New WPI and CDC XMRV sequences in genbank

[bullybeef]

Raisch found a C virus in a cell line which may be the same.

Also see: http://www.patentstorm.us/applications/20100166797/fulltext.html

The most significant match in the full length viral genome database is to a xenotropic murine type C retrovirus known as DG-75.....

 

[RustyJ]

Also see: http://www.patentstorm.us/applications/20100166797/fulltext.html

Grossman was on the Raisch team. He knew DG-75 came from an me/cfs patient, which is presumably why he dived off in that direction.

 

[Bob]

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.

Just on a very narrow point of fact, retroviruses can recombine and so can change quickly without evolving. In other words, they can change large amounts of genetic material just by recombination.

On a wider point of discussion, I don't personally think it's important whether we label something XMRV or not. I think it's more important to ask questions relating to whether these viruses have similarities to each other, whether they are related in any way, whether they have a similar behaviour, whether they cause a similar immune response, whether there might be a similar source for them, and - most importantly for us - whether they are present in ME patients. I hope that Lipkin will be able to answer the latter question.

 

[currer]

If they can reproduce in human cell lines, they can reproduce in us. They probably all can cause the same pathology.

RRM, How can you say they reflect different infections when they are probably no more diverse than different HTLV strains? Remember that as far as we can tell, these retroviruses are similar enough to have all crossed into human cell lines by the same method - from miice to human tumour grafts.

The virologists arguing about strains is an irrelevance from the point of view of the patients, if they have MLV related illness, and those doctors who are trying to investigate retroviral involvement in ME.

Here I will be very interested to see what strain is found in Dr Snyderman's leukaemia. There was talk about getting it sequenced so it will be fascinating to see which viral strain it most nearly resembles.

Rusty, when you say pseudotyping like mad - do you really mean that? Are these X/P MLVs really inserting themselves into other viruses? Or did you mean that they are highly infectious in cell lines?

 

[RRM]

Just on a very narrow point of fact, retroviruses can recombine and so can change quickly without evolving. In other words, they can change large amounts of genetic material just by recombination.

Although this is true, strictly speaking, you would not expect recombinations to end up on another already existing branch on a phylogenetic tree. The chances of this happening are astronomically low. That is why phylogenetic evidence is considered to be very robust (and no, the Switzer conference abstract from Retrovirology does not challenge this). But I must admit that a true analysis has only really been done with the Lo sequences and not with this Grossberg isolate, and it would be nice if Grossberg (or someone with specific qualifications, like Katzourakis) would do this to see how it exactly clusters with other known sequences.

On a wider point of discussion, I don't personally think it's important whether we label something XMRV or not. I think it's more important to ask questions relating to whether these viruses have similarities to each other, whether they are related in any way, whether they have a similar behaviour, whether they cause a similar immune response, and most importantly whether they are present in ME patients. I hope that Lipkin will be able to answer the latter question.

I agree to a large extent, and that is also why I used the very wide monicker of "something". As long as Mikovits/Ruscetti can find "something" to discriminate between patients and controls using their methodology, it's fine by me.

However, I don't agree with it in the context of the Grossberg JHK sequence. That people were not just finding XMRV was known long before this, since Lo et al. (or even before that if you count conference presentations). However, this Grossberg finding was specifically hailed as an argument in favor of the idea of XMRV itself having evolved beyond what was thought possible by current research (e.g. Paprotka et al.). It's hard to maintain that. And, as such, looking at XMRV itself isn't too narrow.

 

[RustyJ]

Rusty, when you say pseudotyping like mad - do you really mean that? Are these X/P MLVs really inserting themselves into other viruses? Or did you mean that they are highly infectious in cell lines?

Thats what Grossman/Raisch found. But I guess what I was really getting at is that it is odd these new variants are not being found anywhere else (except of course, in us, depending on who you believe) and not in mice. So one conclusion is that MLV contaminant are recombining in the lab to form the new viruses, swapping bits of each other.

I am not all the sure that anyone has really confirmed the sequences of the original viruses, except by partial sequences, and theory, and terms like 'close to' etc. So where did they come from? Eg XMRV/SP62 varies from Moloney by quite a bit.

 

[currer]

There was a suggestion made a while ago that well adapted retrovirus could be created by putting different human tissues into mice, and the human tissue would naturally become infected with the MLV from the mouse most well adapted to that cell line, breast, lung, prostate, blood etc.

In this way you could select for the ideal mouse/human infection for a tissue type.

Can anyone remember the researcher who mentioned this?

These MLVs have had fifty years to adapt - isnt that how long the tissue grafting has been done? There are quite possibly some well adapted human MLVs in laboratories.

 

[RustyJ]

There was a suggestion made a while ago that well adapted retrovirus could be created by putting different human tissues into mice, and the human tissue would naturally become infected with the MLV from the mouse most well adapted to that cell line, breast, lung, prostate, blood etc.

In this way you could select for the ideal mouse/human infection for a tissue type.

Can anyone remember the researcher who mentioned this?

Different MLVs have different integration points, this is well accepted in mouse studies. The MLV/lymphoma studies talked about integration sites. There is some work being done on HIV which is now looking at new variants, currently undetected by PCR, and unaffected by HAART, with link to progressive neurological damage - sound familiar.

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020234

MLV favors integration near transcription start regions and favors active genes only weakly..

 

[Bob]

Although this is true, strictly speaking, you would not expect recombinations to end up on another already existing branch on a phylogenetic tree. The chances of this happening are astronomically low. That is why phylogenetic evidence is considered to be very robust (and no, the Switzer conference abstract from Retrovirology does not challenge this). But I must admit that a true analysis has only really been done with the Lo sequences and not with this Grossberg isolate, and it would be nice if Grossberg (or someone with specific qualifications, like Katzourakis) would do this to see how it exactly clusters with other known sequences.

I don't have much knowledge about the recombination issue, but my understanding was that many different MRVs could break apart and recombine with each other, and that this is a common occurance. Thus PMLV and XMLV etc. particles could combine with each other. Is that not the case? Recombination is supposed to be an extremelly common occurance, and so if viral particals (from related viruses) are freely available in the the same substrate, then I would have thought that recombinations would easily end up on "another already existing branch on a phylogenetic tree". That was my understanding anyway - please correct me if you think I am wrong.

As an example VP29 and VP184 are said to be recombinants of XMRV and Moloney MLV:
http://www.retrovirology.com/content/7/1/111

However, I don't agree with it in the context of the Grossberg JHK sequence. That people were not just finding XMRV was known long before this, since Lo et al. (or even before that if you count conference presentations). However, this Grossberg finding was specifically hailed as an argument in favor of the idea of XMRV itself having evolved beyond what was thought possible by current research (e.g. Paprotka et al.). It's hard to maintain that. And, as such, looking at XMRV itself isn't too narrow.

I don't know much about JHK, but I would agree (going from my very little knowledge about it) that it doesn't look to me like XMRV has 'evolved' into JHK or vica versa. However, if there are any MRVs associated with ME then there might be a variety of them causing the same or similar symptoms, and so JHK could be relevant for ME patients whether it is closely related to XMRV or not. The fact that JHK is related in some way to XMRV could be significant in ways that we are possibly not even yet aware of.

 

[RRM]

There was a suggestion made a while ago that well adapted retrovirus could be created by putting different human tissues into mice, and the human tissue would naturally become infected with the MLV from the mouse most well adapted to that cell line, breast, prostate, blood etc.

In this way you could select for the ideal mouse/human infection for a tissue type.

Can anyone remember the researcher who mentioned this?

No, but that is in essence very basic evolutionary logic. In fact, I've argued before that this is also very good evidence of 22Rv1 being the origin of XMRV in itself: 22Rv1 is exceptionally well suited for XMRV, better than any other known cell line (or environment).

And the same really applies to really everyting: if I tomorrow decide to propagate elephant liver tissue through parrots, then eventually (after the right amount of time, which of course could be very long) that elephant liver tissue will become infected with a parrot virus that is "accidentally" well suited to the elephant liver tissue. Parrot viruses will mutate/recombinate in the tissue, but all of them will die, because they can't survive in elephant liver tissue. Only when, through sheer chance, a mutation/recombination will "create" a virus that can accidentally survive and replicate in its new environment, it will also survive and replicate.

This is exactly why it is no surpise that many cell lines have become infected and there is also not much that can be done about this.

 

[currer]

RRM said ;
This is exactly why it is no surpise that many cell lines have become infected and there is also not much that can be done about this.

It is a surprise that this obvious danger was ignored for so long, though.

 

[RRM]

I don't have much knowledge about the recombination issue, but my understanding was that many MRVs could break apart and recombine. Thus PMLVs and XMLVs etc., could combine with each other. Is that not the case? Recombination is supposed to be an extremelly common occurance, and so if viral particals (from related viruses) are available in the the same substrate, then I would have thought that recombinations would easily end up on another already existing branch on a phylogenetic tree. That was my understanding anyway - please correct me if I am wrong.

If A and B recombine, then this is only so in the sense that it will end up on the (existing) branch of A or the existing branch of B, but it's unlikley to turn up on the existing branch of C.

It's basically the same as drawing a family tree: if a scientist takes blood from my parents and me, he can (very probably) draw the correct family tree from analysing a partial fragment. If the analyzed partial region from my DNA consisted of just a single stretch of my father's DNA then it would be impossible to put me on my mother's branch (and vice versa), but then I'd still branch with my father's DNA (and not someone else's). Perhaps you could argue that I could possible match my uncle's DNA better by some chance event, but then I would still essentially be on the same branch and very close to the correct spot on the tree. And it would be incredibly unlikely that this partial recombination would accidentally match the milkman's DNA.

 

[Bob]

There was a suggestion made a while ago that well adapted retrovirus could be created by putting different human tissues into mice, and the human tissue would naturally become infected with the MLV from the mouse most well adapted to that cell line, breast, lung, prostate, blood etc.

In this way you could select for the ideal mouse/human infection for a tissue type.

Can anyone remember the researcher who mentioned this?

These MLVs have had fifty years to adapt - isnt that how long the tissue grafting has been done? There are quite possibly some well adapted human MLVs in laboratories.

The retroviruses found in human cell lines clearly have an affinity for human tissue, because they live and replicate in human tissue.
I would have thought that this means that they could very easily infect humans, although a full human immune system (present in the human body but not present in the cell lines) could possibly stop an infection very early on in the process (the jury is out on that).
From our current knowledge, it looks like the novel MRV/MLV viruses found in the cell lines have formed as a result of recombination events and a small amount of evolution, or genetic mutations. The recombination event together with the genetic mutations could be the mechanism that allows them to thrive in human tissue, whereas many other MLVs do not thrive in human cell lines.
It could be the case that these viruses thrive most in the type of human cells of the specific cell line in which they are found. That would make sense because each tissue is a unique cellular environment, so I would have thought a virus could do best in certain tissues, rather than others. I think that's widely accepted isn't it? It certainly is with bacteria. (I can't think of an example of a virus that has an affinity for a specific tissue off the top of my head, but i'm sure that there are some.)

 

[Jemal]

This is exactly why it is no surpise that many cell lines have become infected and there is also not much that can be done about this.

Though a lot of researchers seem to be surprised by the amount of infected cell lines?

 

[RRM]

RRM said ;
This is exactly why it is no surpise that many cell lines have become infected and there is also not much that can be done about this.

It is a surprise that this obvious danger was ignored for so long, though.

I don't know if it has been ignored. For instance, the Coffin/Stoye letter that was posted in JDJ's latest blog indicates that people were aware of the situation and dangers of these kinds of things.

The problem is: what are the alternatives? We could stop doing research using animals, but I think that would be a case of throwing out the baby (or rather, 100 babies) with the bath water. Alternatively, we could use animals that share less homology with humans, but this is a real Catch 22:

The more distant the animal, the harder it will be to propate human tissue (and thus the longer it will take and thus the more chance of chance recombinations to happen). Moreover, testing in these animals will be less valubale to understanding human disease. In the most extreme case, if macaques (ignoring ethical issues) were as easy to "breed" as mice it would from one standpoint be "great" to use them instead of mice: it would be relatively easy to propagate human tissue and test results would be more "refelictive" of human infection than mice experiments. On the other hand, it would be "very bad", because with macaques, you'd have the largest chances of "breeding" some lethal and horrific human pathogen.

In an extreme case from the other side, we could use spiders. On one hand, this again would be "great" because we wouldn't less chances of any of the spider viruses jumping into the human tissue and creating a real human pathogen, but from the other hand it would be "bad" because I guess it's very hard to propagate human tissue in non-mammals and even if we get some results in some experiments, it's not very likely that these results will be of use in the fight against human disease.

 

[Bob]

If A and B recombine, then this is only so in the sense that it will end up on the (existing) branch of A or the existing branch of B, but it's unlikley to turn up on the existing branch of C.

Well, yes, that's likely to be correct most of the time, but I think I've lost the thread of this discussion, so I think i'll stop now.

I think I was just responding to what you said earlier:

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.

I agree that they are distinct viruses, or variants.
But the (hypothetical) human infection of both XMRV and PMRV could possibly be from the same source, at the same time.
And a variety of similar MLV viruses could possibly cause the same (or very similar) symptoms.
And for the sake of discussion, assuming that human infection is possible, if it is possible that MLV recombination events can occur inside the human body (I don't know if this is possible) then PMRV could have been formed inside the human body after infection by various MLV viral particles.
There seem to be very many potential possibilities about which we know very little at this stage.

 

[Sam Carter]

The retroviruses found in human cell lines clearly have an affinity for human tissue, because they live and replicate in human tissue.
I would have thought that this means that they could very easily infect humans, although a full human immune system (present in the human body but not present in the cell lines) could possibly stop an infection very early on in the process (the jury is out on that)....

Hi Bob,

As you've pointed out later in your post one cannot assume that a virus capable of replicating in a human cell-line is also capable of infecting a human being.

This is an important issue that is so often overlooked.

Regarding Grossberg's JHK virus this work needs replicating before any confidence can be placed in it. I would have thought that had it been present the groups who also looked for related-MLVs as well as XMRV (Tang et al 2011, Luczkowiak et al 2012, Simmons G et al 2011, Shin et al 2011 etc) would have found it.

 

[Bob]

I don't know if it has been ignored. For instance, the Coffin/Stoye letter that was posted in JDJ's latest blog indicates that people were aware of the situation and dangers of these kinds of things.

The problem is: what are the alternatives? We could stop doing research using animals, but I think that would be a case of throwing out the baby (or rather, 100 babies) with the bath water. Alternatively, we could use animals that share less homology with humans, but this is a real Catch 22:

Clearly there is a potential danger from MLV viruses (and potential novel MRV viruses), that thrive in labs and human cell lines, that has been hitherto ignored, either by choice or from ignorance, or choosing to be ignorant.
They have only just started to test many of these cell lines for MLVs, so there was a large degree of ignorance about what viruses were present in which cell lines.

Personally, I don't think that cell line research should be stopped because of these viruses, but safety procedures need to be put into place to protect lab workers and the public. And for safety procedures to be put into place, we need as much knowledge as possible about what viruses are present in which cell lines.

And it doesn't seem to be a very good idea to use contaminated substrates to create vaccines.
It's only a matter of time before a mutated novel MLV, which thrives in a human tissue cell line, infects a human and goes wild, if it hasn't happened already.

 

[Bob]

Hi Bob,

As you've pointed out later in your post one cannot assume that a virus capable of replicating in a human cell-line is also capable of infecting a human being.

This is an important issue that is so often overlooked.

Yes, I agree with you Sam.

Like I said earlier, I think the jury is still out on whether an XMRV infection in a human can be successful or not. i.e. will the human immune system always eradicate the virus so that an infection cannot take hold? There have been conflicting papers published about the effectiveness of the immune system against XMRV.

Regarding Grossberg's JHK virus this work needs replicating before any confidence can be placed in it. I would have thought that had it been present the groups who also looked for related-MLVs as well as XMRV (Tang et al 2011, Luczkowiak et al 2012, Simmons G et al 2011, Shin et al 2011 etc) would have found it.

Yes, I agree with you here as well... All research needs to be replicated to be validated...
I hope that if there are any pathogens involved in ME, then Lipkin's second (non-XMRV) study will find them.

 

[RRM]

I agree that they are distinct viruses, or variants.
But the (hypothetical) human infection of both XMRV and PMRV could possibly be from the same source, at the same time.

If you mean that people could have gotten infected with both XMRV and PMRV from the same "source" (e.g. another person), I agree.

But I don't think it is realistically possible that some people could have gotten infected with XMRV and some with PMRV, all from the same ancestral sequence. The sequences are just too distant for that to have happened - I believe there's a couple of million years of evolution between them. Although you could theoretically argue that these sequences reflect a recombination of the MLV in question with XMRV and that just the MLV-part was sequenced (and therefore it appeared on that part of the tree), it simply lacks any evidence in support of it.