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New WPI and CDC XMRV sequences in genbank

barbc56

Senior Member
Messages
3,657
Eco, I missed this. Interesting.

@Alex. BB, Bob, et. al.

It appears people are confusing not believing in XMRV in our illness with being negaive, a denialist and also not wanting people to post about XMRV when nothing could be further from the truth.

Barb. C. :>)
 

natasa778

Senior Member
Messages
1,774
It appears people are confusing not believing in XMRV in our illness with being negaive, a denialist and also not wanting people to post about XMRV when nothing could be further from the truth.

Barb. C. :>)

When I don't believe something is linked to my illness I don't read those posts or visit those threads, or get in any way involved unless topics crop us somewhere in passing. That is sort of a natural path, no? If you don't believe XMRV or anything similar is involved in 'your' illness why on earth are you reading here and posting same questions and comments over and over and over and over again?
 

barbc56

Senior Member
Messages
3,657
When I don't believe something is linked to my illness I don't read those posts or visit those threads, or get in any way involved unless topics crop us somewhere in passing. That is sort of a natural path, no? If you don't believe XMRV or anything similar is involved in 'your' illness why on earth are you reading here and posting same questions and comments over and over and over and over again?

Just because I don't believe xmrv is involved in my illness, it would be silly to not keep up with what is going on. If someone reading is on the fence or doesn't know all the sides of the story, I hope we can all contribute to show all the different perspectives of this topic.

I try to read as many topics as possible. I also want to be an informed consumer. I've learned a lot from reading all sorts of threads. Someone with a different opinion might make me pause and think about a subject in more detail.

No one on this board should be asked why they post. IMHO, it's rather rude and if someone has teh evul intentions, they won't say so. This makes it kind of a moot point.

But I think we need to get back on topic or make a separate thread.

Over and out. :>)
 

barbc56

Senior Member
Messages
3,657
Partial molecular cloning with novel consensus PCR primers of the murine JHK retrovirus of human origin, is NOT, repeat NOT a variant of the Xenotropic murine leukemia virus-related virus (XMRV.) Its closest relative is the retrovirus isolated from VCaP cells as shown in the Blast report as mentioned in my post 108. It will updated by Grossberg to reflect this change. Just look at the Blast report. No need to state erroneous information to confuse people.

Eco

I can see from the blast why you are saying the JHK virus is not related. What does that mean in practical terms in relation to our illnes? I may have missed this as we seem to be off topic so maybe I need to read this thread from the beginning. :rolleyes:

Thanks.

Barb. C. :>)
 

RRM

Messages
94
When I don't believe something is linked to my illness I don't read those posts or visit those threads, or get in any way involved unless topics crop us somewhere in passing. That is sort of a natural path, no? If you don't believe XMRV or anything similar is involved in 'your' illness why on earth are you reading here and posting same questions and comments over and over and over and over again?
It would be pretty simple for you and the others to "solve" the problem I've seen discussed during the past previous pages: you can simply block individual users. The fact that this isn't being done, indicates that it's not just about discussing the matter with like-minded people. Discussing things in an open forum is just as much about spreading your ideas, and in this context (mis)information can, and should be critiqued.

And critique is a good thing. Consider this recent topic for instance. The exact same "BWG thoughts" were posted on another forum almost two months ago, where only proponents posted. Aside from one poster who made a general comment about coding, nobody really questioned any of the three main arguments. However, when you look at responses to the post on this site, you'll see that of the three arguments, one was factually totally wrong (the non-sequencing of cultures, as Ruscetti opted not to do PCR after culture but WB), one was contradicted by pretty compelling evidence (the sequence data from the two healty controls didn't match the sequence data from the spiked controls), while the remaining argument (about the 30% positivity rate) could be reasonable explained by another mechanism.

Now, regardless if you agree with all of these counterarguments (I'd say it's pretty hard not to in at least two instances), I would argue that you should be glad that you are visiting a site where not every pro-argument is swallowed hook, line and sinker. Even if you wouldn't agree with (some of) my points in the above example, it would still be a good thing that you have considered my arguments and found them to be worthless - it would make your opinion that the original post was correct more valuable than without considering them.

I could again argue about this all day, but as nobody has said it better than J.S. Mill (although he used quite a lot of words also ;)):

[Mankind] is capable of rectifying his mistakes by discussion and experience. Not by experience alone. There must be discussion, to show how experience is to be interpreted. Wrong opinions and practices gradually yield to fact and argument: but facts and arguments, to produce any effect on the mind, must be brought before it. Very few facts are able to tell their own story, without comments to bring out their meaning. The whole strength and value, then, of human judgment, depending on the one property, that it can be set right when it is wrong, reliance can be placed on it only when the means of setting it right are kept constantly at hand. In the case of any person whose judgment is really deserving of confidence, how has it become so?

Because he has kept his mind open to criticism of his opinions and conduct. Because it has been his practice to listen to all that could be said against him; to profit by as much of it as was just, and expound to himself, and upon occasion to others, the fallacy of what was fallacious. Because he has felt, that the only way in which a human being can make some approach to knowing the whole of a subject, is by hearing what can be said about it by persons of every variety of opinion, and studying all modes in which it can be looked at by every character of mind. No wise man ever acquired his wisdom in any mode but this; nor is it in the nature of human intellect to become wise in any other manner.

The steady habit of correcting and completing his own opinion by collating it with those of others, so far from causing doubt and hesitation in carrying it into practice, is the only stable foundation for a just reliance on it: for, being cognizant of all that can, at least obviously, be said against him, and having taken up his position against all gainsayers knowing that he has sought for objections and difficulties, instead of avoiding them, and has shut out no light which can be thrown upon the subject from any quarterhe has a right to think his judgment better than that of any person, or any multitude, who have not gone through a similar process.
 

RRM

Messages
94
I can see from the blast why you are saying the JHK virus is not related. What does that mean in practical terms in relation to our illnes? I may have missed this as we seem to be off topic so maybe I need to read this thread from the beginning. :rolleyes:

Thanks.

Barb. C. :>)

Basically, the JHK sequence was seen by some as evidence that XMRV is more diverse than previously thought, and more diverse than could reasonably be explained by its creation in a cell line in the early nineties. The problem with the argument can be illustrated with the following joke:

Q: How many legs does a dog have if you call the tail a leg?
A: Four. Calling a tail a leg doesn't make it a leg.

Although Grossberg called his JHK isolate "XMRV" in its Genbank entry, it wasn't. Another scientist (I presume A.D. Miller) called this to Grossberg's attention and Grossberg subsequently corrected it in Genbank.

In pratical terms, it means that some thought the JHK finding had something to do with the ME/CFS findings (though, rather indirectly), but it appears that it doesn't.
 

barbc56

Senior Member
Messages
3,657
Thanks.

Basically, the JHK sequence was seen by some as evidence that XMRV is more diverse than previously thought, and more diverse than could reasonably be explained by its creation in a cell line in the early nineties. The problem with the argument can be illustrated with the following joke:

Q: How many legs does a dog have if you call the tail a leg?
A: Four. Calling a tail a leg doesn't make it a leg.

Although Grossberg called his JHK isolate "XMRV" in its Genbank entry, it wasn't. Another scientist (I presume A.D. Miller) called this to Grossberg's attention and Grossberg subsequently corrected it in Genbank.

In pratical terms, it means that some thought the JHK finding had something to do with the ME/CFS findings (though, rather indirectly), but it appears that it doesn't.

Thanks RRM. I went through this thread again and found some posts that helped me understand some of this. I may have left out some of the numbers of the posts but will come back and do that. Thanks to all who contributed these. I am sure there are some that I missed.

http://phoenixrising.me/?p=5568

Eco's posts #35.

TWIV #136

http://www.ncbi.nlm.nih.gov/nuccore/JF274252.1

According to Dr. Grossberg's website, "the JHK virus is an enveloped, relatively fragile particle containing RNA, reverse transcriptase, and prominent, knobbed glycoprotein projections. Although the JHK virus resembles a retrovirus (but 35% smaller than most other retroviruses), it is clearly not like any of the known human retroviruses as determined either by polymerase chain reactions or electron microscopy. The JHK-3 B-lymphoblastoid cell line that constitutively produces the JHK virus (and the Epstein-Barr virus as well) has the antigenic markers of immature B-lymphocytes by flow cytometry. cDNA libraries produced by reverse transcription of JHK viral RNA have been constructed and are being analyzed; the sequences determined of the many clones produced have so far revealed no significant homology with known viruses. The possible etiological role of the JHK virus in diseases that may involve B-lymphocytes, such as leukemia, lymphoma, chronic fatigue syndrome or immuno-dysfunctional states, remains to be determined [8,9,10]." It would appear that the JHK virus differs from XMRV judging by Grossberg's information.
#108-
Post #108

JHK-3 BLAST.pdf?

Now, I will include your above two posts. #145 and 146.

The quote you have above by Abraham Lincoln was my signature on another forum, LOL!! ;)

I like the other quote. It would be a good one to put on my office wall. (read desk at home with a bulleting board next to it.):D

Barb C.:>)
 

Firestormm

Senior Member
Messages
5,055
Location
Cornwall England
Is there a link to this naming/renaming of JHK development at all? Just wondering how one has come by the information. Not doubting it but would like a look-e-loo if I may :D

Not that I understand sequencing!
 

bullybeef

Senior Member
Messages
488
Location
North West, England, UK
But the JHK virus was isolated from a patient with ME in 1989:

See: http://www.patentstorm.us/patents/5827750/description.html?forumid=331851


The JHK virus was initially isolated from Patient 1. Patient 1 is a 40-year old woman who had experienced a relatively acute onset of severe fatigue, marked easy fatiguability, difficulties in mentation, neuromuscular symptoms, immunologic anergy, and no haematologic evidence of leukemia or lymphoma. These symptoms lasted about three years and led to a diagnosis of CFIDS.....Samples of Patient 1's blood were taken in January, April, and September of 1989, and February 1990.


Obviously JHK isn't VP62 which seems to mean XMRV when it is used in negative publications, so Grossberg probably means JHK is a human gamma retroviral variant. His Genbank entry still clearly states the organism is "XMRV", but it is of the JHK-3 strain: http://www.uniprot.org/uniprot/G0WKJ6


And regardless of whether it is a XMRV, it is still a retrovirus that was isolated from a patient with ME over 20 years ago, yet only added to Genbank in Oct 2011. Based upon this, the US government have been quite happy to allow this discovery to remain without the need of "replication" (or rather another scientist loosely attempting to validate the discovery) or retraction. In other words, they have been aware for sometime people with ME are carrying a retrovirus, something that also ties in with EBV.


And knowing that ME was first coined Chronic EBV in the US in the 1980s, that has too much of a coincidence.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
But the JHK virus was isolated from a patient with ME in 1989:

See: http://www.patentstorm.us/patents/5827750/description.html?forumid=331851

Obviously JHK isn't VP62 which seems to mean XMRV when it is used in negative publications, so Grossberg probably means JHK is a human gamma retroviral variant. His Genbank entry still clearly states the organism is "XMRV", but it is of the JHK-3 strain: http://www.uniprot.org/uniprot/G0WKJ6


And regardless of whether it is a XMRV, it is still a retrovirus that was isolated from a patient with ME over 20 years ago, yet only added to Genbank in Oct 2011. Based upon this, the US government have been quite happy to allow this discovery to remain without the need of "replication" (or rather another scientist loosely attempting to validate the discovery) or retraction. In other words, they have been aware for sometime people with ME are carrying a retrovirus, something that also ties in with EBV.


And knowing that ME was first coined Chronic EBV in the US in the 1980s, that has too much of a coincidence.

Hopefully this sort of pathogen would pop up in Lipkin's non-XMRV study, if it's in many ME patients.
 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
The problem with the RRM's argument can be illustrated with the following:

Q: How many XMRVs does a me/cfs patient have?
A: One, if we call all MLVs/MRVs XMRV, hundreds if we call them JHK-3, VP42, S-162, etc
A2: None, if we look only for VP-62, and don't bother looking in tissue for any MLVs


According to Dr. Grossberg's website, "the JHK virus is an enveloped, relatively fragile particle containing RNA, reverse transcriptase, and prominent, knobbed glycoprotein projections. Although the JHK virus resembles a retrovirus (but 35% smaller than most other retroviruses), it is clearly not like any of the known human retroviruses as determined either by polymerase chain reactions or electron microscopy. The JHK-3 B-lymphoblastoid cell line that constitutively produces the JHK virus (and the Epstein-Barr virus as well) has the antigenic markers of immature B-lymphocytes by flow cytometry. cDNA libraries produced by reverse transcription of JHK viral RNA have been constructed and are being analyzed; the sequences determined of the many clones produced have so far revealed no significant homology with known viruses. The possible etiological role of the JHK virus in diseases that may involve B-lymphocytes, such as leukemia, lymphoma, chronic fatigue syndrome or immuno-dysfunctional states, remains to be determined [8,9,10]."



This quote is unchanged from 2009, and most likely paraphrased from his 1997 paper, which is pre the XMRV Science paper, or at least the very early days. He changed the genbank entry to XMRV late last year, so he at least thought it was XMRV for quite a long time. The reasons for his turnabout in the last few weeks are unknown.

It would appear that the JHK virus differs from XMRV judging by Grossberg's information.

Note sure who made this statement, but it doesn't necessary follow from the Grossberg quote.

All other information on the patent remains the same, so most probably a problem with nomenclature.

JHK-3 is a gammaretrovirus. It was found only in the blood of a me/cfs patient, not in the blood of a normal control, nor to my knowledge in cell lines as a contaminant as yet.

Sorry, while I was compiling, other posts came in... some repetition.
 

RRM

Messages
94

bullybeef

Senior Member
Messages
488
Location
North West, England, UK
It does look like Grossberg has modified his entry on Jan 19th 2012 to remove "XMRV" (which is fine because when they use "XMRV" they really mean VP62, and in that sense "XMRV" is dead, in fact it has never been alive in nature), and replaced it with MLV-related JHK human retrovirus.
See: http://www.ebi.ac.uk/cgi-bin/sva/sv...ION28813-1327317397-1&index=0&view=1409200631


So little change there then. ;) Still looks like a HGRV to me. :D
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
JHK-3 is a gammaretrovirus. It was found only in the blood of a me/cfs patient, not in the blood of a normal control, nor to my knowledge in cell lines as a contaminant as yet.

I thought JHK has been found in a cell line bullybeef? Are you saying that the specific strain JHK-3 hasn't been found in a cell line yet?
 

RRM

Messages
94
The problem with the RRM's argument can be illustrated with the following:

Q: How many XMRVs does a me/cfs patient have?
A: One, if we call all MLVs/MRVs XMRV, hundreds if we call them JHK-3, VP42, S-162, etc
A2: None, if we look only for VP-62, and don't bother looking in tissue for any MLVs

A classic strawman. I have never said that XMRV is defined by VP62 or any other single sequence. I have never said that people should only look for VP62 (or only in tissue, but I don't see what that has to do with the discussion anyway).

Calling something XMRV just doesn't make it so. That is a simple fact.

This is not XMRV, not because I don't want it to be, or not because Grossberg decided not to call it XMRV, but because known XMRV sequences cluster together and this sequence clusters somewhere else on a phylogenetic tree. It means they are distinct findings. It's basically the same as with Lo's sequences. Although they were similar to XMRV, one could not have reasonably evolved into the other into a relatively short period of time, and therefore they are disctinct. And therefore they reflect, if true at all, different infections.
 

bullybeef

Senior Member
Messages
488
Location
North West, England, UK
I thought JHK has been found in a cell line bullybeef? Are you saying that the specific strain JHK-3 hasn't been found in a cell line yet?


According to the study, the JHK-3 strain is from the human B-lymphoblastoid cell line, Bob: http://www.ncbi.nlm.nih.gov/pubmed?term=Grossberg SE jhk


Also see: http://www.patentstorm.us/patents/5827750/description.html?forumid=331851

Different amounts of JHK-3 cell DNA (1 ?g, 3 ?g and 10 ?g), presumably containing JHK provirus, were introduced by cationic liposome-mediated transfection (Felgner, et al., Proc. Natl. Acad. Sci., USA, 84:7413-7417, 1987) into three B-lymphoblastoid cell lines (from Dr. William Sugden, University of Wisconsin, Madison.) One line, HH514, was EBV-positive and two lines, BJAB and Wilson, were EBV-negative. After transfection, the BJAB cells did not grow, but the Wilson and HH514 cells propagated well. After 6 weeks supernatant fluid was centrifuged at 200,000g to obtain a pellet, and the pellet and cells examined by electron microscopy. The HH514 cells transfected with 10 ?g of JHK cell DNA were positive for 80-nm virions and incorporated 3 H-uridine such that the 200,000g viral pellet gave a characteristic peak of TCA-precipitable radioactivity in a sucrose density gradient. Thus, transfection with JHK-3 cell DNA was successful, providing additional evidence that JHK virus is a retrovirus.
 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
I thought JHK has been found in a cell line bullybeef? Are you saying that the specific strain JHK-3 hasn't been found in a cell line yet?

The operative word is 'contaminant'. As far as I know Raisch found a C virus in a cell line which may be the same. Grossberg later claims it came from an me/cfs patient.

At the moment, the contamination folk are pinning their argument on the fact that because they haven't found the virus in us, it must either be a lab artifact or in mice. As far as I know, none of the strains referred to in the prior posts have been found in mice. Yet it is pseudotyping like crazy in cell lines in labs.