XMRV complete proviral genome, isolate S-162

[anciendaze]

Dusty Miller's response could have been prerecorded.

At the outset of the controversy, the groups claiming XMRV was a new retrovirus had said it was 94% similar to a mouse virus (X-MLV) and 95% similar to an endogenous sequence. You might have heard the fulminations of 'ERV' on the subject last year. Take away the endogenous sequences, and you are left with mouse viruses. By defining XMRV into that tiny gap you can easily render any claim vulnerable.

A later wrinkle is apparent in this response, the new game plan is to define XMRV as the virus in 22Rv1 which is a contaminant by definition, since nobody wanted it there. Insistence on the particular deletion is Miller's criterion, not the original authors. He is entitled to his opinion. I am not required to accept it. (Nullius In Verba.)

What we have again is a report of a gamma retrovirus, very similar to a virus found in mice, isolated from a human patient. Harvey Alter was willing to accept his results as supporting such a finding, and those differences were substantial, because he knows hepatitis C is more variable.

If the charge of contamination doesn't work against the results from Ukraine/Lithuania, we should expect to hear about the drinking habits of people in the region. There may no longer be bounds on acceptable tactics.

 

[Ernie]

Response from Dr. Mikovits:



Not exactly sure what this all means, but here it is.

Hope you had permissions to post those e-mails!

 

[kday]

One-party consent in my state, so yes I have permission.

However, people always bring up arguments about law, copyright, ethics, etc, so I guess, I'll just delete them.

 

[Ernie]

Probably a good idea being one party state doesn't mean anything, it's about the e-mail being the property of the originator. That would not be you.

 

[omerbasket]

One-party consent in my state, so yes I have permission.

However, people always bring up arguments about law, copyright, ethics, etc, so I guess, I'll just delete them.

Besides, who is even talking about rules? Here you have a person who is willing to snwer your questions - and who actually does it very quickly, and you are thanking her by publishing her words without first getting her approval, even though you know that when a person sends an email to another person, especially when it's a scientist, he expects these emails to remain confidential unless who woukd give his approval to publish them?
It's not about law, it's about dignity and respecting a person who respects you and showed it by answering your email quickly - and I tend to believe that it was also answered politely, since I have emailed Dr. Mikovits many times, and her answers were always very polite.

It disgusts me that you think that the reason for which you should or should not delete that post is the law, and not dignity and respect.

 

[omerbasket]

A later wrinkle is apparent in this response, the new game plan is to define XMRV as the virus in 22Rv1 which is a contaminant by definition, since nobody wanted it there. Insistence on the particular deletion is Miller's criterion, not the original authors. He is entitled to his opinion. I am not required to accept it. (Nullius In Verba.)

Wow, I didn't notice that and I thank you for mentioning it. XMRV was first isolated from prostate cancer tissues that came from human beings - not from cell lines that were developed in the laboratory, and therefore not from the 22Rv1 cell line. Miller and Coffin can theorize that the XMRV that was found in prostate cancer tissues is a result of a contamination that came from the 22Rv1 cell line - but that is just a thoery right now, it is not proven, and there it is very much controversial. Therefore, refering to the virus from 22Rv1, in such a delicate way, and talking about it as if this is the reference for XMRV, seems odd, as until today the reference was VP62, and although they are very similar, it's not only that they are not the same, but it is the change in the wording - saying "XMRV from 22Rv1" instead of "XMRV VP62" that sounds as if people are trying to get their theory - that XMRV is just a contamination that came from the 22Rv1 cell line - to be thought of as a proven thing.

On another issue:

XMRV or not, we humans seem to harbour an awful lot of mouse retroviruses
Somewhere along the line this can't all be explained by contamination anymore, I think. It's like the boy crying "Wolf!" all the time. There comes a time when that doesn't work anymore...

Anyway, Miller might have published some research some of us don't look favourably upon, at least he is responding to questions.

I totally agree with you: It seems to me that when it's almost identical to VP62 they are saying that it is evidence that it's just a contamination, and when it is just closely related, just 95% identical, they are saying that it is not even the same virus. Which again is wierd, because HIV-1 has strains that are "just" 85% identical to one another, and HCV have strains that are "just" 79% identical to one another. They are talking about the deletion VP62 and about the phylogenetic trees. My questions are: Could it not be that mutation caused the deletion/dissapearment of deletion? Is the phylogenetic tree evidence so strong that it is proving that this is not the same virus - as opposed to those strains of HIV-1 that are just 85% identical to one another but are still called by the same name - and even though the similarity here is significantly bigger (95%)?

And I do agree with you, Jemal - at least he is responding to emails. He has a different opinion than some of us, but at least he treats us with respect, and in this day and age it's something too. That is, ofcourse, not to say that we should take every word from him as if we can be 100% sure that it is true and proven.

 

[Ecoclimber]

S-162 Sequence and Miller's Analysis

I asked Miller for his comment below was his reply.

This Lithuanian sequence is not very close to XMRV, and really could not have originated from XMRV by spread in humans. It doesn't have the characteristic glycogag deletion of XMRV, and is only 96% identical to the 22Rv1 XMRV, with 69 sequence gaps (see attached alignment). It potentially could be a new human retrovirus, but it should not be called XMRV.

Take a look at the phylogenetic tree at the end of the attachment to see how the Lithuanian sequence (S-162 at bottom) is related to all other sequences in GenBank. It hangs out on its own, essentially no closer to the XMRV group (middle of tree) than to the DG-75 retrovirus group (near the top).

My guess is that this Lithuanian sequence is another mouse retrovirus sequence, but we'll need to wait for the paper describing the origin of this sequence to find out.


Dusty Miller

Note: Open attach document in Adobe Reader

Permisson to post.

 

[jace]

omerbasket answered eco's post before he posted it!

I totally agree with you: It seems to me that when it's almost identical to VP62 they are saying that it is evidence that it's just a contamination, and when it is just closely related, just 95% identical, they are saying that it is not even the same virus. Which again is wierd, because HIV-1 has strains that are "just" 85% identical to one another, and HCV have strains that are "just" 79% identical to one another. They are talking about the deletion VP62 and about the phylogenetic trees. My questions are: Could it not be that mutation caused the deletion/dissapearment of deletion? Is the phylogenetic tree evidence so strong that it is proving that this is not the same virus - as opposed to those strains of HIV-1 that are just 85% identical to one another but are still called by the same name - and even though the similarity here is significantly bigger (95%)?

A phylogenic tree is an artificial construct, an attempt at making a graphic representation of reality, and not in any way "proof" of anything. IMHO.

 

[asleep]

Miller's Catch-22

I asked Miller for his comment below was his reply.

This Lithuanian sequence is not very close to XMRV, and really could not have originated from XMRV by spread in humans. It doesn't have the characteristic glycogag deletion of XMRV, and is only 96% identical to the 22Rv1 XMRV, with 69 sequence gaps (see attached alignment). It potentially could be a new human retrovirus, but it should not be called XMRV.

Take a look at the phylogenetic tree at the end of the attachment to see how the Lithuanian sequence (S-162 at bottom) is related to all other sequences in GenBank. It hangs out on its own, essentially no closer to the XMRV group (middle of tree) than to the DG-75 retrovirus group (near the top).

My guess is that this Lithuanian sequence is another mouse retrovirus sequence, but we'll need to wait for the paper describing the origin of this sequence to find out.


Dusty Miller

Note: Open attach document in Adobe Reader

Permisson to post.

There is nothing interesting or scientific about Miller's position. He's just shuffling words around in an attempt to define XMRV out of existence.

Step 1: Find a cell line (22Rv1) that produces infectious XMRV (produced from human cells with a demonstrated tropism for XMRV no less!).

Step 2: Cobble together a patchwork hypothesis about how XMRV originated during the creation of this cell line. NOTE: There is no need to provide any evidence other than conjecture, nor is there any need for the hypothesis to even explain all the observed data. The only important thing is that the "contamination" label sticks and gets propagated through the media.

Step 3: Through common usage and other means, attempt to redefine XMRV as the precise sequence expressed by 22Rv1.

Step 4: If anyone publishes sequences close to 22Rv1 XMRV, claim that the lack of variation is further "proof" of contamination. If anyone publishes sequences with greater variation (indicative of a genuine human pathogen), claim that it must be something else entirely by virtue of its difference from your freshly redefined single-strain XMRV.

Step 5: Congratulations! You've successfully defined XMRV as a "contaminant" and placed it beyond the scope of scientific inquiry. You may now claim a hollow semantic victory. Game, set, match, if you happen to live in la-la-land. Unfortunately, no one is buying what you're selling.

In summary, according to Miller's logic, no one can ever publish sequences that support XMRV as a human pathogen, by definition not logic. Any sequence will either be labeled as further proof of contamination or as a different virus.

Ecoclimber, I don't know why you would cite some half-baked theory from Miller. He has proven himself to be a "contamination" zealot, not a scientist. The only credibility the man has left is that which is mistakenly afforded him by those incapable of looking past the extra letters appended to his name.

 

[Ecoclimber]

S-162 Sequence and Miller's Analysis Further Comments

omerbasket answered eco's post before he posted it!


A phylogenic tree is an artificial construct, an attempt at making a graphic representation of reality, and not in any way "proof" of anything. IMHO.

The response to your post raises a legitimate question: how similar do sequences need to be to be considered in the same group?


ALL retroviruses are related, but that doesn't mean we don't find differences that allow us to put these viruses into different groups. What we really need is more "XMRV" sequences to make sense of XMRV phylogeny (that is, their ancestral relationships).



In the case of HIV, there are so many sequences available from humans and monkeys that we can tell from which monkeys the human HIV strains derived. Indeed, HIV strains in humans are divided into clades of closely-related viruses. Sequence variation within a clade is much less than between clades, and if you look at a phylogenetic tree of all HIV sequences, the clades can be clearly distinguished.



For XMRV we only have a few completely-sequenced isolates, and they are all more than 99.8% identical. Along comes a virus that is only 96% identical, and is missing several characteristic features that differentiate XMRV from other retroviruses. Without additional data, we can't call it XMRV. If the scientists, who still claim that XMRV is present in humans, would provide more sequences of the different strains of XMRV they find in humans, we could see what the natural variation is.



The sequences would need to form a continuum of changes, representing a continuum of mutations that occur as the virus evolves. Alternatively, we might find a cluster of viruses similar to XMRV and a cluster similar to the Lithuanian S-162 virus. Then we could legitimately call these different virus families.

In response to the question, "Could it not be that mutation caused the deletion/disapierment of deletion?". To make the deletion disappear [sic], the virus would need to add the exact 15 bases that are missing in XMRV but are present in other retroviruses. This would be highly unlikely (1 chance in 4^15, or about 1 in a billion).


Response from Dusty Miller

 

[omerbasket]

Who said that it would only add the disappeared 15 bases (if that's what Miller means, it's possible that I'm getting it wrong)? What if it would add 50 bases, and from those 50 bases, bases number 14 to 28 (15 bases) would happen to be in the spots of those 15 bases that had deletions?

 

[VillageLife]

There are probably loads of strains of XMRV.

Still all XMRV what ever way you want to look at it.

it will be very interesting to see if this strain of XMRV they have found is the same one in most people in lithuania.

Just like the other one is mostly the same in the UK / USA.

 

[omerbasket]

Two more things to add to what I've said in my last message:
1) I didn't think about it at first, but actually, it would seem more likely to me that VP62 is a strain of XMRV that had undrewent more mutation than the Lithuanian strain - meaning, the Lithuanian strain, in my opinion (and while remembering that my knowledge here is little), is more likely to be an ancestor of VP62 than the other way around, and that is because:

Deletions remove one or more nucleotides from the DNA. Like insertions, these mutations can alter the reading frame of the gene. They are generally irreversible: though exactly the same sequence might theoretically be restored by an insertion, transposable elements able to revert a very short deletion (say 12 bases) in any location are either highly unlikely to exist or do not exist at all. Note that a deletion is not the exact opposite of an insertion: the former is quite random while the latter consists of a specific sequence inserting at locations that are not entirely random or even quite narrowly defined.

http://en.wikipedia.org/wiki/Mutation
So it seems to me that it's more likely that the Lithuanian XMRV existed before VP62, and that VP62 is a mutation of the Lithuanian XMRV. Now, look at the following theory: The Lithuanian XMRV existed in Lithuania before any type of XMRV existed in the USA. In at least one of the people infected with the Lithuanian XMRV, the virus underwent a mutation that caused the 15 base pairs deletion that we see in VP62 and the almost-identical sequences (like the WPI full sequences). That person then travelled to Nevada and infected a person from Nevada with that XMRV, which is like VP62. On another occasion, another person from Lithuanian - this time a person that is infected with the Lithuanian XMRV - travelled to Boston (the Lo/Alter study included 25 patients from Dr. Komaroff's clinic, which is in Boston - so I guess most of them were from the Boston area) and infected a person from Boston with the Lithuanian XMRV. That would even make some since, because Dr. Hanson had told us that the MLV-related viruses that she found in her Lyndonville (New-York) cohort are more like the sequences found by Lo and Alter then the sequences found by the WPI. And While Nevada is one of the places in the USA that is the most far away places from Boston or New-York, Lindonville (New-York) and Boston are relatively very close. So it would make more since when the highly identical sequences would be found in relatively close places, and a somewhat divergent sequences would be found in a reltively far-away places.
One must remember that this theory is simplified: You don't have to have just one person with a deletion in the Lithuanian XMRV, you can have many such people. And they don't have to travel directly to Nevada, they can infect someone from Britain, for example, and that someone might infect someone from the netherlands, and that someone might infect someone from Nevada. And you don't have to have just VP62 in Nevada - you might have also the sequences from Lyndonville, Boston or Lithuania - but you might have them in a lower number of people.

2) There is already at least 1 example (it's just the one that I know of) of a known mutation that the same gene in our body underwent, and still it is the same gene - and it's also more common in one place of the world (Europe) than in other places:

For example, a specific 32 base pair deletion in human CCR5 (CCR5-?32) confers HIV resistance to homozygotes and delays AIDS onset in heterozygotes.[44] The CCR5 mutation is more common in those of European descent

http://en.wikipedia.org/wiki/Mutation
So you see, here we have a 32 base pair deletion in a gene - but it's still called by the same name (with a subtype). Moreover, it seems that this subtype of the gene is more common in one place of the world (europe) than in other places - so it fits with the theory that XMRV VP62 is more common in certain areas of the world than in other areas. This might explain the negative studies: If the WPI test is sensitive enough, and can find viruses that are, for example, "just" 95% identical to VP62 (and also with mutations not just in one place, but in several different places accross the strain), it's possible that what they are finding in the UK is a mutation of VP62 (actually, as I've said, it seems to me that it's the other way around - that VP62 is a mutation of that virus, but who knows...), but they cannot know that because they haven't yet sequenced the full virus.

Anyway, it all comes back to one thing: That is why your test should be extremely sensitive; That is why you, at this time, should only use tests that were clinically validated (and if you think that they are giving false results - you should first try them, and then, if you think that the results are false, you should explain why, or even make experiments that would give evidence or proof that the results from these tests were false); And that is why, at this time, a scientist must keep an open mind and remember that had we known everything, we either had a cure to all of the diseases, or we would have known about diseases that no matter what one would do, it is impossible to find a cure for them. But we are not there yet, right?

 

[kday]

That person then travelled to Nevada and infected a person from Nevada with that XMRV, which is like VP62.

I can't comment on the virology aspect so much, but Lithuanians infecting people in Nevada is actually not that far-fetched.

A lot of Lithuanians (and people from other countries too) come to Tahoe in the summer to work. For an example, when I lived there, I worked with 3 my last summer job (a few years ago). They had 15 or so people in their house (guys and girls), the majority being from Lithuania.

Let's blame the Lithuanians!

 

[Jemal]

Let's blame the Lithuanians!

No, it's obvious it's the gibbon apes that got to us.

 

[omerbasket]

Was the first known ME/CFS outbreak in Incline Village in the summer? It might give us a very tiny hint if it was (and if it wasn't, it won't really give us even a tiny hint to the contrary - because it could be that the virus was transmitted in the summer but the people just developed it later; And that the first know cases were not the first cases, or came to the doctor who diagnosed them after several months; Or that the virus was transmitted in another time in the year, because I guess there are some Lithuanians there in those times too; And anyway, even if it was in the summer, it is ofcourse, a very tiny hint).

 

[anciendaze]

Hoping to clarify without extending a flame war, I'd like to explain something fundamental to evolution of both species and sequences. The chance of identifying a 'missing link' or actual ancestor is virtually zero. It is safer to assume you are always dealing with descendants with a common ancestor. This may be close or distant. The question is how close.

In terms of editing distance, any deletion is only one operation away from the original sequence. The Lithuanian sequence could be very close to the common ancestor with XMRV, despite the deletion. Other differences must be considered.

The probability quoted for filling a 15-bp deletion is impressive. By this standard, the thousands of bp missing from pre-xmrv1 or 2 could be dismissed as effectively impossible to fill. If another sequence containing that 15-bp sequence and matching surrounding bp is available for recombination, things get much easier.

 

[jace]

omerbasket:

Was the first known ME/CFS outbreak in Incline Village in the summer? It might give us a very tiny hint if it was

From Osler's Web:

" By the end of summer 1984, Dr Carol Jessop counted 15 such cases in her practice at the Lyon-Martin Health Center" (in SF, CA)

"Inga Thompson ... Her home was in Reno,... she fell ill in the summer of 1984"

"The North Carolina Symphony was comprised mostly of younger musicians. Their average age was thirty eight... In August of 1984 several orchestra members began to experience a strange panoply of symptoms..."

The first cases recorded in Incline Village seem to have been in late summer 1984. No clues to dates other than
"Late in September the careworn woman departed for Houston as was her custom." and "By early December the Alder Street clinican (Peterson) had tested all of his weary patients for.....results were negative."

Hope this helps.

Oh, and I should add, Incline Village was not the first outbreak. Maybe that's not what you meant, but for clarification, check the timeline here

 

[ukxmrv]

In Oslers Web there is a tentative attempt to create a "patient zero" around a South African woman who visited the USA.

Lithuanians would only have started to travel to work abroad after the fall of the iron curtain? We have Lithuanian people working in the UK now but they didn't arrive until the Russians began to travel.

From Wiki

Lithuania was again absorbed into the Soviet Union for nearly 50 years. In the early 1990s, Lithuania restored its sovereignty and in the following years became integrated into the European political structures.