2 more studies that found, you guessed it, zero XMRV

Jemal

Senior Member
Messages
1,031
Likes
65
And finally, many of the remaining negative studies have explicitly drawn woefully illogical conclusions (as has been pointed out by others ad nauseum). To me this definitely sets off alarm bells regarding motivations and/or competence. If you can't form a logical conclusion, can the rest of your study be that well designed? Why would competent, well-intentioned scientists overreach so drastically in a way that is indistinguishable from an attempt to bury this finding?
Yeah, a lot of these studies come to some outrageous conclusions. It does make me wonder how scientific these studies were, so I agree with your point.
I also agree with Cort though that there seem to be certain unusual requirements to detect this virus.
 

urbantravels

disjecta membra
Messages
1,333
Likes
527
Location
Los Angeles, CA
I think there are four key studies - the Blood Working group, Singh, the CAA/Glaxo Smith Kline study and Lipkin.

Dr. LeGrice told me he thinks the mouse DNA (contamination) issue will be resolved within 3 weeks! The Blood Working Group will announce findings as soon as they get - they know the patients are suffering under all this controversy. Their assay will hopefully be done by XMAS or early next year.

From your lips to God's ears, Cort!

But...if Le Grice thinks it's all about to be straightened out soon...why was he singing such a long and repetitive song about contamination in his talk on Science Day??
 

urbantravels

disjecta membra
Messages
1,333
Likes
527
Location
Los Angeles, CA
Also - I guess we're not quite to the point yet where peer reviewers for scientific papers are going to send the authors of scientific publications back to the bench because they're clearly using inadequate methods for detection. At least the cat is out of the bag now that there's been SO much open discussion of assay methods, people can't pretend forever that the inadequate methods are somehow going to settle the question of whether the virus(es) are present.

I hope, hope, hope the assay standardization happens SOON, so that we don't get more publications, using inadequate methods, to provide more fodder for those who are just all to eager to console the poor patients about having gotten their hopes up again....
 

Esther12

Senior Member
Messages
13,774
Likes
28,359
But...if Le Grice thinks it's all about to be straightened out soon...why was he singing such a long and repetitive song about contamination in his talk on Science Day??
'Sorted out' doesn't necessarily mean 'shown to be false'. He could think it's a quite likely possibility, and be in the midst of experiments which will settle the matter one way or the other.
 

currer

Senior Member
Messages
1,409
Likes
861
Hi. We already know that XMRV is not very infectious sexually. ME/CFS does not show up with great frequency between sexual partners. It seems to transmit in families via some other mechanism. We also know that gay men and drug abusers are not the usual ME/CFS patient. That patient is usually female. So I cannot see the point of the Barnes/Mclure study. Why study groups that are known not to be usually associated with ME/CFS? Why go to great lengths to show something that is already known? A number of these research studies reveal that the authors know little about the features of the illness and are not thinking deeply enough.
 

Mark

Senior Member
Messages
5,238
Likes
6,201
Location
Sofa, UK
There are only two general reasons for the discrepancy: 1) the original claim is false (e.g. contamination, false postives, etc) or 2) the followup attempts are inadequate in some fashion (e.g. issue w/ method or process). I believe that if one is both competent and well-intentioned, then he/she would willingly and proactively acknowledge and investigate both possibilities. A competent and well-intentioned person doesn't (as has happened in most of these cases) state unequivocally that the first option is the only possibility and then launch into a PR crusade to discredit the original claim.
This is a cast-iron point. No scientist can be unaware of the issue of investigator bias. Any good science should be conducting their investigations of scientific questions with an open mind, and taking pains to ensure their objectivity. And yet there is abundant evidence regarding many of the negative studies that their authors did not believe the results would be positive. Even going so far, in Wessely's case to say "I don't think we're going to find it..." and then after the briefest of pauses..."nope, see, we didn't find it - told you so!".

As to what is going on in their heads regarding their true motivations for not believing they will find anything...well, I hate to see people trying to look inside other people's heads, so it is much better not to speculate, and to simply observe the evidence that demonstrates those preconceptions and biases. Asleep has listed a few possibilities, there are many, and I don't know which ones apply to which individuals.

But "My expectation is that we will not... [find it]" is a subtle phrase, if you look up "expectation" in a dictionary...
 

Mark

Senior Member
Messages
5,238
Likes
6,201
Location
Sofa, UK
Hi. We already know that XMRV is not very infectious sexually. ME/CFS does not show up with great frequency between sexual partners. It seems to transmit in families via some other mechanism.
Sorry currer but that's not proven to my satisfaction. There are yet more possibilities which seem interesting to me...

If XMRV rarely becomes a replicating infection, and does so only to a limited extent and under very specific conditions, then it's quite possible that when sexual or other transmission of XMRV occurs, only a tiny amount of XMRV is transmitted. That transmission could lead to a very, very slow build-up of latent XMRV infection, and perhaps disease symptoms only become evident when a critical threshold has been passed, or when some other factor like a separate infection enables active replication. So in a sense XMRV would not be 'very' infectious sexually, but it would be infectious and a slow, gradual build-up. This seems to fit anecdotal evidence of long-term partners showing signs of infection after many years.

Those instances of familial transmission could equally be masked if only a small percentage of people are susceptible to disease as a result of infection, or again, if only certain circumstances allow the virus to replicate.

I agree that it does now appear likely that infection can take place through more casual routes - I have (virtual) money on the sweat hypothesis for example - but I still think there's a very good chance it is regularly transmitted sexually.

Whatever the explanation I think it's clear that there are some confounding factors involved in the pathology and disease progression that make most tentative partial conclusions seem contradictory to other evidence at first glance. But that's exactly what you would expect of a good "stealth virus"...

ETA: Plus I'm not convinced there is any good evidence about familial transmission of ME/CFS to make the oft-repeated claim that it doesn't seem to be infectious. In terms of accepted biomarkers, at least, there isn't any rock-solid data on anything else, and there's never been a reliable way to measure ME/CFS other than patient reports of illness, and even regarding that the data hasn't been remotely well-collected, so I don't see how we can take it as a given that it doesn't tend to spread between partners.
 

Jim

Senior Member
Messages
79
Likes
14
But...if Le Grice thinks it's all about to be straightened out soon...why was he singing such a long and repetitive song about contamination in his talk on Science Day??
keep in mind le grice also said this: "We’re not far from a controlled clinical trial." sounds like a treatment trial to me, which obviously means he believes in xmrv or mlv's.
 

Hope123

Senior Member
Messages
1,264
Likes
1,082
Hi Mark, thanks for your reply.
I was only making some general points as I think we can spend a lot of time, (and time is what WE have in abundance) hairsplitting the available evidence. Although I think there are some very clever people contributing to this site and I value their posts - and yours.
Isn't there a PR patient survey that bears out what I said? The rate of family contacts with CFS/ME was much higher than sexual contacts. Incidentally I live in a place with a high percentage of gay men in the population so if CFS could be spread sexually I think I would have noticed. Just anecdotal I know!
I still think that the discrepancy in these new studies between the prostate cancer findings (which are not contested) and the CFS ones is strange. Surely if one is contamination the other is also suspect. But no, its always the CFS findings that are attacked.
I cannot get the complete study report. But I notice no-one replied to my earlier question about the HIV patients. Were they recently diagnosed (and untreated) or had they been on retrovirals? I am really curious to know.
This is what I understand:

1. Very few studies on ME/CFS transmission. Back in Incline Village and other related outbreaks, they did early studies which showed that spouses were not at higher risk than the general population but there were several family clusters (including Nevada and upstate NY). Also several other outbreaks (high school, professional symphony group, etc.) argues against just sexual transmission as the only or even main route although as others have said, it's possible if this is a virus, in certain states, might be able to be more sexually transmitted than at other times.

2. This is the 3rd study by my count using PCR showing no XMRV in HIV patients. Haven't read this one but the other two had a fair number of untreated HIV subjects.
 

lansbergen

Senior Member
Messages
2,512
Likes
2,687
I cannot get the complete study report. But I notice no-one replied to my earlier question about the HIV patients. Were they recently diagnosed (and untreated) or had they been on retrovirals? I am really curious to know.
Methods. Two cohorts of HIV-1infected individuals were
tested for XMRV, 1 for patients with acute and 1 for those with
chronic HIV-1 infection (Table 1). The cohort of patients with
chronic infection included Swiss participants from the Swiss-
Spanish Intermittent Therapy Trial, described elsewhere [11].
All patients were not receiving therapy at the time of sampling
and had received a median duration of 26 months (range, 8.5
44.5 months) of highly active antiretroviral therapy at study
entry. The median time not receiving therapy for the cohort
was 14 months (range, 319 months). The second HIV-1
infected group of patients were recruited from a study of acute
HIV-1 infection at St. Marys Hospital, London [12]. Plasma
samples were obtained from these individuals prior to receipt
of antiretrovirals. For both cohorts, plasma samples andPBMCs
were stored in 80C freezers and liquid nitrogen, respectively,
for up to 6 years.
 

acer2000

Senior Member
Messages
815
Likes
644
I wanted to post this language which comes from the other study to be released at the same time as the two mentioned at the top of this thread.

http://www.journals.uchicago.edu/doi/abs/10.1086/656146

Detection of Xenotropic Murine Leukemia Virus–Related Virus in Normal and Tumor Tissue of Patients from the Southern United States with Prostate Cancer Is Dependent on Specific Polymerase Chain Reaction Conditions Bryan P. Danielson,1 Gustavo E. Ayala,2,3 and Jason T. Kimata1 Departments of 1Molecular Virology and Microbiology and 2Pathology, and 3Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas

Journal of Infectious Diseases
The study found the following - A) That XMRV showed up in 22% of prostate cancer patients that they tested B) it was not correlated with the RNASE mutation as was originally hypothesized (ie people with normal RNASE QQ genese had it as well) C) it infected not just malignant cells in the people who carried it, and D) infection with XMRV didn't seem to correlated with severity of prostate cancer.

In the discussion section they state:

Our screen of patients with prostate cancer confirms the presence of XMRV among patients with prostate cancer in the United States. We detected XMRV DNA in normal and tumor tissue, indicating that nonmalignant cells may be susceptible to infection. In agreement with recent studies, we find no correlation between the presence of XMRV infection and the R462Q polymorphism of RNASEL, confirming that the population at risk of infection is not confined to homozygous carriers of the Q variant [7, 8].

Interestingly, 3 independent studies, including 2 surveys of German prostate tissue specimens and a screen of English chronic fatigue syndrome patients, found little to no evidence of XMRV infection [9, 10, 13]. However, in agreement with studies performed in the United States, we found the presence of XMRV in prostate cancer tissues [6, 7, 14]. It is possible that XMRV is mostly absent from the European population. If so, it would be interesting to uncover the reason for this geographic distribution. Alternatively, the inability to detect XMRV in Europe may possibly reflect genetic differences between American and European strains. However, this seems unlikely considering the high degree of sequence conservation among XMRV isolates and the variety of primer target sequences used for detection among the studies in Europe [6, 8–10, 13]. Additionally, the failure to detect XMRV may be attributable to differences in the detection techniques employed. We have found that detection of XMRV required rather specific conditions. For instance, at least 600 ng of prostate tissue DNA was necessary for reliable detection with our PCR assay. XMRV was detected in 3.2% of the patients when we initially used 100–140 ng of prostate tissue DNA, compared with 22.2% of the patients when we used 650 ng. Additionally, we found that detection of XMRV from patient specimens, but not from LNCaP cells infected in vitro, depended on the gene targeted in the PCR assay. We were unable to detect XMRV in the patient tissue samples by nested PCR with primers specific for the gag and pol genes, regardless of whether 100 or 650 ng of DNA was used as template. We found the gag primers to be at least 10- fold less sensitive than the env primers, and the pol primers tended to amplify a competing region from the human genome (data not shown). It is unclear whether these deficiencies account for the inability to detect XMRV in patient samples or whether XMRV is mainly present as an incomplete provirus in the cells of these patients. Nonetheless, the difficulty associated with detecting XMRV in patient samples may perhaps explain studies that do not detect the virus among large cohorts.

We found our nested PCR assay for XMRV env to be capable of detecting 1 infected cell per 1105 uninfected LNCaP cells in 1 of 3 samples with use of 600 ng of DNA. The fact that the PCR-positive tissue specimens tested positive in only 1 or 2 of 3 replicates may indicate that XMRV provirus is present at a very low copy number. This interpretation would be consistent with another report [7]. Alternatively, it is possible that the quality of the tissue specimens was low because of preservation, handling, and the duration of storage prior to DNA isolation. However, we were able to genotype the patients for R462Q with use of 20 ng of DNA without difficulty.
Of note is the comment:

Additionally, we found that detection of XMRV from patient specimens, but not from LNCaP cells infected in vitro, depended on the gene targeted in the PCR assay. We were unable to detect XMRV in the patient tissue samples by nested PCR with primers specific for the gag and pol genes, regardless of whether 100 or 650 ng of DNA was used as template. We found the gag primers to be at least 10- fold less sensitive than the env primers, and the pol primers tended to amplify a competing region from the human genome (data not shown). It is unclear whether these deficiencies account for the inability to detect XMRV in patient samples or whether XMRV is mainly present as an incomplete provirus in the cells of these patients. Nonetheless, the difficulty associated with detecting XMRV in patient samples may perhaps explain studies that do not detect the virus among large cohorts.
Basically what I take from that statement is that the sequences that they have to amplify to find XMRV are different if they aren't going to culture it in the LNCaP lines. So the same assay wouldn't work with both types of samples and this might account for why some assays have failed to find the virus.
 

Cort

Phoenix Rising Founder
Messages
7,371
Likes
2,125
Location
Arizona in winter & W. North America otherwise
Additionally, we found that detection of XMRV from patient specimens, but not from LNCaP cells infected in vitro, depended on the gene targeted in the PCR assay. We were unable to detect XMRV in the patient tissue samples by nested PCR with primers specific for the gag and pol genes, regardless of whether 100 or 650 ng of DNA was used as template. We found the gag primers to be at least 10- fold less sensitive than the env primers, and the pol primers tended to amplify a competing region from the human genome (data not shown). It is unclear whether these deficiencies account for the inability to detect XMRV in patient samples or whether XMRV is mainly present as an incomplete provirus in the cells of these patients. Nonetheless, the difficulty associated with detecting XMRV in patient samples may perhaps explain studies that do not detect the virus among large cohorts.
I think this points out how much they are still learning. I think we should rely on the opinions of the people who have the most expertise in this virus; that would Dr. Singh and Sandra (and therefore) Frank Ruscetti. Dr. Singh has been studying this type of virus for 10 years - when I talked to her she said she was not at all surprised at how much difficulty researchers were having. (She also said she didn't contamination was an issue).

Its amazing how messy science really is. Weiss's commentary, which I didn't think was particularly powerful actually, was obviously persuasive to some researchers but this is Dr. Singh's mileu; it's not LeGrice's focus and its certainly not Dr. Houghton's focus - so I, for one, am going to stand on Dr. Singhs opinion like it's a rock. Her study should be finishing up pretty soon and hopefully it won't take too long before we know the results.

Her study, the Blood Working Group, the Lipkin study and the CAA/GSK studies all sound like they are going to be more comprehensive than any coming before them and the Singh and CAA/GSK study will more closely follow the WPI's techniques. I imagine this set of studies will be definitive. Let's wait on them.
 

Cort

Phoenix Rising Founder
Messages
7,371
Likes
2,125
Location
Arizona in winter & W. North America otherwise
I had always heard that CFS was not infectious but the PR forum poll on family members with this disorder or similar is intriguing. I just met somebody who has ADHD and autism and CFS in her family and we did see all that overlap in the Cheney report at the Workshop. I think there's still alot of ground to cover in that area.

With the patient data repository/Treatment Review program we will be picking all that up.
 

Mark

Senior Member
Messages
5,238
Likes
6,201
Location
Sofa, UK
I had always heard that CFS was not infectious but the PR forum poll on family members with this disorder or similar is intriguing.
Thinking this through...

If CFS were partially or wholly caused by any environmental factor, then in at least some proportion of cases, that environmental factor must be expected to be shared by some proportion of groups of people who live together.

If CFS were partially or wholly explained by some genetic factor, then there would be a family association.

If CFS were partially or wholly explained by a virus, then again there would be a detectable association with family members.

Heck, even if it were all down to purely psychological factors, you'd expect it to cluster in families to some extent.

Whatever it is, you have to be at increased risk if a family member has it.

But there's no evidence of family association. So what?

The received wisdom that there's no such association just leads me to question where that received wisdom comes from - sure ain't from comprehensive study of us!

Personally, I have always assumed that my own condition may very well be contagious, to such an extent that, even in the absence of any direct evidence, I have always been very worried that I might infect my friends. Two family members, one related by adoption, acquired rare and ideopathic chronic illnesses at roughly the same time as me. And I have long suspected that I infected one friend who came down with what sound like very similar symptoms to my own after we shared a hotel room in Amsterdam for a few days...which points towards my theory of potential transfer through sweat, on towels, at a time of high infectivity on one side and lowered immune capability on the other...

All anecdotal, so scientists may discount this evidence if they choose...

None of my friends have ever been at all worried about getting infected. I guess if they secretly doubt I'm really sick, it would be less of a concern. But I reckon that psychology of the population at large is the real reason why we have always heard that CFS is not infectious...

Studying this question by survey would have been so easy and so cheap. Large population of CFS sufferers: how many people do you know personally who have CFS/developed CFS while you knew them/ have ideopathic conditions/etc? Compare with general population. Design survey carefully. Cheap and easy.

Of course, you would have to find us first. And you would have to give a damn...
 

jace

Off the fence
Messages
856
Likes
181
Location
England
Back to negative studies, briefly. I posted this on another forum - short and sweet. I can't see anything wrong with the logic:


I think I'm right in saying that all the high-profile negative studies find no XMRV at all anywhere. None in controls, none in study cohort.

This alone should be enough to discredit their methods (and it has to be method, as G says, and not cohort, or they would have found the background infection of 4 - 7%) unless it is believed that XMRV does not exist anywhere. No-one is saying that, are they? No one is disputing the truth of the budding XMRV virus, taken by electron microscope, no one is saying there is no XMRV in prostate cancer.

IMHO if a study finds zero XMRV it is ipso facto discredited.
 

Mark

Senior Member
Messages
5,238
Likes
6,201
Location
Sofa, UK
IMHO if a study finds zero XMRV it is ipso facto discredited.
I agree Jace, with the exception that if such a study describes its blood-collection and storage methodology and its testing methodology thoroughly, attempts to test a 'known positive' sample from somebody who can find XMRV, and simply states as its conclusion something along the lines of "we were unable to find XMRV in any samples using this methodology" rather than overreaching wildly and irresponsibly, then they have the potential to add to scientific knowledge by clarifying what does not work for the detection of XMRV. The majority of the negative studies have drawn conclusions that their results do not support, and some have even gone to efforts to speculate beyond those findings in the press. That's what discredits them.
 

Cort

Phoenix Rising Founder
Messages
7,371
Likes
2,125
Location
Arizona in winter & W. North America otherwise
Back to negative studies, briefly. I posted this on another forum - short and sweet. I can't see anything wrong with the logic:


I think I'm right in saying that all the high-profile negative studies find no XMRV at all anywhere. None in controls, none in study cohort.

This alone should be enough to discredit their methods (and it has to be method, as G says, and not cohort, or they would have found the background infection of 4 - 7%) unless it is believed that XMRV does not exist anywhere. No-one is saying that, are they? No one is disputing the truth of the budding XMRV virus, taken by electron microscope, no one is saying there is no XMRV in prostate cancer.

IMHO if a study finds zero XMRV it is ipso facto discredited.
No study is validated until independent labs verify it - that's why they go through this process. If it didn't have to be verified we wouldn't see all these people spending all this money trying to find it so I disagree - only when they figure out what is causing the disparities will they be to say whose results are right and whose are wrong. I still think that most groups feel they are doing everything right - that they are using methods they believe can find the virus - and it is eluding them.

I don't know how the 'we don't think XMRV is there group' can explain away the budding virus - I assume they have some way to do that or they wouldn't be making their statements.

But I think we should all hold our horses until the big studies come out; the Blood Working Group should be making an announcement in the next month or so about the contamination and I would assume the blood storage issues. The Singh and CAA/GSK studies have been underway for awhile. The NIH knows about all the controversy and the disparate findings and yet they put together an expensive study with a top researcher to work things out. That indicates to me that they think this issue is hardly resolved (they wouldn't do that if they really thought it was contamination) - that's a big positive for me. The lack of positive results is disappointing but no one know how this will turn out.

I would note that the latest study used the clone Dr. Mikovits warned about.
 

currer

Senior Member
Messages
1,409
Likes
861
Thanks for posting the Houston study, Acer2000. It looks like thoughtful and careful research and shows how tricky finding XMRV is. I thought their discussion very revealing. I remember Dr Singh saying on TWIV that the low hanging fruit had already been picked where virus detection was concerned. I cannot usually download the complete papers to read but what seems wrong to me about the negative studies is the reliance on one simple approach. I dont think a virus in CFS/ME would be EASY to detect or it would have been detected years ago. The researchers have to expect a difficult search.
In Britain CFS/ME is considered to have some genetic association. A recent study (I cant remember which one) did find a higher incidence in family members - not necessarily close family, cousins uncles that sort of thing, which suggested a genetic susceptibility. Among my friends with CFS/ME there is a definate association between CFS and autistic spectrum disorders in families. This is a newly discovered association and a worrying one. I also have friends with CFS/ME who think they have infected their partner.
I suppose a micrograph of a budding virus could be any virus budding out of a cell. Can it be conclusively proven that THIS virus is XMRV?
 

Hope123

Senior Member
Messages
1,264
Likes
1,082
I don't know how the 'we don't think XMRV is there group' can explain away the budding virus - I assume they have some way to do that or they wouldn't be making their statements.

.
The older "rumor viruses" article by Voisset? that Kurt posted a long time ago talks about this and how it could be an artifact of the techniques or budding endogenous retroviruses (which can happen) rather than a true exogenous virus about to lyse. One method it suggested resolving something like this is to get the photo at the same time using antibodies specific for the exogenous virus of interest. In that case, you get both the "budding virus" and some confirmation that this is an exogenous virus. Of course, there are probably steps in the technique I am not aware of that could still cause artifact.
 

currer

Senior Member
Messages
1,409
Likes
861
Hi. A friend has just pointed out to me why the Weiss paper (which was not well argued) is so persuasive. IT REMINDS RESEARCHERS HOW DAMAGING MISTAKES ARE TO THEIR CAREERS. It is much safer to publicly declare that you are not convinced by new work. You can change your mind without loss of reputation when it becomes clearer what the general consensus is. Weiss has reminded researchers how he nearly made a BAD mistake. They do not want to be next. Judy Mikovits has been very brave in standing by her findings.