New WPI and CDC XMRV sequences in genbank

[ukxmrv]

Dr Mikovits said at the IiME conference in London that HTLV is the virus to think about rather then HIV. With HTLV she said that the virus could be sequenced from the same patient 40 years later and it would be the same.

Also remember Dr Magiorkinis in the Lancet

(start)
Once a virus is endogenised, it is forced to follow the evolutionary rate of the host. Since XMRV is integrated in cell-lines the virus evolution is restricted to the host's pace of evolution, and viral descendants have none or minimum sequence diversity. Thus, if a contaminated product, previously cultured in cell-lines, is administered to people then the infections would provide the evolutionary patterns reported by Hue and colleagues.4 If the immunological data reported by Lombardi and colleagues5 are correct, then we need to trace the common source for these infections to prevent possible public health concerns. Products from cell-lines should be the first candidates.

 

[Bob]

Dr Mikovits said at the IiME conference in London that HTLV is the virus to think about rather then HIV. With HTLV she said that the virus could be sequenced from the same patient 40 years later and it would be the same.

Also remember Dr Magiorkinis in the Lancet

(start)
Once a virus is endogenised, it is forced to follow the evolutionary rate of the host. Since XMRV is integrated in cell-lines the virus evolution is restricted to the host's pace of evolution, and viral descendants have none or minimum sequence diversity. Thus, if a contaminated product, previously cultured in cell-lines, is administered to people then the infections would provide the evolutionary patterns reported by Hue and colleagues.4 If the immunological data reported by Lombardi and colleagues5 are correct, then we need to trace the common source for these infections to prevent possible public health concerns. Products from cell-lines should be the first candidates.

Yes, so even if all of the known XMRV sequences were almost identical, then it wouldn't prove that they were contamination.

Also, the P variety of MLV-related viruses is proof of variety.
Just because it has a different name doesn't make it a different virus.
Harvey Alter specifically said that he considers X and P types to be different varieties of the same virus.

 

[Jemal]

CDC has posted more XMRV sequences to Genbank. According to IMEA it's more proof that XMRV is not contamination:

http://imeassoc.com/New_CDC_XMRV_sequences.html

 

[Bob]

CDC has posted more XMRV sequences to Genbank. According to IMEA it's more proof that XMRV is not contamination:

http://imeassoc.com/New_CDC_XMRV_sequences.html

They are the CDC's (Switzer's) genbank sequences listed on the opening post of this thread.
They're from Switzer's negative prostate cancer paper that we've discussed before.
Switzer concludes in his published paper that the genetic variety of the sequences is consistent with human infection.

 

[Jemal]

They are the CDC's (Switzer's) genbank sequences listed on the opening post of this thread.
They're from Switzer's negative prostate cancer paper that we've discussed before.
Switzer concludes in his published paper that the sequences' genetic variety demonstrates wild human infection.

Are they the same? I have no idea. I did see several new CDC sequences submitted on 20 june:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&cmd=search&term=xmrv

They also appear above the Lithuanian sequence...

As this thread was created earlier, I assumed these were new or at least different?

 

[Bob]

Are they the same? I have no idea. I did see several new CDC sequences submitted on 20 june:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&cmd=search&term=xmrv

They also appear above the Lithuanian sequence...

As this thread was created earlier, I assumed these were new or at least different?

You can tell by the 'Accession' reference number that they are the same sequences...
They do seem to have changed the date for some reason... Maybe some of info has been updated or added to.

 

[Jemal]

You can tell by the 'Accession' reference number that they are the same sequences...
They do seem to have changed the date for some reason... Maybe some of info has been updated or added to.

Ah, too bad... I thought it was something new. Several recent articles popped up in a Google search.

 

[Bob]

Ah, too bad... I thought it was something new. Several recent articles popped up in a Google search.

I can't remember if we started a new thread about the significance of Switzer's sequences, did we Jemal?
This is a lesson to me that we need to start new threads about significant things like that so that other people see the info.
A new thread would also show up in a google search, and google alerts.

 

[Jemal]

I can't remember if we started a new thread about the significance of Switzer's sequences, did we Jemal?
I think this is a lesson to me that we need to start new threads about significant things like that so that other people see the info.
A new thread would also show up in a google search, and google alerts.

I don't think we did. I agree Switzer's negative study is very significant, because it did find some XMRV and he ruled out contamination.

 

[Bob]

New sequence published.

Xenotropic MuLV-related virus RKO, complete genome
Zhang,Y.-A., Maitra,A., Hsieh,J.-T., Rudin,C.M., Peacock,C., Karikari,C., Brekken,R.A., Stastny,V., Gao,B., Girard,L., Wistuba,I., Frenkel,E., Minna,J.D. and Gazdar,A.F.
29-JUN-2011
Xenotropic MuLV-related virus RKO, complete genome.
JF274252
http://www.ncbi.nlm.nih.gov/nuccore/JF274252.1

 

[eric_s]

Looks like this one is 100% identical to VP-62.

 

[Jemal]

A new XMRV sequence submitted to Genbank?
http://www.ncbi.nlm.nih.gov/nuccore/HM119591.1
(posted 1 aug)

Partial molecular cloning with novel consensus PCR primers of the murine JHK retrovirus of human origin, a variant of the Xenotropic murine leukemia virus-related virus (XMRV)

This is an article about it:
http://imeassoc.com/New_XMRV_evidence.html

See also:

Is XMRV related to the JHK retrovirus found in CFS patients and discovered by Sidney Grossberg, M.D.?

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.

http://www.ncf-net.org/forum/2010winter2.htm

Looks like Dr. Grossberg now thinks JHK is (closely?) related to XMRV.

 

[eric_s]

As if things have not been confusing enough already...

 

[Jemal]

As if things have not been confusing enough already...

Yeah, also I have no idea if this is good or bad news. Maybe several researchers have been looking at the same (family of) virus(es) all along, who knows...

 

[Bob]

Thanku Jemal, I want to add it to my list on the opening post, just to keep it up to date, but there's something wrong with the edit facility for old posts.

I'll talk to admin about it.

---------------------------------------------------------------

The rest of this post, is just for my own notes, so please ignore...

Last updated 3rd August 2011.

BBC, Medical College of Wisconsin
Partial molecular cloning with novel consensus PCR primers of the murine JHK retrovirus of human origin, a variant of the Xenotropic murine leukemia virus-related virus (XMRV)
Halligan,B.D., Sun,H.-Y., Cashdollar,L.W., Kushnaryov,V.M. and Grossberg,S.E.
01-AUG-2011 (Submitted 14-APR-2010)

Xenotropic MuLV-related virus 5' LTR, partial sequence; and gag protein (gag) gene, partial cds.
HM119591
http://www.ncbi.nlm.nih.gov/nuccore/HM119591.1

 

[Jemal]

Also, I think HHV-6 and this JHK virus are connected? Which could mean all these viruses (including XMRV) that have been found in ME/CFS patients are connected somehow and maybe part of a family?

I think it was Dr. Deckoff-Jones that wrote an article that explained several researchers, like Knox, went the HHV-6 route in favor of XMRV (stating XMRV is contamination). What if XMRV, HHV-6, etc are all connected? That would be mind-boggling.

 

[Countrygirl]

Also, I think HHV-6 and this JHK virus are connected? Which could mean all these viruses (including XMRV) that have been found in ME/CFS patients are connected somehow and maybe part of a family?

I think it was Dr. Deckoff-Jones that wrote an article that explained several researchers, like Knox, went the HHV-6 route in favor of XMRV (stating XMRV is contamination). What if XMRV, HHV-6, etc are all connected? That would be mind-boggling.

Has this been posted? (Sorry, I haven't had time to read the thread yet.)



http://www.ncf-net.org/forum/ncftruths.html?forumid=331851



The basic thing you should know is that nearly all ME/CFIDS patients have a virus called HHV-6A and inside that is a retrovirus that one researcher has named the JHK virus. This has been known and kept quiet as we have continued to suffer for many years.



In an earlier patent, Dr. Sidney Grossberg, a world renown virologist from the Medical College of Wisconsin, wrote (# 5,827,750 on 10/98) "The human virus on which the present invention is based has not been classified as to which virus family it belongs, but it most nearly resembles a retrovirus ....The present invention relates to the detection of the presence of an NMA (neuromyasthnia) virus that is associated with CFIDS." He goes on to talk of the "protein spikes in the envelope" which are called peplomers and these spikes are characteristic of a retrovirus. He calls this retrovirus the "JHK virus." He mentions that the retrovirus that is close to the same size is called the "mouse mammary tumor virus." In his only publication on the virus, one that went unannounced by the CFIDS Association despite their funding of him, Grossberg writes ( Res Virol, 1997; 148(3): 191-206 ), "The human B-lymphoblastoid cell line, designated JHK-3, with pre-B-cell characteristics, chronically produces two viruses, Epstein-Barr virus (EBV) and JHK virus, an apparently novel retrovirus...most nearly resembling C-type retroviruses." Professor Cocchetto admitted that the driving force behind uncovering this research was reading Hillary Johnson's Osler's Web: Inside the Labyrinth of Chronic Fatigue Syndrome. In fact, he shared this quote from the book by Dr. Sidney Grossberg, "We may have a genetic recombination of herpes and retrovirus here."


The JHK RV was first discovered by Grossberg in 1989, and he first applied for a patent for it with Konstance Knox (!) in 1994.

Now it is in the GenBank as a XMRV variant, so was he the first discoverer of the RV?

C.G.

 

[heapsreal]

There are a number of herpes viruses that supposedly 90% of the population have been exposed by age 40 and have antibodies to. What i find interesting is that there arent many who are positive to the 3 main herpes viruses connected to cfs ie ebv, cmv, hhv6, same have 1 and some have 2 but not many have 3. I have tested consistently to cmv, cfs onset to ebv but now neg and neg to hhv6, this is antibodies to these viruses. u would think that many of us would be positive to all 3 but from what i have read this seems rare. My thoughts are that maybe most cfs have active herpes viruses to all 3 but due to immune defiencies from all 3 infections, we are only able to produce antibodies to only 1 or 2. Maybe an underlying retrovirus is causing the immune defiency or maybe when all 3 are active, this is whats causing the immune defiency or a combination of herpes viruses and retrovirus. My cfs started with active infections to 3 herpes viruses with 6 months ie ebv, cmv and chickenpox, maybe this is enough to permanently lower immunity and allow these viruses to work deper into our tissues and cfs which make it harder for our immune system to irradicate and after trying to fight these infection after sveral months, our immune system just wares out. So bottom line is my theory is that we get all these infections with in a short period of time which causes all the problems, maybe geting these infections spread out of a number of years is easier for our immune system to contain. Those that dont have antibodies to any of these infections maybe due to a really crappy immune system that just cant produce antibodies. Maybe this is why testing is so unreliable and a long term trial of av.s is needed, of cause av's cant irradicate these viruses but cant lower their viral load and give partial improvement.

This is all just my unscientific opinion from reading/researching herpes infections and retroviral infections. bottom line, no cure but improvement in condition is possible with av's and immune modulation. gee i wish i studied more at school and persued biomedical science.

cheers!!!

 

[eric_s]

Quoted from your link, Countrygirl:

HHV-6A can destroy CD4 and CD8 cells as well as Natural Killer (NK) cells.

These are exactly the ones where i have low counts... Maybe i should get tested for HHV-6A...

 

[eric_s]

It would be good if the NCF put dates to it's articles, i have no idea when this was written, probably some years ago.