Snake oil, snake oil, get your fresh snake oil here!
Hi, I tried to post this 14 hours ago but my phone exchange crashed and I lost internet. So here is my reply to Hue:
Disease-associated XMRV sequences are consistent with laboratory contamination
Stphane Hu1*, Eleanor R. Gray1*, Astrid Gall2*, Aris Katzourakis3, Choon Ping Tan1,
CharlotteJ. Houldcroft2, Stuart McLaren2, Deenan Pillay1, Andrew Futreal2, Jeremy A. Garson1, Oliver G.Pybus3, Paul Kellam1,2 , Greg J. Towers1
1MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, UniversityCollege London, 46 Cleveland St, London W1T 4JF, United Kingdom
2Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
3Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom
This paper is a much more serious attempt at showing contamination than we have so far seen. In a nutshell, XMRV is (according to them) derived from contaminated human cell lines, which have then reinfected other cell lines and vectors, becoming close to ubiquitous in labs.
They still do not explain why controls don't keep testing positive, but they do have plausible explanations for the source of the contamination. Basically, XMRV is a real virus but it is loose in labs all over the place. It could be in many lab cultures, not just prostate cancer. Because of this even a sample that tests negative for mouse DNA or mouse mitochondrial DNA could still be contaminated. No amount of testing for mouse contamination can rule this out.
Comments have already been made on this thread about issues with primers. We need to know more about the primers used (although it could be in the original papers of Lombardi or Lo/Alter, I need to go back and check) before much more can be said.
I do not know enough about statistical phylogenetic analysis to comment much on this part of the science. It would take a lot of research to get a handle on this: I know enough to know it is a very deep topic.
Of particular interest in this paper is the observation that hypermutation by APOBEC3G is much more prevalent in the cell line versus patients (81 times versus 5). The cell line version of the virus is much more evolved and damaged than prostate cancer XMRV isolates.
This of course does not allow for the probable variation in CFS patients with MLVs. This was not discussed in this paper. They confined their analysis to prostate derived XMRV, although they do note that virus isolated from prostate cancers appear to be XMRV and Moloney MLV recombinations.
They did not discuss the possibility that such ubiquitious XMRV contamination might be itself a source of infection, originally from the cell line 22Rv1, but since this was derived from still earlier cell lines it is hard to say when this all started. Since most mammals are potential hosts, this virus could be spreading in labs. They had better hope its not pathogenic! If this virus is such a loose cannon, and causes any disease, we could have a real problem!
A number of hospitals have been loci for ME outbreaks since 1934 - does anyone have an idea as to how many? I am sure of two, but there could be many more. I vaguely recall several more, I but am very unsure about this.
In a quick search I was unable to find a reference for 22Rv1 prior to 1999: the title and abstract directly imply that this cell line was developed just prior to 1999:
In Vitro Cell Dev Biol Anim. 1999 Jul-Aug;35(7):403-9.
A new human prostate carcinoma cell line, 22Rv1.
Sramkoski RM, Pretlow TG 2nd, Giaconia JM, Pretlow TP, Schwartz S, Sy MS, Marengo SR, Rhim JS, Zhang D, Jacobberger JW.
Cancer Research Center, Case Western Reserve University, Cleveland, Ohio 44106, USA.
PMID: 10462204
This abstract refers to a culture line: CWR22R which was used to develop the 22Rv1 cell line. Does anyone know when prostate cancer cell lines were first developed? The earliest reference I found with a quick search was:
Morphological and biochemical studies of virus (SV40) transformed prostatic tissue.
Fraley EE, Paulson DF.
J Urol. 1969 May;101(5):735-40. No abstract available.
PMID: 4305419
However, Pubmed is a limited resource when looking back, it may be that this is just the limit of digital indexing. Cell line cultures date back to the early 1900s - I think I recall reading they date back to prior to 1910.
This paper also raises the contamination issue in a bad way. If the XMRV virus is a common contaminant, it may well be that there are issues with lab contamination in many or most cell lines, including those used for vaccine manufacturing. It might also be that many patients have similar XMRV sequences because we keep being infected from a common source such as vaccines. Rather than closing the door on XMRV, this paper is a pandora's box. I still think they are wrong, but I wonder if I am just hoping they are wrong because the implications are very disturbing. Against this we have the problem that if cell lines were a common source, then their would be far greater diversity in patients; wait, isn't that the case? They are finding reduced diversity in prostate cancer not CFS.
So while it is possible that XMRV is a contaminant (but I still want the experimental controls issue explained), it is also possible that many of the problems raised in this paper are due to the virus spreading from labs: the common source may be the labs involved in virus and cancer experimentation, and vaccine manufacture. Medical personel are among the most common ME patients, as are airline personel, teachers and long distance cyclists (who compete internationally). All of these groups (with the possible exception of teachers) will have had lots of vaccinations.
So, if we consider this paper might be correct, we now we need to (if it hasn't already been done):
1. Test all stored XMRV positive samples for mouse contamination, but with the understanding that a negative does not mean they are not contaminated. A positive shows contamination, a negative for mouse DNA is always inconclusive.
2. Check common lab cell lines including those used in the vaccine industry for contamination. Just checking for mouse contamination is not enough - we need to search very diligently for XMRV.
3. Check vaccines themselves for XMRV contamination.
4. Check the specific cell lines used in culturing for XMRV to ensure they are not contaminated (I don't think they are, this should have been tested and controlled for, but there is no substitute for hard evidence). If large numbers of controls have been cultured and found to be negative, then this is very strong evidence that the contamination theory is wrong. I am about to go back and reread Lombardi et. al. 1999 and all the associated stuff, plus the WPI sources. This might take a while ...
(PS Some hours later: it still seems clear that WPI, Lo and Alter have all checked this multiple times.)
5. There is speculation that the kinds of viral mixes necessary for XMRV genesis begin back in 1932 or prior in California - there was a thread on this a few weeks back We need to find if any samples from that time exist anywhere, and if so have them tested. I would be very doubtful that there was any evidence, but I wonder if children or grandchildren of people who were in the 1934 epidemic could not be tested. This date was selected because the first highly probable cases of ME date back to 1932, and the first highly probable epidemic was 1934 in a hospital in California. Note there was a paper on phylogenetic analysis of XMRV that puts its origin in California at just prior to this time:
The mouse "xenotropic" gammaretroviruses and their XPR1 receptor
Retrovirology 2010, 7:101 doi:10.1186/1742-4690-7-101
Christine A Kozak (ckozak@niaid.nih.gov)
I am not a fan of consipiracy theories in any form, and vaccine contamination theories qualify for that I think because it ties in with many CFS conspiracy theories I have read. I would like all this to be proven wrong. In all probability it is wrong, the contamination issue is a non-issue, but we need evidence one way or another. Hard evidence trumps speculation, whether it be speculation from patients like me or from XMRV researchers. Proof should be undeniable. It if is contraversial it is not proof.
Bye
Alex
PPS I have deliberately ignored issues here about antibodies, staining, viral replication etc because that would make a long post longer...
PPPS It is also not clear if XMRV is an integrated virus or an infective virus. I took that they were talking about infective virus, not just integrated endogenous virus.