Discussion in 'XMRV Research and Replication Studies' started by Jemal, Dec 12, 2011.
And here we go...
If I remember correctly some scientists said these kind of viruses would be quickly extinguished in our blood, meaning the virus would not be able to establish a foothold. Does this research challenge that?
yes Jemal That would have been Levy that was saying that at the webnar for the blood group studies results.
Very interesting and telling find Jemal.. ty
Hi Jemal, I agree with GaryK, this has indeed been claimed. The argument goes that native blood defences quickly destroy XMRV. To me this meant something other than it being impossible to infect someone - it meant the infection rate is low. This is of course what we see in ME, another match. However, now we know that once the virus is there the defences go down. This will allow the virus to spread, particularly in tissues as opposed to blood. It will be interesting to see if any further information along this line comes out. It certainly raises questions. Bye, Alex
The complement reaction described by Levy would be a problem for free virions, but viruses infecting immune cells need not spread this way. Infected immune cells can transfer virus through immunological synapses formed during normal functioning of the immune system. This allows virus to spread between B-cells, T-cells and dendritic cells, for example. They can also form virological synapses with adjacent cells. From the outside it is not at all clear that you can distinguish such a synapse spreading infection from those without any virus. This takes place readily in infection by HTLV. The virus actually uses the cytoskeleton like a rail system to move from cell to cell without ever floating free. Migrating lymphocytes can thus carry virus all over the body.
Also, the envelope of the virus in 22Rv1, which was his positive control, may not be the same as the XMRV envelope, even without considering natural pseudotyping. Other examples from work on MMTV show a virus using debris from bacteria in the gut to confuse immune response to its envelope proteins.
This is not the devastating criticism claimed.
I have a few questions. Not disagreeing with you, anciendaze, just trying to clarify.
Confusing for me anciendaze. Virus in 22Rv1 is VP-62 which became known as XMRV? I think you are saying we probably don't have vp-62?
This study suggests previous papers which state otherwise may be due to a discrepancy in A3G detection due to selection and sensitivity of A3G antibodies.
Again not sure what you are getting at here. Irrespective of whether cell to cell transmission can occur, one of the central arguments of those saying there are no HGRVs is that APOBEC3G stops it. This paper directly attacks that premise. Or have I misinterpreted your comment (likely).
Do you have any references that show MLVs doing this, that I could use? Does anyone?
I don't think we have VP-62, though that is not what I'm saying there. VP-62 is a chimera pieced together from multiple sources. It is very likely the envelope is significantly different from the envelope of the virus in 22Rv1. This is particularly relevant to arguments about detecting antibodies.
What you stated there was what I meant. The confusion may be due to uncertainty about which criticism I was talking about.
Cell-to-cell transmission is well documented in a number of viruses, so I don't count that as special pleading. I don't have references handy concerning MLVs, but there is a huge literature to search. It definitely takes place with HTLV, another retrovirus infecting immune cells, as referenced. That is also a situation where the ratio of latent to active virus is high. If I happen across a specific reference for MLVs I'll post it. In mice there are plenty of free MLV virions, so this mode of transmission may be less important, and harder to detect.
I'm trying to say that assumptions about detecting free virions may be convenient, but unjustified. Once a retrovirus gets into mobile immune cells the possibilities for further transmission within an infected individual, without free virions, increase dramatically. Transmission to other individuals is more dependent on free virions.
This has a bearing on efforts to treat HIV-1 infection. Current treatments are fairly good at stopping transmission to other individuals, but don't come close to eliminating infection.
Did everyone also read the comment by Dusty Miller concerning this study? He questions some of the conclusions. The science is above me, so I have no idea if his points are valid or not.
Good pick up Jemal.
I am not sure, but it seems he is not disagreeing that the virus does replicate, but is disputing the use of the term "efficient", hence the rate of replication. A somewhat arbitrary point if any replication whatsoever causes pathology.
I cannot help but think his response is just to muddy the waters.
Hi RustyJ, the Dusty Miller comment is the point I have been making all along. Restriction factors slow and limit. They do not stop. Sure, given enough time in a non-replicating cell-free viral sample they will eventually attack all the virus, but a replicating virus that is incorporated into the genome and not silenced by methylation or another mechanism could still pump out more virus if infected cells are present. Further, cell to cell transmission will allow virus to avoid blood restriction factors, so it then depends on what each cell type can do. In addition the main route of infection is likely to be via mucus membranes, including nose, mouth, gut and lungs. If there are cell types in there that have reduced resistance, either due to dysfunction from whatever cause or simply lower restriction capacity, then they offer a route of entry.
It might only require one virus to successfully infect a person.
So these facts mean that the infection rate is low. This however is deceptive. How common are these pathogens? With a very low rate of infection, but a very high prevalence of pathogen (I am referring to all MLLVs, not any one) then some people will be infected on a regular basis. In many cases the immune system will detroy it (by destroying the infected cells) but this will not always be the case.
So I expect MLLVs, should they ever be clearly validated as infecting people, to infect at a low rate, to infect across a wide geographical area based on viral prevalence and immune compromising risk in those areas, and to spread through tissue (not blood) in a very slow fashion. This means that runaway short term epidemics are rare, and might require something as a viral source (e.g. contaminated food) or as an immune toxin (e.g. mold, other poisons), or both. The old observation that sporadic ME is ten times more common than epidemic ME fits this interpretation. I am not even going to bother addressing incubation periods for ME epidemics, I have answered that so many times now.
Also, I suspect that if MLLVs are ever shown to be infectious to any human population it will be many different kinds, not one, for a large enough population (e.g. country). For there to be only one some additional mechanism must be involved.
Thanks from me too Jemal. I don't know how you pick all these up but am pleased you do. I had only just received the full paper as it happens - not even looked at it all yet - and I had no idea there was even a comments section attached to this Journal! What a muppet
There still - from my perspective - seems to be some confusion about all these studies when it comes to terminology and generalisation.
I mean this one is about XMRV [period]. And whilst scientists might infer that similar processes occur with other MLVs Miller and the authors and ourselves should perhaps stick to the subject in hand, no?
'This report claims two major conclusions (last paragraph of Abstract):
1. XMRV replicates efficiently in prostate epithelial cells by downregulating A3G expression.
2. Our data suggest a novel mechanism by which retroviruses can counteract the antiviral effects of A3G proteins.
Neither conclusion is supported by the data.'
This is where I would have needed to consult a scientist lol.
I cannot and would not attempt to interpret such data, so I am glad those with the expertise do - I would expect nothing less of them.
I do hope Miller's concerns prompt a response from the authors I really do. I mean this is how science proceeds, no? Anyway, am glad he said what he did but I shall still try to read the whole paper myself.
'Many publications to date have shown that XMRV can be mutated by APOBEC3 proteins (A3A - A3G) present at various levels in human cells.'
THIS is the point I believe.
Inject or observe XMRV into blood or cells and APOBEC3 (believed to attack viruses including retroviruses) will mutate (alter) the retrovirus to such an extent as to render it ineffective, defunct, dead.
The question seems to be - to what extent APOBEC affects XMRV, and whether what (assuming something does) remain - is capable of doing it's assumed nastiness even after having been bashed about, no?
'Sequencing of the RNA genomes of XMRV viruses produced from particular human cells shows that some genomes are intensely mutated (hypermutated) while others show only background mutation rates likely due to errors in reverse transcription.'
Again to my layman's eye this also seems key. Within XMRV and once APOBEC has smashed into it - some of the nasty bits of the virus are affected to a much, much greater extent that others. And they seem to know - roughly - to what extent this occurs:
'Rates of hypermutation vary for viruses produced from different human cells, from almost none for XMRV produced by 22Rv1 prostate cancer cells (Paprotka et al., 2010), to ~25% for DU145 prostate cancer cells (Paprotka et al., 2010)...'
This next is for me also key:
'...to almost 100% for virus produced by human peripheral blood mononuclear cells (PBMC) (Chaipan et al., 2011).
The results obtained for human PBMC clearly show that XMRV is not able to circumvent the effects of A3 restriction in human cells.'
Now from my point of view - as a human - that's a good thing, right? I mean isn't that saying that my blood (assuming it is doing its' job) smashes the bad bits of XMRV to death? You see I ask because I am not sure but I think that is what is being said - that XMRV in human blood is enveloped by APOBEC to such an extent that the virus is so mutated as to render it, well, harmless I guess. But questions remain of course...
The main ones in relation to this paper appear to be the conclusions drawn from their study of prostate cell responses.
Whereby XMRV rather than being rendered unrecognisable is somehow able to replicate most effectively in two (?) cell lines by avoiding the APOBEC response (or the bit that would normally smash retroviruses). Which is kind of like I guess what HIV does, isn't it?
Miller offers an explanation and a way to check that what he is offering is correct:
'Lastly, there is a simple explanation for the decrease in A3G levels the authors report; that A3G packaging into virions, which is required for virus hypermutation, is responsible for the decrease in cellular levels of A3G. This possibility would be easy to address by assay for A3G associated with XMRV virions in the cell culture medium. If so, there is no reason to propose an A3G regulatory mechanism involving XMRV.'
At this point a response from the authors would be most welcome I should think, indeed here too:
'What about the authors' second major conclusion, that their findings suggest a novel mechanism by which retroviruses* can counteract the antiviral effects of A3G proteins?
The mechanism, if any, is certainly not robust, and its existence is not supported by the data provided.
At the very least, the authors should measure A3G mRNA levels in infected and uninfected cells to see if XMRV might be regulating A3G transcription, which would suggest the production of some transcription factor by XMRV, and might provide some support for the suggested regulatory mechanism.
This experiment is critical for the authors' claim that XMRV downregulates A3G expression.'
Note: Please do let me know if my attempts at simplification through use of common language above is 'wrong'. As I said I do find the complexities of all this science rather confusing, and whilst interesting, I don't think it can always be seen to draw the cast iron conclusions that might be perceived elsewhere. I think science is fluid and a continuous learning process - well hopefully
(*I haven't read the paper as I said but Miller's reference to 'retroviruses' in this context might be taken literally to mean ALL retroviruses but I don't think so - I think he/the authors mean something perhaps unique to XMRV. But I don't know.)
My question is if Miller is saying that XMRV does not replicate efficiently in prostate cancer cells or is he just questioning the mechanism cited by the authors used to come up with their conclusions but he believes they do replicate efficiently. Either, none, both?
I am probably showing my ignorance here but Miller's rebuttal reads to me that he is saying XMRV does not replicate efficiently in prostate cancer cells. This is very difficult reading/ process and I'm not sure if my above questions are even relevant.
Just thought of something. Maybe I need to look up Miller's previous studies?
Hope this makes sense.
I also thought Miller's response was a little unfocussed. As Firestormm mentioned above, the mechanism of downregulation is being disputed by Miller. As for the rest, I did read it to be a disagreement over the rates of replication, or at least how those rates were derived. However, whether XMRV efficiently replicates or not, it still replicates. Miller's response is, in effect, an acknowledgement of that point and essentially supports the contention that XMRV can replicate, despite APOBEC3G.
I essentially agree, Alex. However I suspect that amplification events involving the hypermutated virus and subsequent MLV infections may play a greater role. This may be one explanation for both epidemic and non epidemic situations. The Hackett paper used the word 'surprised' (I am relying on memory here) when describing the amplification event in the macaques. I think this mechanism will be the key to a great many questions.
But if XMRV is a contaminant/benign, does it really make a difference? Just asking.
Hi barbc56, yes, even then, this is why. First, XMRV probably doesn't infect people, though we await Lipkin et. al. and future prostate cancer studies to be certain. Second, it could indeed be benign - but we do not know that.
Here is why its important. Its about RISK MANAGEMENT. Lets assume it is finally proven beyond any doubt that XMRV does not infect any person, and that even if it did its totally benign. So we ignore it. Then the next pathogen thought to be in a similar situation comes along. Fine, we have a precedent. Ignore that too. Then the next. Then the next. This is a numbers game. At some point if this is standard policy we are going to ignore something nasty, maybe something very very nasty. From a risk management perspective its a bad idea. From this perspective a suggestive or weak probabilistic argument for non-infection or non-pathogenicity is completely inadequate. We need strong data from well designed studies to say something is sufficiently low risk to be ignored. Otherwise we are gambling with human health ... which so many government agencies have been doing with ME by the way, regardless of the cause. So those saying that weak evidence should preclude further study are either ignoring or unaware of the risk this establishes. In time that risk is going to bite a whole lot of people very severely.
I don't really buy into that. If evidence proved otherwise, science would pursue it. Should we still be pursuing the theory of alchemy simply because there is a minute possibility of this happening, even if it's not probable with the scientific information we have today?
Risk management is a good model, however I think the science has moved to the point showing the risk is not there. Whether XMRV or whatever it's now called should still be studied or not is a separate issue.
But like you I await the Lipkin study.
Barb C. :>)
I like to think that studying XMRV as a novel gammaretrovirus will lead to a greater understanding as to how and why it functions and what its' limitations are. And yes, is it even capable of a) infecting humans in vivo and b) what possible disease could it cause and c) yes, is it capable of causing human disease (and if so what and how and to what extent i.e. probability).
Of course should another paper ever be published establishing an association with human infection and more importantly with my condition - then my interest would be piqued even more! But I don't think that is very likely - though one can never discount it - or some portion of it - I don't suppose.
XMRV might also be a candidate for - dare I say it - gene therapy I suppose. Whatever - it has been a fascinating opportunity to watch the discovery of a new virus, the currently accepted explanation of how it arose, and to see how it operates/might operate. Will have to see how the research progresses now.
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