Just spotted this today -- the authors appear to have carefully controlled for mouse contamination (using the mitochondrial DNA assay), and found that 2 of 12 CFS patient samples were positive for MLV-GAG region sequences...they were unable to find other genes related to MLVs...sound familiar? Again, if all these patients that come up negative for mouse DNA come up positive for MLV GAG -- but not for env or other genes...maybe people are looking for the wrong genes...the title of the paper is somewhat misleading but perhaps necessary to get it published "Xenotropic and polytropic murine leukemia virus-related sequences are not detected in the majority of patients with chronic fatigue syndrome", it is by an Italian group --Paolucci et al. and you can find it here
Do you mean that the negative studies could have been looking for the wrong sequences of pol and env? That other sequences are probably present?
ReplyDeleteThanks
I mean that is certainly possible; most people are looking for sequences based on what we know of the XMRV VP62 sequence (yes, lab generated or not), or other MLV-type viruses. Is it possible that an MLV has recombined with something with a slightly different sequence that isn't picked up by these primer sequences - I think so -- is it probable? Other explanations may include more rapid degradation of the non-gag regions of MLV...is that more probable than the first suggestion? What I think is very interesting is that if every finding of MLVs in mouse negative human samples is due to undetectable contamination-- then why is the GAG region the only region consistently picked up? Under the assumption it has come directly from mouse, it would be present at the same level as the associated genes, eg env. So why don't we see env? I'm just asking!
ReplyDeleteThank you. Sorry for the questions, if you are too busy to answer don't worry.
ReplyDeleteCould it be a different type of retrovirus that is providing the env?
Do you have any examples of regions degrading faster than others?
hmmmm...I am too busy but just quickly -- my guess is it could be...maybe one that is not even typically considered a retrovirus...examples of regions degrading faster...not off the top of my head, but when the human genome was being sequenced, CpG rich areas were much more difficult to sequence and often under-represented in genome libraries, to my recollection -- certain types of sequences would also be more susceptible to nuclease attack...imho this would be less likely than the first theory.
ReplyDeleteSo another animal might be involved, not just a mouse?
DeleteOr maybe it's our own Junk ERV combining with the MLVs and creating a retrovirus?
Thanks for you time Dr O'Keefe.
Deletenp...I love science -- can't help myself...junk erv is closest...
ReplyDeleteHi Dr O'Keefe,
ReplyDelete(sorry to sign anonymous)
My post was the one suggesting that maybe Junk ERV & the MLVs are maybe combining, thanks your reply.
Kind regards Crafter Kate.
Silly scientists. Looking for mouse contamination, when the professionals like Mikovits get their results with VP62 plasmid contamination:
ReplyDeleteIn July, [Dr. Mikovits] says, she found it—an entry from March 2009 indicating that a culture of the XMRV virus had been placed into the same incubatorwith the rest of the lab’s blood samples.
Of course, Dr. Mikovits knew nothing, did nothing, was out of town when this happened and therefore completely innocent. Dr. Keefe, with your solid expertise in XMRV, I expect you run your lab the same way as the fine Dr. Mikovits? Anything else would be below you, I'd say.
If others are taking it upon themselves to do things that Dr Mikovits would not have condoned then it is they who will have to answer questions. This was also after the bulk of the testing for Lombardi et al. had taken place, so what was the reason for this?
DeleteTony why do you say VP62 when the article says culture? Where are you getting your information from?
Just one more thing: Did the fine authors appear to have carefully controlled for VP62 plasmid contamination as well? You know, the stuff Dr. Silverman found in the CFS samples he got from Dr. Mikovits, as a renowned researcher in matters XMRV, like you Dr. Keefe, surely knows?
ReplyDeleteDr Silverman found contamination in his lab. This is the data Dr Mikovits presented in Ottawa showing that there was no VP62 plasmid in the original samples.
Deletehttp://3.bp.blogspot.com/-LE3KbJjEN2g/TnzsXvAzL0I/AAAAAAAAAEE/Otc07jeQbFs/s1600/Slide07.jpg
And this data from an independent lab that retested samples and found no contamination either.
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good question Tony - they did control for plasmid contamination, by sequencing the products they amplified. They are actually most closely related to known polytropic MLVs.
ReplyDeleteProfessor Denise, please see my LONG response to Dr. Jamie Deckoff-Jones comments about your excellent findings at "Thomas Hennessy, jr. Boca Raton, Florida" on Facebook, and check out our websites at www.rescindinc.org and www.may12.org THANKS FOR ALL YOUR HARD WORK! xo TMH
ReplyDeleteIf it is a recombinant virus that cannot be picked up by "primer sequences", could it still be found by NGS?
ReplyDeleteSorry I dont know much about this stuff.
Thank you
Sue
yep. Primer sequences are biased - they are designed based on the sequence you are trying to find...but if that sequence is really different, you might not find it -- NGS can be unbiased, by using "random" primers. I hope this helps!
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Ahhh, those were the times. Kindling false hope in CFS-patients with spurious positive results!
ReplyDeleteBut not to worry, if you want someone to add XMRV plasmid to your samples and create positive results in your lab: Just give Dr. Mikovits a call, she is available on the job market!
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