for the past year all efforts have been placed soley on xmrv! let us all hope that this paper puts a final end to this retrovirus infection theory! there are numerous other serious ongoing research with regards to the following... c.pneumonaie,dr.charles stratton vanderbilt university...drs. garth/nancy nicolson mycoplasma with 45% of the hiv virus envelope,institute for molecular medicine, california... ciguetera 'epitope' toxins university of hawaii with a link to low level radiation...also a prominent neuro surgeon in the u.s.a. found 300 consecutive cfs/fibro patients with chiari malformation and/or cervical spinal stenosis and last dr.a.martin lerner on herpes viral ebv,cmv and hhv-6 causing heart muscle problems and successfully treated with herpes antivirals...it is now time to put the phycological babblers behind and serious and long awaited research to years of patient complete neglect. this is not what medicine is all about!i have met countless nurses and doctors whose lives have been trashed by this disease and there is absolutely nothing this disease cannot take from you.i call on the british prime minister/government in 2011 to give this disease the complete and urgent funding it deserves and especially to all the children who suffer day in and day out from this illness. stop with your 'all in the mind attitudes'and put the money in to protect the spread of this and safeguard the world's blood banks.talk does not solve issues but serious funding will find the cause(s)as dr. nancy klimas of miami, florida once said,'i would rather have hiv than cfs'... to all of you researchers who try to find answers may god bless all of you...to all mankind a merry xmas and health to everyone in 2011...sincerely aidan walsh southampton,united kingdom...p.s. it is a monster of a disease and not ones imagination...
Competing interests
None declared
Baysian knowledge is not Scientific knowledge
Gerwyn Morris, PA institute
13 January 2011
A consideration of Hue et al, 2010
The paper states
"To consider the provenance of XMRV we sequenced XMRV from the cell line 22Rv1, which is infected with an MLV-X that is indistinguishable from patient derived XMRV."
The virus expressed by the 22Rv1 cell line has been sequenced and has the unique nucleotide sequences in the env and gag regions which identify it as XMRV 123, therefore it is the same virus. The cell line originates from a patient suffering from prostate cancer in 1993(4). Taking the evidence as a whole the explanation that the origin of XMRV expressed by these cells in that patient, in which case the difference in sequence was not derived from replication in an immortalised cell line but was representative of wild type XMRV in 1993 and yet Towers et al seem determined to adhere to their speculative viewpoint that this is a virus acquired by these cells, via passage through mouse cell lines. This seems irrational bearing in mind that there is no known MuLV virus which has the characteristic 24 nt deletion in the gag leader or the same sequences in the env su region (1).
It continues: "Bayesian phylogenies clearly show that XMRV sequences reportedly derived from unlinked patients form a monophyletic clade with interspersed 22Rv1 clones (posterior probability >0.99). The cell line-derived sequences are ancestral to the patient-derived sequences (posterior probability >0.99)."
This is clearly been represented as objective scientific evidence when in fact it is not, and directly contradicts experimental scientific evidence. This is an example of Baysian inference based on a computer model and should not be portrayed as objective or scientific (5, 6). Baysian mathematics is a probability estimate of a hypothesis being true. The Baysian methodology rests on the idealised assumption that human beings make decisions on a purely rational basis and that knowledge can be gained by using reason and inductive logic alone. In a Baysian analysis an ideally rational (free of political or emotional biases) individual assigns a probability of truth to the hypothesis in question at the beginning of the analysis, which is called a prior position. There then follows an analysis via the input of new information, and the posterior probability of the hypothesis being true (from the perspective of the person(s) conducting the analysis) is inferred.
In other words the prior view can heavily influence if not determine the posterior inferential probability of truth.
The model does not work at all if the person constructing the prior has an intransigent view regarding the hypothesis in question. A rational person (for example) would not simply add information into the analysis which favours his/her initial viewpoint and exclude that which does not. If this does happen then the outputs, as well as neither objective or scientific, are not even correct in Baysian reasoning. The following summary re Baysian methodology is provided for the reader (5).
*Prior information may not be accurate - generating misleading conclusions. *The way of inputting prior information (choice of prior) may not be correct, and highly subjective *Prior data is a construct made by judgements regarding relevance. *There is no one "correct way" of inputting prior information and different approaches can give different results. *Results aren't objective and cannot stand by themselves.
We will turn to the information omitted from this analysis later. This is an excerpt from the Stanford encyclopedia of philosophy:
Quote
"In Bayesian Confirmation Theory, it is said that evidence confirms (or would confirm) hypothesis H (to at least some degree) just in case the prior probability of H conditional on E is greater than the prior unconditional probability of H: Pi(H/E) > Pi(H). E disconfirms (or would disconfirm) H if the prior probability of H conditional on E is less than the prior unconditional probability of H.
This is a qualitative conception of confirmation. There is no general agreement in the literature on a quantitative measure of degree of confirmation or degree of evidential support.) hypothesis H could be defined as Pi(H/E) − Pi(H).
One potential problem with this proposal is that it has the consequence that no evidence can provide much evidential support to a hypothesis that is antecedently very probable, because as the probability of H approaches one, the difference goes to zero.
So even if H is very probable at the time that evidence E is acquired, we can ask how much evidential support E would provide for H if we had no other evidence supporting H."
The key points from the above is that the Evidence chosen, E, is both selective and subjective.
The other point is that E as chosen in this study provides little evidential support for the predetermined position of these authors that XMRV is a contaminant. Other lines of evidence are needed which have been omitted from this analysis.
"Furthermore, pol sequences apparently amplified from PC patient material (VP29 and VP184) are recombinants of XMRV and Moloney MLV (MoMLV) a virus with an envelope that lacks tropism for human cells."
This is clearly presented as evidence that XMRV is a contaminant. It is known that the pol gene of XMRV consists of polytropic and xenotropic sequences (1, 17). It is also known that the human genome plays host to Moloney Murine leukaemia Pol sequences (7) and that acquisition of such sequences would actually be evidence of a recombinant which would be expected if XMRV was a human replicating MuLV class virus (8].
XMRV has been compared to MoMulv by different researchers and found to be very similar, but an entirely different virus (1,9). In fact the env proteins of XMRV and MoMulv only have a homology of 54% (9). The reverse transcriptase of XMRV has different biochemical activity and three dimensional structure when compared to MoMulv (10).
"Considering the diversity of XMRV we show that the mean pairwise genetic distance among env and pol 22Rv1-derived sequences exceeds that of patient-associated sequences (Wilcoxon rank sum test: p=0.005 and p<0.001 for pol and env, respectively). Thus XMRV sequences acquire diversity in a cell line but not in patient samples."
The hypothesis here seems to be that somehow a sequence acquires sequence diversity in cell lines while not doing so in the same cells in a living human being. No mechanism is proposed.
The authors who first isolated and sequenced XMRV concluded that the sequence variability in the POL genes between the three sequenced clones was 5 orders of magnitude higher than could be accounted for by PCR assembly and could only be explained by the viruses being independently acquired by the patients studied (1).
"These observations are difficult to reconcile with the hypothesis that published XMRV sequences are related by a process of infectious transmission."
These observations in fact can easily support the other scientific evidence (omitted by this computer simulation). As already mentioned if the XMRV in the cell line pre-existed in the patient with prostate cancer then all the observations support that XMRV is an active oncovirus.
Towers and others are clearly assuming that such a virus can only be transmitted horizontally despite a wealth of scientific evidence to the contrary. Gammaretroviruses are transmitted from one generation to the other (11,12) and cause cancer by inserting into the GpG regions of tumour suppressing genes leading to their silencing (13,14). XMRV was originally discovered integrated into Human DNA (1) and has shown to be integrated into the tumour suppressing gene (NFATc3) (2) and has demonstrated a distinct preference for integrating into genes associated with cancer (15).
Finally we look at the rationality of the analysts themselves both in terms of the evidence they omitted from the analysis and how they came to formulate the hypothesis in the first place. XMRV was first isolated by Urisman and others in 2006 (1), when it was isolated from polyadenylated RNA and also detected in samples taken directly from embedded tissue samples. Now polyadenylated RNA is extremely pure so would not have contained any viral DNA. They amplfied either viral mRNA and/or genomic RNA. Either way a replicating virus must be involved as naked genomic RNA is rapidly degraded. The authors observed viral nucleic acid in the nucleus and saw it integrated into DNA and saw nucleic acid clustered just outside the nucleus. This is either cDNA or MRNA. They also detected viral proteins.
The genetic makeup of the person was a variable, linking the presence or absence of XMRV which was only found in stromal cells and not in any epithelial cells, thus displayed cellular tropism. The sequence variability in pol was greater than that for gag and 5 orders of magnitude higher than could be accounted for by that created by PCR. How does the theory that XMRV is a contaminant account for these observations?
XMRV has been found integrated into genes associated into genes implicated in causing cancer (2) and indeed shows a distinct preference for such sites (15). Antibodies to XMRV isolated from patients with PCR have been found using serological methods specific to that isolated virus (9) (16)
PCR is the least sensitive method for isolating XMRV (or polytropic variants) (16) (9) (3). XMRV has been detected with multiple assay methods many used directly on patient samples.
LnCAP (the cells used in the Lombardi et al 2009 study) do not express XMRV cells naturally (16)
XMRV was not isolated by PCR but by DNA/RNA hybridisation microarrays (virochip). Its sequence is unique compared to other MuLV viruses be they endogenous or exogenous which have their sequences recorded in repositories.
Recovery of wild type XMRV by PCR using primers constructed to detect the gag gene sequences of the VP62 clone is impossible even in people known to be positive using other PCR primers (19).
The XMRV from 22RV1 cells cannot be the source of wild type XMRV. The 22RV1 cell line originated from a prostate cancer patient in 1993 (4). XMRV was isolated from a patient whose blood sample was taken in 1984! (3, 17)
Thus was the hypothesis formed by this group a product of scientific observation? Clearly not. It was a belief, and cannot be the product of rational decision making. Moreover the bulk of evidence relating to the hypothesis of XMRV being a contaminant was omitted from the analysis. All this evidence supports the view that XMRV is an infectious retrovirus. Is this omission consistent with rational analysis? I would submit that it is not. Therefore this analysis at its best is neither objective or scientific does not even adhere to the principles of conducting a Baysian computer analysis.
It would be a sad day indeed if computer simulations were given preference over experimental scientific evidence.
References: 1. Urisman A, Molinaro RJ, Fischer N, Plummer SJ, Casey G, Klein EA, Malathi K, Magi-Galluzzi C, Tubbs RR, Ganem D, et al: Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog 2006, 2:e25. 2. Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH: An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors. Proc Natl Acad Sci U S A 2007, 104:1655-1660. 3. Lombardi, V.C.; Ruscetti, F.W.; Das Gupta, J.; Pfost, M.A.; Hagen, K.S.; Peterson, D.L.; Ruscetti, S.K.; Bagni, R.K.; Petrow-Sadowski, C.; Gold, B.; Dean, M.; Silverman, R.H.; Mikovits, J.A. Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science 2009, 326, 585-589. 4. Pretlow, T. G., S. R. Wolman, M. A. Micale, R. J. Pelley, E. D. Kursh, M. I. Resnick, D. R. Bodner, J. W. Jacobberger, C. M. Delmoro, J. M. Giaconia, and T. P. Pretlow. 1993. Xenografts of primary human prostatic carcinoma. J. Natl. Cancer Inst. 85:394-398. 5. Brian Dennis; Statistics and the Scientific Method in Ecology; Nat. of Scientific Evidence: Statistical, Philosophical, and Empirical Considerations: pp 327-378 http://www.math.ualberta.ca/~irl/summer_school/lecture_notes/stats1.pdf 6. KT Kelly, C Glymour; Why Bayesian Confirmation Does Not Capture the Logic of Scientific Justification; Tech Rep CMU-PHIL-138; Carnegie Mellon. http://www.hss.cmu.edu/philosophy/techreports/138_Kelly.pdf 7. D L Mager and J D Freeman; Human endogenous retroviruslike genome with type C pol sequences and gag sequences related to human T-cell lymphotropic viruses; J Virol. 1987 December; 61(12): 4060–4066. 8. H van der Putten, W Quint, J van Raaij, ER Maandag, IM Verma, A Berns; M-MuLV-induced leukemogenesis: integration and structure of recombinant proviruses in tumors. Cell (1981) 24: 729-39. 9. Schlaberg R, Choe DJ, Brown KR, Thaker HM, Singh IR: XMRV is present in malignant prostatic epithelium and is associated with prostate cancer, especially high-grade tumors. Proc Natl Acad Sci U S A 2009, 106:16351-16356. 10. T. Ndongwe, SG Saralianos et al; Biochemical, Structural, and Inhibition Studies of XMRV Reverse Transcriptase; 11th Annual Symposium on Anitviral Drug Resistance, poster 5 http://antiviralresistance.org/abstract_poster5_2010.pdf 11. Panthier JJ, Gounon P, Condamine H, Jacob F.; Pattern of expression of ecotropic murine leukemia virus in gonads of inoculated SWR/J mice; J Virol. 1989 May;63(5):2134-42. http://www.ncbi.nlm.nih.gov/pubmed/2539508 12. A H Sharpe, J J Hunter, R M Ruprecht, and R Jaenisch; Maternal transmission of retroviral disease and strategies for preventing infection of the neonate; J Virol. 1989 March; 63(3): 1049–1053. http://jvi.asm.org/cgi/reprint/63/3/1049.pdf 13. F Martin, S Ladoire, G Mignot, L Apetoh and F Ghiringhelli; Human FOXP3 and cancer; Oncogene, (24 May 2010) | doi:10.1038/onc.2010.174 14. Emily C. Knouf, Michael J. Metzger, Patrick S. Mitchell, Jason D. Arroyo, John R. Chevillet, Muneesh Tewari, and A. Dusty Miller; Multiple Integrated Copies and High-Level Production of the Human Retrovirus XMRV (Xenotropic Murine Leukemia Virus-Related Virus) from 22Rv1 Prostate Carcinoma Cells; Journal of Virology, July 2009, p. 7353-7356, Vol. 83, No. 14 http://jvi.asm.org/cgi/content/full/83/14/7353#R14 15. Kim, S., N. Kim, B. Dong, D. Boren, S. A. Lee, J. Das Gupta, C. Gaughan, E. A. Klein, C. Lee, R. H. Silverman, and S. A. Chow. 2008. Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer. J. Virol. 82:9964-9977. 16. Arnold RS, Makarova NV, Osunkoya AO, Suppiah S, Scott TA, Johnson NA, Bhosle SM, Liotta D, Hunter E, Marshall FF, et al: XMRV infection in patients with prostate cancer: novel serologic assay and correlation with PCR and FISH. Urology 2010, 75:755-761 17. Lo, S.C.; Pripuzova, N.; Li, B.; Komaroff, A.L.; Hung, G.C.; Wang, R.; Alter, H.J. Detection of MLV-related virus gene sequences in blood of patients with chronic fatigue syndrome and healthy blood donors. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 15874-15879. 18. Wong KS, Li YJ, Howard J, Ben-David Y. Loss of p53 in F-MuLV 14induced-erythroleukemias accelerates the acquisition of mutational events that confers immortality and growth factor independence. Oncogene. 1999 Sep 30;18(40):5525-34. 19. BP Danielson, GE Ayala and JT Kimata; 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; J Infect Dis. (2010) 202 (10): 1470-1477. doi:10.1086/656146
is this really the final straw?
21 December 2010
for the past year all efforts have been placed soley on xmrv! let us all hope that this paper puts a final end to this retrovirus infection theory! there are numerous other serious ongoing research with regards to the following... c.pneumonaie,dr.charles stratton vanderbilt university...drs. garth/nancy nicolson mycoplasma with 45% of the hiv virus envelope,institute for molecular medicine, california... ciguetera 'epitope' toxins university of hawaii with a link to low level radiation...also a prominent neuro surgeon in the u.s.a. found 300 consecutive cfs/fibro patients with chiari malformation and/or cervical spinal stenosis and last dr.a.martin lerner on herpes viral ebv,cmv and hhv-6 causing heart muscle problems and successfully treated with herpes antivirals...it is now time to put the phycological babblers behind and serious and long awaited research to years of patient complete neglect. this is not what medicine is all about!i have met countless nurses and doctors whose lives have been trashed by this disease and there is absolutely nothing this disease cannot take from you.i call on the british prime minister/government in 2011 to give this disease the complete and urgent funding it deserves and especially to all the children who suffer day in and day out from this illness. stop with your 'all in the mind attitudes'and put the money in to protect the spread of this and safeguard the world's blood banks.talk does not solve issues but serious funding will find the cause(s)as dr. nancy klimas of miami, florida once said,'i would rather have hiv than cfs'... to all of you researchers who try to find answers may god bless all of you...to all mankind a merry xmas and health to everyone in 2011...sincerely aidan walsh southampton,united kingdom...p.s. it is a monster of a disease and not ones imagination...
Competing interests
None declared
Baysian knowledge is not Scientific knowledge
13 January 2011
A consideration of Hue et al, 2010
The paper states
"To consider the provenance of XMRV we sequenced XMRV from the cell line 22Rv1, which is infected with an MLV-X that is indistinguishable from patient derived XMRV."
The virus expressed by the 22Rv1 cell line has been sequenced and has the unique nucleotide sequences in the env and gag regions which identify it as XMRV 123, therefore it is the same virus. The cell line originates from a patient suffering from prostate cancer in 1993(4). Taking the evidence as a whole the explanation that the origin of XMRV expressed by these cells in that patient, in which case the difference in sequence was not derived from replication in an immortalised cell line but was representative of wild type XMRV in 1993 and yet Towers et al seem determined to adhere to their speculative viewpoint that this is a virus acquired by these cells, via passage through mouse cell lines. This seems irrational bearing in mind that there is no known MuLV virus which has the characteristic 24 nt deletion in the gag leader or the same sequences in the env su region (1).
It continues:
"Bayesian phylogenies clearly show that XMRV sequences reportedly derived from unlinked patients form a monophyletic clade with interspersed 22Rv1 clones (posterior probability >0.99). The cell line-derived sequences are ancestral to the patient-derived sequences (posterior probability >0.99)."
This is clearly been represented as objective scientific evidence when in fact it is not, and directly contradicts experimental scientific evidence. This is an example of Baysian inference based on a computer model and should not be portrayed as objective or scientific (5, 6). Baysian mathematics is a probability estimate of a hypothesis being true. The Baysian methodology rests on the idealised assumption that human beings make decisions on a purely rational basis and that knowledge can be gained by using reason and inductive logic alone. In a Baysian analysis an ideally rational (free of political or emotional biases) individual assigns a probability of truth to the hypothesis in question at the beginning of the analysis, which is called a prior position. There then follows an analysis via the input of new information, and the posterior probability of the hypothesis being true (from the perspective of the person(s) conducting the analysis) is inferred.
In other words the prior view can heavily influence if not determine the posterior inferential probability of truth.
The model does not work at all if the person constructing the prior has an intransigent view regarding the hypothesis in question. A rational person (for example) would not simply add information into the analysis which favours his/her initial viewpoint and exclude that which does not. If this does happen then the outputs, as well as neither objective or scientific, are not even correct in Baysian reasoning. The following summary re Baysian methodology is provided for the reader (5).
*Prior information may not be accurate - generating misleading conclusions.
*The way of inputting prior information (choice of prior) may not be correct, and highly subjective
*Prior data is a construct made by judgements regarding relevance.
*There is no one "correct way" of inputting prior information and different approaches can give different results.
*Results aren't objective and cannot stand by themselves.
We will turn to the information omitted from this analysis later. This is an excerpt from the Stanford encyclopedia of philosophy:
Quote
"In Bayesian Confirmation Theory, it is said that evidence confirms (or would confirm) hypothesis H (to at least some degree) just in case the prior probability of H conditional on E is greater than the prior unconditional probability of H: Pi(H/E) > Pi(H). E disconfirms (or would disconfirm) H if the prior probability of H conditional on E is less than the prior unconditional probability of H.
This is a qualitative conception of confirmation. There is no general agreement in the literature on a quantitative measure of degree of confirmation or degree of evidential support.) hypothesis H could be defined as Pi(H/E) − Pi(H).
One potential problem with this proposal is that it has the consequence that no evidence can provide much evidential support to a hypothesis that is antecedently very probable, because as the probability of H approaches one, the difference goes to zero.
So even if H is very probable at the time that evidence E is acquired, we can ask how much evidential support E would provide for H if we had no other evidence supporting H."
The key points from the above is that the Evidence chosen, E, is both selective and subjective.
The other point is that E as chosen in this study provides little evidential support for the predetermined position of these authors that XMRV is a contaminant. Other lines of evidence are needed which have been omitted from this analysis.
"Furthermore, pol sequences apparently amplified from PC patient material (VP29 and VP184) are recombinants of XMRV and Moloney MLV (MoMLV) a virus with an envelope that lacks tropism for human cells."
This is clearly presented as evidence that XMRV is a contaminant. It is known that the pol gene of XMRV consists of polytropic and xenotropic sequences (1, 17). It is also known that the human genome plays host to Moloney Murine leukaemia Pol sequences (7) and that acquisition of such sequences would actually be evidence of a recombinant which would be expected if XMRV was a human replicating MuLV class virus (8].
XMRV has been compared to MoMulv by different researchers and found to be very similar, but an entirely different virus (1,9). In fact the env proteins of XMRV and MoMulv only have a homology of 54% (9). The reverse transcriptase of XMRV has different biochemical activity and three dimensional structure when compared to MoMulv (10).
"Considering the diversity of XMRV we show that the mean pairwise genetic distance among env and pol 22Rv1-derived sequences exceeds that of patient-associated sequences (Wilcoxon rank sum test: p=0.005 and p<0.001 for pol and env, respectively). Thus XMRV sequences acquire diversity in a cell line but not in patient samples."
The hypothesis here seems to be that somehow a sequence acquires sequence diversity in cell lines while not doing so in the same cells in a living human being. No mechanism is proposed.
The authors who first isolated and sequenced XMRV concluded that the sequence variability in the POL genes between the three sequenced clones was 5 orders of magnitude higher than could be accounted for by PCR assembly and could only be explained by the viruses being independently acquired by the patients studied (1).
"These observations are difficult to reconcile with the hypothesis that published XMRV sequences are related by a process of infectious transmission."
These observations in fact can easily support the other scientific evidence (omitted by this computer simulation). As already mentioned if the XMRV in the cell line pre-existed in the patient with prostate cancer then all the observations support that XMRV is an active oncovirus.
Towers and others are clearly assuming that such a virus can only be transmitted horizontally despite a wealth of scientific evidence to the contrary. Gammaretroviruses are transmitted from one generation to the other (11,12) and cause cancer by inserting into the GpG regions of tumour suppressing genes leading to their silencing (13,14).
XMRV was originally discovered integrated into Human DNA (1) and has shown to be integrated into the tumour suppressing gene (NFATc3) (2) and has demonstrated a distinct preference for integrating into genes associated with cancer (15).
Finally we look at the rationality of the analysts themselves both in terms of the evidence they omitted from the analysis and how they came to formulate the hypothesis in the first place.
XMRV was first isolated by Urisman and others in 2006 (1), when it was isolated from polyadenylated RNA and also detected in samples taken directly from embedded tissue samples. Now polyadenylated RNA is extremely pure so would not have contained any viral DNA. They amplfied either viral mRNA and/or genomic RNA. Either way a replicating virus must be involved as naked genomic RNA is rapidly degraded. The authors observed viral nucleic acid in the nucleus and saw it integrated into DNA and saw nucleic acid clustered just outside the nucleus. This is either cDNA or MRNA. They also detected viral proteins.
The genetic makeup of the person was a variable, linking the presence or absence of XMRV which was only found in stromal cells and not in any epithelial cells, thus displayed cellular tropism. The sequence variability in pol was greater than that for gag and 5 orders of magnitude higher than could be accounted for by that created by PCR. How does the theory that XMRV is a contaminant account for these observations?
XMRV has been found integrated into genes associated into genes implicated in causing cancer (2) and indeed shows a distinct preference for such sites (15). Antibodies to XMRV isolated from patients with PCR have been found using serological methods specific to that isolated virus (9) (16)
PCR is the least sensitive method for isolating XMRV (or polytropic variants) (16) (9) (3). XMRV has been detected with multiple assay methods many used directly on patient samples.
LnCAP (the cells used in the Lombardi et al 2009 study) do not express XMRV cells naturally (16)
XMRV was not isolated by PCR but by DNA/RNA hybridisation microarrays (virochip). Its sequence is unique compared to other MuLV viruses be they endogenous or exogenous which have their sequences recorded in repositories.
Recovery of wild type XMRV by PCR using primers constructed to detect the gag gene sequences of the VP62 clone is impossible even in people known to be positive using other PCR primers (19).
The XMRV from 22RV1 cells cannot be the source of wild type XMRV. The 22RV1 cell line originated from a prostate cancer patient in 1993 (4). XMRV was isolated from a patient whose blood sample was taken in 1984! (3, 17)
Thus was the hypothesis formed by this group a product of scientific observation? Clearly not. It was a belief, and cannot be the product of rational decision making. Moreover the bulk of evidence relating to the hypothesis of XMRV being a contaminant was omitted from the analysis. All this evidence supports the view that XMRV is an infectious retrovirus. Is this omission consistent with rational analysis? I would submit that it is not. Therefore this analysis at its best is neither objective or scientific does not even adhere to the principles of conducting a Baysian computer analysis.
It would be a sad day indeed if computer simulations were given preference over experimental scientific evidence.
References:
1. Urisman A, Molinaro RJ, Fischer N, Plummer SJ, Casey G, Klein EA, Malathi K, Magi-Galluzzi C, Tubbs RR, Ganem D, et al: Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog 2006, 2:e25.
2. Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH: An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors. Proc Natl Acad Sci U S A 2007, 104:1655-1660.
3. Lombardi, V.C.; Ruscetti, F.W.; Das Gupta, J.; Pfost, M.A.; Hagen, K.S.; Peterson, D.L.; Ruscetti, S.K.; Bagni, R.K.; Petrow-Sadowski, C.; Gold, B.; Dean, M.; Silverman, R.H.; Mikovits, J.A. Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science 2009, 326, 585-589.
4. Pretlow, T. G., S. R. Wolman, M. A. Micale, R. J. Pelley, E. D. Kursh, M. I. Resnick, D. R. Bodner, J. W. Jacobberger, C. M. Delmoro, J. M. Giaconia, and T. P. Pretlow. 1993. Xenografts of primary human prostatic carcinoma. J. Natl. Cancer Inst. 85:394-398.
5. Brian Dennis; Statistics and the Scientific Method in Ecology; Nat. of Scientific Evidence: Statistical, Philosophical, and Empirical Considerations: pp 327-378 http://www.math.ualberta.ca/~irl/summer_school/lecture_notes/stats1.pdf
6. KT Kelly, C Glymour; Why Bayesian Confirmation Does Not Capture the Logic of Scientific Justification; Tech Rep CMU-PHIL-138; Carnegie Mellon. http://www.hss.cmu.edu/philosophy/techreports/138_Kelly.pdf
7. D L Mager and J D Freeman; Human endogenous retroviruslike genome with type C pol sequences and gag sequences related to human T-cell lymphotropic viruses; J Virol. 1987 December; 61(12): 4060–4066.
8. H van der Putten, W Quint, J van Raaij, ER Maandag, IM Verma, A Berns; M-MuLV-induced leukemogenesis: integration and structure of recombinant proviruses in tumors. Cell (1981) 24: 729-39.
9. Schlaberg R, Choe DJ, Brown KR, Thaker HM, Singh IR: XMRV is present in malignant prostatic epithelium and is associated with prostate cancer, especially high-grade tumors. Proc Natl Acad Sci U S A 2009, 106:16351-16356.
10. T. Ndongwe, SG Saralianos et al; Biochemical, Structural, and Inhibition Studies of XMRV Reverse Transcriptase; 11th Annual Symposium on Anitviral Drug Resistance, poster 5 http://antiviralresistance.org/abstract_poster5_2010.pdf
11. Panthier JJ, Gounon P, Condamine H, Jacob F.; Pattern of expression of ecotropic murine leukemia virus in gonads of inoculated SWR/J mice; J Virol. 1989 May;63(5):2134-42. http://www.ncbi.nlm.nih.gov/pubmed/2539508
12. A H Sharpe, J J Hunter, R M Ruprecht, and R Jaenisch; Maternal transmission of retroviral disease and strategies for preventing infection of the neonate; J Virol. 1989 March; 63(3): 1049–1053. http://jvi.asm.org/cgi/reprint/63/3/1049.pdf
13. F Martin, S Ladoire, G Mignot, L Apetoh and F Ghiringhelli; Human FOXP3 and cancer; Oncogene, (24 May 2010) | doi:10.1038/onc.2010.174
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Competing interests
None declared