patient myself. I’ve been too ill to work for at least 15 years, and was ill off and on during the several decades before that. It seems clear to me at this point that my illness involves a disregulation of the immune system–the extensive blood tests I had done last fall showed sky-high cytokines.
Personally, I’m looking forward to seeing the results of Dr Lipkin’s study. If the link between XMRV and CFS doesn’t pan out, I will be disappointed but then must look ahead to the next line of inquiry. I just finished reading “The Emperor of All Maladies”, a history of cancer. Excellent book! But daunting to realize just how much labor goes into each tiny increment of understanding of complex disease. The biggest fear of ME/CFS patients, I think, is that if XMRV does not turn out to be the solution, that researchers will wander off and forget our illness. I think one positive thing XMRV has done is to introduce some researchers to this illness, and educate them on how debilitating it can be. Maybe some of those people will continue to think about the biological underpinnings, and a possible treatment.Thanks in advance for your comments.
Â
Prof. Racaniello,
Regarding your comments about the antibodies to XMRV in this week’s virolohy blog and an earlier comment in an (online) edition of  WSJ ( “He says that other viruses have proteins that are highly related to XMRV proteins. If the patients then test positive for antibodies, “it looks like they have antibodies to XMRV but they are not specific to that virus.—)
What does this practically mean?
– Does it mean there is another virus in these patients blood? If so, because the proteins are so related to XMRV proteins, would it be plausible it’s a (p)MLV (like found by Lo et al.)? Or could it be any virus? How can scientists find out which virus it is?
– If these antibodies are not caused by a virus, what other explanations could there be for the antibody reponse?
Another closely related question I have is regarding the contamination argument.
 If contamination is so widely spread, wouldn’t it be plausible humans already got in contact with the virus? (lab workers, vaccines etc.) I know Levy speculates XMRV is quickly inactivated by human serum, but isn’t this in contrast with the rhesus macaques studies, who show a low-grade infection and recently demonstrated XMRV was sexually transmittable?Â
Professor Racaniello I am curious if I am miss interpreting the Knox paper results, maybe you can shed some light on this. It appears to me that the western bolt shows a p30 & p15 band in the CFS column also I am seeing some type of reactivity in the 2nd round PCR lane for patient 19, for both of these examples I aligned a ruler across the the positive control and the samples and they seem to line up suggesting that Knox et al. did detect the virus in patient samples but reported everything as negative does this seem right?? Thank so much for the work you do.
We are doing an all-XMRV TWiV tomorrow (3 June), hopefully with
retrovirologist Steve Goff joining us, and I will try to answer some
of your questions then – we also have a long queue of XMRV questions
as well for that episode.
Annette Whittemore is correct, as they do not challenge the findings.
If XMRV really is a contaminate, why is Dr.Lipkin going to continue with his multi-million $ NIH study. As an ME/CFS patient who just wants to get well, I would much rather see that money used to explore what is really making us ill. If it is, as Dr. Levy stated in his NYT article…..toxins being produced by an overactive immune system….let’s have study done on that.
I think ME patients are being portrayed as desperate fools (XMRV-Mikovits/WPI cultists) when all we want to know is what is making us sick and a treatment to help us feel and function better.
Don’t get me wrong many, many of us our thankful for the light WPI and Co. have shed on this much neglected disease…but if their hypothesis is wrong…let’s move on…time, money and precious lives are being wasted each and every day.
We do, however, want bio-physical research not more psycho mumbo-jumbo….there have been 20+ years of those studies and we are still sick, while more and more people/children get sick everyday.
If 1+ million dollars is going to be poured down the drain to prove to us that XMRV really is just a contaminate….it will be just another disappointment in a long history of disappointment and lack of progress in this disease.
I’ll be curious to listen to your TWIV w/Dr. Goff tomorrow….hope AD stays home.
Thanks.
I hope Vince and company address, on his podcast tomorrow, how Drs. Singh, Silverman, etc. remain justified in continuing their own XMRV research in prostate and breast cancer.Â
‘Thing is, reading Singh’s responses to Mindi Kitei, Singh isn’t backing down on her own research. Supposedly, her XMRV isn’t a contaminant. I’m not buying it, any more than I buy her implying that we need more blood studies with ME/CFS before looking at tissue/autopsy samples, ridiculous considering especially what happened with XMRV in the macaques.
No sour grapes – if XMRV is a million-to-one lab creation, there’s
little reason for Likpin’s study to proceed, or WPI or Yale to be
allotted XMRV studies with GWI vets. Let’s move on. I just don’t see how there’s room for Singh and Paprotka to both be completely right. If WPI was wrong, Singh and Silverman were also wrong for the same reasons.
But will they be asked to retract papers, or patents? No – and I don’t even see it’s warranted for the Lombardi team, even if Mikovits’ outside assertions may have misled many patients and autism parents, nor to stop the alleged hordes of patients grasping for anti-retrovirals. Mikovits may be very stubbornly wrong, but I’m sorry, Mikovits/WPI are not Andrew Wakefield, although some would like to portray them that way.
Now whether Lombardi and Lo/Alter should have been published without proof of DNA integration, that’s another story. In my view, this call for retraction is either the editors’ way of taking the focus off Science’s own double-mistake, a political ploy suggested by someone outside the scientific peer-review process, or both.
I think you are right on, Warbler512. And you’d be surprised who would
agree with you. As for retraction of papers – in my view that should
be reserved for outright fraud. When science is wrong, it is corrected
by other research, and the wrong science simply fades away.
I really hope you try and answer these questions as you would about any human retrovirus. Â But after your comments here, based on an absence of evidence, nothing will surprise. Â
You statements are not logical.  The main reservoir for this virus is not the blood but tissue.  They are working at the limits of PCR.  Hence why it is necessary to increase the sensitivity of  any assay.  Only two groups testing people with ME/CFS have done this.  Lombardi and Lo.  You are also ignoring, not surprisingly, the serology results, EM and isolation of the virus.  Claims about only one taq polymerase working are also incorrect, if you have been following closely.
Validation can be achieved through multiple methods and assessment by other labs. Â This is why Science published Lombardi. Â It passed every additional requirement that Coffin asked for. Â Therefore there are known positives. Â This is normal practice when dealing with a new novel virus. Â
Claiming that someone is wrong without evidence to support that claim, nullifies your argument. Â
Replication does not consist of applying one or several variables from a study, you have to use them all. Â None of the negative papers, even those who have bothered with a culture and antibody assay have failed to replicate. Â Thus you are clinging to straws if you think that this is applying the scientific method. Â These culture and serology assays are also riddled with their own issues, which if applied to other human retroviruses would fail to detect.
Luckily for all, more studies that can detect the virus will soon be published ad then we can get away from those who have forgotten basic science.
If these comments had any scientific data to back them up, then those who want to say the XMRV variant of the virus is contamination should withdraw their patents on this virus.  That would include  Abbott labs and Singh.  Singh has said in interview that it is an XMRV-like virus she is findings.  But she has not published anything on this.  They should also make it plain they don’t intend to make money off the other variants of HGRVs, unless they are really not convinced.
There are many studies about the connection of immune activation and CFS. I completely agree that even minor funding could be able to not only lead to a better understanding of CFS but to tests and treatment as well.Â
I think that you have missed my point. Either XMRV causes (strictly: “is associated with”)Â CFS or not. Although on the basis of the available evidence this looks unlikely, it cannot be completely discounted. (This is being generous in the eyes of some.) We have two possibilities.
From the tone of your posts, you don’t appear to able to acknowledge even the possibility that XMRV is *not* associated with CFS (or is not a human pathogen). You seem to be lacking in objectivity. Instead, you disappear into a very high degree of detail, a degree of detail that is simply not needed for most scientific questions. The methods used have been close enough to find this virus if it’s really there.
I am not clinging to anything. I am simply watching this unfold with interest. I have no emotional attachment to one outcome over the other. Personally, I would far rather XMRV is associated with human disease – but it is not up to me! It either is, or is not.
NB you could substitute “is associated with CFS” for “is a human pathogen” if you like. It seems to me equally unlikely that XMRV is associated with prostate cancer.
Interesting journey, though.
There are several very basic errors in the above post. The Supporting Online Materials from Paprotka et al. (1) clearly state that they screened 89 strains of inbred and wild mice. Rather than the authors having failed to look for pre-XMRV’s 1 and 2 in wild mice, it seems that you have failed to look at the available information.
The authors do acknowledge that it cannot be proven that the initial CWR22 tumor was not infected with XMRV, they conclude for a substantial number of reasons that XMRV arose in the manner described in the paper- “Our screen of 89 inbred and wild mice (Fig. S4) failed to detect XMRV as an endogenousprovirus in any of these strains. Thus, it is very unlikely that original CWR22 tumor was infected with XMRV derived from an endogenous XMRV provirus. Furthermore, the NU/NU and Hsd mice are the only mice among the 12 nude mouse strains that we analyzed that contain both PreXMRVâ€1 and PreXMRVâ€2 (Fig. 2D). Taken together, the possibility is remote that the CWR22tumor was originally infected with XMRV—which would have to come from an extremely rareputative endogenous XMRV provirus—and by coincidence was transplanted into rare nudemice that harbor both parental proviruses. Although the possibility that the CWR22 tumor wasinitially infected with XMRV can never be completely excluded, we conclude that it is far morelikely that XMRV arose through recombination between PreXMRV-1 and PreXMRVâ€2 during passaging of the CWR22 xenograft in nude mice.”â€1 and PreXMRVâ€2 (Fig. 2D). Taken together, the possibility is remote that the CWR22tumor was originally infected with XMRV—which would have to come from an extremely rare
putative endogenous XMRV provirus—and by coincidence was transplanted into rare nude
mice that harbor both parental proviruses. Although the possibility that the CWR22 tumor was
initially infected with XMRV can never be completely excluded, we conclude that it is far more
likely that XMRV arose through recombination between PreXMRV-1 and PreXMRVâ€2 during passaging of the CWR22 xenograft in nude mice.”1 and PreXMRVâ€2 during passaging of the CWR22 xenograft in nude mice.”Â
The 22rv1 cell line might or might not have ever been in the WPI’s lab, but materials were sent from Silverman’s lab to the WPI which could account for how XMRV came to be at the WPI. As for none of the cell lines currently in use by the WPI being contaminated by XMRV, WPI representatives have mentioned several times that they have 4 different cell lines derived from patients, with these cell lines expressing XMRV that is virtually identical to the 22rv1 virus. The WPI would probably say well of course, it came from the patients, but it could have just as easily been the result of contamination. For a similar discussion, the comments on the paper  ‘Unintended spread of a biosafety level 2 recombinant retrovirus’ deal with this exact issue. Talk about hiding in plain sight!
As for this paper not saying anything about this virus not infecting humans, this is correct. That is why there are several other papers with do deal with this exact subject such as the accompanying paper in Science, Knox et al., in which the authors found that XMRV is deactivated in human serum, as well as several other older papers which demonstrate that XMRV is inhibited by APOBEC.
Â
1. Supporting Online Material forRecombinant Origin of the Retrovirus XMRVRecombinant Origin of the Retrovirus XMRVhttp://www.sciencemag.org/content/suppl/2011/05/31/science.1205292.DC1/1205292s.pdf
Â
2. Unintended spread of a biosafety level 2 recombinant retrovirus
http://www.retrovirology.com/content/6/1/86/comments
Â
Incorrect. The authors state they check 15 strains for PreXMRV-1 & 2. The strains are listed and are all lab mice. You are quoting the strains they checked for XMRV.
“We screened 15 mouse strains, which included 12 nudemice, for the presence of XMRV, PreXMRV-1, andPreXMRV-2 using XMRV-specific primers, primers thatamplified XMRV or PreXMRV-1, and PreXMRV-2-specificprimers (Fig. 2D and fig. S2). None of the mouse strainscontained XMRV and only the Hsd and the NU/NU outbrednude strains contained PreXMRV-1 (Fig. 2D and fig. S6). Sixof the 15 mouse strains contained PreXMRV-2, but only theNU/NU and Hsd mice contained both PreXMRV-1 andPreXMRV-2 (Fig. 2D and fig. S6).”amplified XMRV or PreXMRV-1, and PreXMRV-2-specificprimers (Fig. 2D and fig. S2). None of the mouse strainscontained XMRV and only the Hsd and the NU/NU outbrednude strains contained PreXMRV-1 (Fig. 2D and fig. S6). Sixof the 15 mouse strains contained PreXMRV-2, but only theNU/NU and Hsd mice contained both PreXMRV-1 andPreXMRV-2 (Fig. 2D and fig. S6).”
Whether HGRVs are the cause of any disease has not been the subject of any paper at this time. The scientifc data supports that this retrovirus is infecting humans and is associated with prostate cancer and ME/CFS. There is no scientific evidence of contamination.  This would require a hypothesis that could account for all the observations. This is absent still. The possibility of mouse contamination and innability of studies to detect HGRVs is not evidence of absence.  The paper here also presents an incomplete proposal.  It is much more likely that the XMRV strain was not created in the lab, but through zoonosis.   This paper should not have been excepted with the conclusions made by the authors and wild mice should have been screened for PreXMRV-1 and 2. But of course no evidence is available to support whether PreXRMV-1 and 2 are ancestral or decendants of the XMRV strain.
That is to skirt around the issue a little, isn’t it? Surely the importance of identifying a novel infectious agent is the potential for it to be actually causing disease?
But anyhow…. All you have to do is substitute “infects humans” for “is associated with CFS/is a human pathogen” and my previous post still stands. Two possibilities – though you acknowledge only one.
If this were to be really shown to be infecting humans somehow I don’t think we would hear you urging caution because “we are uncertain whether this is simply association or actually causation.”
It might take someone with more knowledge of the actual sequences than me to confirm this (@profvrr:disqus ?) but given the extremely high degree of sequence similarity between fragments of pre-XMRV-1 & 2 and XMRV I would expect the screening for XMRV to pick up pre-XMRV. The primers used were XmU3f (which is in the 5′ LTR) and GAGr (which is in GAG) so this assay should at the very least have picked up pre-XMRV-1 (from which the 5′ end of XMRV is derived), meaning in effect all 89 mouse strains were screened for pre-XMRV-1.
Wow now I am really into the detail. Phew!
Cynically, as long as Lipkin proceeds, Fauci’s behind is covered for giving this attention.
If Levy is right about toxins, let’s open up the books on the Ciguatoxin epitope studed at U of Hawaii, which Tom Hennessey brought up in his CFSAC testimony. Perhaps the acute phase lipids, found higher in ME/CFS than even Ciguatera poisoning itself, help keep this thing going as much as the original insult.
Cynically, consider also who was using U Hawaii’s test – Martin at USC, and some clown from the FDA who was patenting a food poison test. FDA has remained absolutely mum about anything regarding this disease; no Ampligen, no blood ban, nothing. Who/what are they covering for? I don’ t know that a food-borne against would explain all cases either, but screw it, lets put everything on the table.
Not at this stage. Â First you have to approach association. Â Work is progressing on proving causation. Â I would speculate we should see something in the next 12 months. Â
The argument in your second paragraph is unclear?
The virus has been stated to be, by several health authorities, to be a human retrovirus. Â The data supports such a conclusion. Â The argument in your third paragraph is unclear?
PreXMRV-1 and 2 are in fact highly dissimilar to XMRV. Â PreXMRV-1 is only 90% similar to XMRV over a 3.6-kb stretch and in PreXMRV-2 only 88% over a 3.1-kb stretch. Â Those viruses have not been detected in any human samples, so I have no idea what you are speculating about now. Â Again, the authors are clear. Â Only 15 strains were tested for PreXMRV-1 and 2. Â They also provide a complete list of those 15 lab strains.
Yes
First time I’m hearing 90% similarity being referred to as “highly dissimilar”
PreXMRV-1 and PreXMRV-2 have been sough in wild mice; the results were reported at last week’s Cold Spring Harbor Retrovirus meeting. I can’t reveal the results here, unless the authors are reading and wish to do so. But remember that the likelihood of XMRV being generated by a different recombination event in wild mice is vanishingly small – a one in 1,000,000,000,000 chance. If such a virus were generated years ago (when CFS as a disease began) it would be very different today. Knox et al showed that passage of VP62 in cultured cells results in more mutations than have been observed in XMRV isolates. You could argue that a very different MLV causes CFS – but there is no evidence for that.Â
When there are people who’ve been diagnosed with CFS before XMRV even existed (according to Paprotka et al.) and are positive for XMRV according to Lombardi et al., and you think that this Paprotka finding is not a problem for the hypothesis that there is an association between XMRV and CFS…
…you must believe in time travel?
You wouldn’t claim they were similar at 88% in one stretch would you? Â Perhaps you would find this easier if you used facts.
The paper does not say that they tested wild mice for preXMRV-1 and 2. Â They specifically state that 15 strains were tested. Â Those named in Figure 2D are lab mice. Â
I am a little shocked that you are talking about unpublished data as if it were valid. Â The statistics in the paper are speculative at best. Â It is not known if PreXMRV-1 and 2 are ancestral or descendants of the XMRV strain. Â It is not known if any of those are in wild mice. Â Therefore the statistic are speculative at best. Â
CFS is a fictions construct and it is not possible to say when it began if there has been no biomarker used for diagnosis. Â Again, speculation. Â
I will come back to the VP-62 in a moment. Â For now I’m shocked.
Paprotka et al is lacking in data. Â It is not possible to conclude where HGRVs originated from based on that paper. Â CFS is also a metaphor and it is not possible to state when the disease “began”. Â
Here are the facts of your so called “dissimilar” sequences.
“The complete sequence of PreXMRV-1 was determined from
the early passage xenografts, the NU/NU and Hsd strains, and
the CWR-R1 cell line. PreXMRV-1 and consensus XMRV
differed by only one base in a 3211-nt stretch of the genome
encoding the 3’ half of pol and the 5’ 2/3 of env. In addition,
the LTRs were nearly identical; PreXMRV-1 had a single
adenine deletion relative to XMRV in a run of 6 adenines.
The two genomes differed by 10% over the remaining 3.5-kb
stretch of gag-pro-pol and by 9% in a 600-nt stretch at the 3’
end of env.”
“A 3.6-kb stretch encompassing the gag
leader region and gag-pro-pol differs by one base from the
consensus XMRV (99.9% identity); in addition, a ô€—½700-nt
region of env is 99% identical to XMRV; however, the LTRs
and the remaining viral genome differ by 6–12% from
consensus XMRV.”
Did you even read the comment you replied to? He is talking about cold spring harbor meeting not CROI. He is saying he can’t reveal the results, how can you claim that he is “talking about unpublished data as if it were valid”.
I’m afraid it has now been reported that this strain of nude mice, NU/NU and Hsd were not used in the preperation of the 22Rv1 cell line.
The authors of the paper have been contacted by the editors of Science and have been asked to deny this fact. We will await their response with interest! Â I believe that this matter is to be discussed in the conference in Belgium. Â
The most likely explanation is that these sequences were actually transferred from humans to the mice. Â Which should have been proposed in the paper. This has been reinforced by the fact that this mouse strain has been kept isolated from wild mice since its creation.Â
Knox et al. used the PCR assay which had only detected gag sequences in 7% of patients in the Lombardi study when testing Dan Petersons patients and reduced the DNA concentration while doing so and for good measure increased the annealing temperatures. Â The likelyhood figures are just plucked out of thin air. Â
Xenotropic Polytropic hybrid MLVs are routinely generated in infected mice. Â The use of PCR assays, which have high analytical sensitivity but unknown clinical sensitivity, should be discouraged as negative findings do not prove the absence of target viral sequences. Â 20 months have been lost because of this fiasco. Â
The data has not been published and you may want to read my other comment.
Take a look at the remainder of PreXMRV-1 and 2 and you will comprehend. Â
How does the results of Harvey Alter at the NIH and Dr Lo of the FDA fit into all this?
They found the retroviral PMLV sequences in ME/CFS patients at 87% versus 4 % of controls in a very well definded cohort of patients gotten from Dr. Anthony Komeroff at Harvard.
Dr. s Alter and Lo said they tested and controlled for contamination even using Dr. Coffins own IAP test. Alter is on record as saying his study was a partially validating study to the NCI/CC/Science paper. So if he found PMLV’s which are part of the larger family of which XMRV belongs.
Why is this finding not being talked about here?
Yes my second paragraph is a bit unclear. To repeat with minor modification:
“I think that you have missed my point. Either XMRV infects humans or not. Although on the basis of the available
evidence this looks unlikely, it cannot be completely discounted. (This
is being generous in the eyes of some.) We have two possibilities.
From
the tone of your posts, you don’t appear to able to acknowledge even
the possibility that XMRV does *not* infect humans. You seem to be lacking in objectivity. Instead, you
disappear into a very high degree of detail, a degree of detail that is
simply not needed for most scientific questions. The methods used have
been close enough to find this virus if it’s really there.”
My third paragraph was not really an argument but more flippant speculation.
To call pre-XMRV-1 & 2 highly dissimilar to XMRV is to be in denial (or to be conveniently referring only to the portion of the genomes that did not contribute to XMRV which misses the point). Yet again I see no evidence that you are conceptually able to grasp two distinct possibilities, either of which could be true. (Though on the basis of the evidence it would seem much more likely that XMRV does not infect humans.)
20 months haven’t been lost at all. This field is advancing much faster than other new infections I have seen. It’s been very interesting to see this all unfold. What it tells us about retroviral recombination events is fascinating and has implications well beyond putative XMRV infection.
Where can we find verification that the authors have been contacted by science? Can you give a link?
Then your position is different: The findings of Paprotka et al. DO challenge Lombardi, but you think the findings of Paprotka ‘are not valid because they’re not backed by data’. That is suddenly a very different position to take than ‘I accept the findings but they do not challenge Lombardi et al., but you knew that, right?Â
Ms. Whittemore said that the Paprotka findings do not challenge Lombardi et al. Specifically, she said that ‘the theory of the origin of XMRV is not relevant to the Lombardi finding’. Remember, this was before she had the chance to actually see the data (“We have not had the chance to review the embargoed Paprotka et al. report”), and therefore she is really talking about the findings and not about the data that is backing these findings (as you are now suddenly resorting to).
Sorry, but that Whiitemore comment is therefore a stupid comment to make. Unless you believe in time travel, that is. : )
“indicates that the virus is nearly identical with XMRV produced from a human prostate tumor cell line called 22Rv1. ”
“Nearly identical” is not good English. Â Identical means “exactly the same”, to qualify it with “nearly” changes the meaning completely. Â A better choice of words would be “similar” which has the additional virtue of being shorter. Â However “similar” would not be as effective in promulgating the spurious argument given in this article.
The second paper you link to above again calls on people with ME/CFS not to take anti-retrovirals. Â Yet ARTs are used as prophylactic against HIV infection in healthy people, and those taking ART with ME/CFS are sick, some so much so that their decision was either to go to Dignitas in Switzerland or have one more go at treatment. Â There are (admittedly anecdotal, but what else do we have?) reports of health improvement from these pioneers. Â Why the continued attempted prohibition?
Clinical trials now!
Sorry, I intended to add this link http://treatingxmrv.blogspot.com/2011/06/comparison-of-methods-for-detection-and.html#comments which is instructive and factual.
The small amount of data in Paprotka et al. has nothing to say about people being infected with HGRVs. Â
If we imagined for a moment that they had further supporting data and the argument of a recombinant being created during xenografting was plausible for the source of one strain of HGRV. Â It still has no bearing on whether the virus is in the human population. These same people would also wish us to believe that the virus is everywhere, which would leave plenty of routes from which the virus could find its way into a human. Â
Infected cell lines have not been in labs detecting the virus in ME/CFS and no evidence exists to show that the samples were contaminated. Â Those 20 positive samples retested by the CDC and the use of the unvalidated IAP assay by Lo support the opposite. Â The virus could have been created 10 years ago, but the date of origin has nothing to say about who is infected now. Â And where did the other strains come from? Â Not XMRV. Â But this is of no concern as the data in Paprotka is lacking and not convincing at all. Â Annette Whittemore is therefore entirely correct.
The evidence supports the conclusion that the virus is infecting humans. Â You are picking and choosing the data that fits your beliefs, perhaps for emotional reasons. Â You are very much in denial, similar to HIV denialists of the 1980s.
It is speculation how many switching events would be needed if the XMRV strain was created from those two PreXMRVs. Â Again, are they ancestral or descendants of XMRV. Â They have no idea. Â Furthermore, the entire issue of lab mice strains infected with them has now been challenged. Â
XMRV is one variant of HGRV. Â That is a human gammaretrovirus.
The authors have been contacted by the editors of Science.Â
20 months have been wasted by those not adhering to the scientific method. Â
ART is only used as prophylaxis against HIV in healthy people where there is clear evidence of a high risk exposure to HIV and there is thought to be benefit. Even then it is a difficult decision and one that has exercised me significantly on a number of occasions as the risk of HIV acquisition is often hard to estimate. Then the drugs are only used for a month and, in the unit where I work, 50% of people don’t finish the course because of the side effects.
Although ART is generally safe, all drugs have side effects which must be balanced against the benefits. ART has some significant side effects. `taking a protease inhibitor for 5 years carries approximately the same risk for a heart attack as being a smoker or being diabetic; that is not insignificant. Tenofovir, a very commonly used drug has kidney toxicity. Abacavir, the main alternative to tenofovir, also increases the risk of heart attack. Raltegravir has the least side effects of all in clinical trials but there are case reports of major depression in patients after starting raltegravir, not a good thing for someone with CFS. Efavirenz is notorious for it’s psychological side effects – most common are weird dreams and a feeling of being spaced out – again probably not helpful if you have CFS! That covers most of the first line drugs that would likely be used.
The available evidence does not suggest a basis for using ART in people with CFS. Even if all these papers found XMRV that still would not prove causation, but it might at least justify a clinical trial (to which I would enthusiastically recruit should it ever happen). However, there is no basis to justify this at present while there is such disagreement amongst the virologists. We are scared of the side effects.
The scientific method includes the possibility that there is more than one explanation for an observation which you do not acknowledge in this case. Your mind is firmly made up no matter what evidence is presented. I put it to you that there are no data, no matter how perfect, that would convince you this virus doesn’t infect humans.
Time hasn’t been wasted at all. If this virus does turn out to be able to infect humans, we will have learned alot about the problems of trying to detect it which would need to be worked out at some point anyway as diagnostic tests are commercialized & scaled up.
Using different methods to answer the same question provides powerful evidence in science. For example, lets say under certain conditions in an experiment an enzyme is upregulated. Showing that the message is upregulated (say by RT-qPCR or northern blot), the protein is upregulated (by western blot perhaps) and the activity of the enzyme is increased (by enzymatic activity assay) is much more powerful than one alone. Slavishly following the only method that has been shown to work leaves you open to repeatedly making the same mistake. Of course it is notable here that multiple methods were originally used to detect XMRV, but all these methods have since been difficult to replicate.
That one “HGRV” strain is the only strain that has been released by the Lombardi et al. authors. You are reframing the argument. Let’s keep it simple:
– Lombardi et al. found XMRV, not a multitude of HGRV strains, in a patient that had been sick since the 80’s.
– Paprotka et al. found that XMRV was created around 1993 (whether you believe the data backs the finding is a seperate issue, as I’ve explained)
– Therefore, you must believe this finding is very relevant to Lombardi et al., or of course you must believe in time travel.
The scientific methods takes account of all data in creating a hypothesis. Â It does not, as the authors of Paprotka have, present a paper that lacks data, ignores data and speculates only on those outcomes they wish to present. Â The evidence strongly supports the virus being human. Â Not one hypothesis has been developed to offer the opposite conclusion. Â No evidence for contamination in those labs has ever been found. Â Find out what the scientific method is before making silly claims.
20 months have been wasted. Â
Lo et al. used different methods to Lombardi et al. Â They found the same virus. Â XMRV is a xentropic and polytropic hybrid. Â Lombardi et al used 4 methods to support the finding. Â Including WB. Â None of the negative papers have replicated their methodology. Â Consequently your final paragraph is irrelevant.
The new strains in the GenBank from the WPI are polytropic and modified polytropic.Â
It is impossible for anyone to conclude that the data in Paprotka et al. supports the virus having been created in 1993. Â The paper should never have been accepted by Science.
So it is acceptable to replicate a study using different methods then? Or would that be… acceptable if you find the result that you want? Your pre-conceived ideas are remarkably strong.
Lo et al. didn’t find the same virus, they found a related virus.
XMRV is a hybrid of what, precisely?