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Further Reflection and Critique of the 4 Contamination Papers

Angela Kennedy

Senior Member
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1,026
Location
Essex, UK
Yes, mouse DNA is not the same as XMRV. But... Many mice have XMRV integrated into their DNA; XMRV started off life as a mouse retrovirus that lost the ability to reinfect mice cells but is still carried in the DNA of many mice. So if you have mouse DNA there's a decent chance it contains XMRV. Put another way, finding contaminating mouse DNA means that any XMRV detected may have come from mouse contamination, not the human patient. Still, not all mice carry XMRV so mouse dna contamination could in theory occur but not be responsible for postive XMRV findings.


Correct, XMRV itself does not carry mouse DNA (well, it might just pick up tiny bits of it, but not enough to be detected by any of the mouse DNA tests discussed in the Retrovirology papers).

However, my point was that the Hue paper suggested the WPI XMRV findings were contaminants from human cell lines, NOT mice.

Other questions then arise: how many mice are believed to carry XMRV (what proportion?) What else do mice carry that might 'contaminate' labs? Lab mice or wild 'house' mice?

People may not have the answers here, I understand. I'm saying there are so many possible confounding issues going on here, for example other infections that might be just 'mice' contaminations (by their logic)? It's a can o' worms.
 

Jim

Senior Member
Messages
79
how many contaminations?

if xmrv was from contamination in the WPI study, how many products would have to be contaminated? i mean, culture, pcr, antibodies, electron microscope, etc - do these tests all use the same cell lines or reagents or test kits (or whatever materials are used to test all these different ways)? or do any of these tests use completely separate materials that never are shared or come into contact with each other, and thus more than 1 would need to be contaminated?
 

Angela Kennedy

Senior Member
Messages
1,026
Location
Essex, UK
if xmrv was from contamination in the WPI study, how many products would have to be contaminated? i mean, culture, pcr, antibodies, electron microscope, etc - do these tests all use the same cell lines or reagents or test kits (or whatever materials are used to test all these different ways)? or do any of these tests use completely separate materials that never are shared or come into contact with each other, and thus more than 1 would need to be contaminated?

Fair question - one of the bods was carrying on as if mouse DNA was on every surface in the land (or at least the labs)- which raises the question of sterilising efficacy (or rather, non-efficacy) - already brought up on one of these threads. It sounds like the lab mice have wild parties every night in all the labs, rolling all over the surfaces of everything- or wild mice are living it up- while no-one's looking, possibly in the evening?

I know- I'm being flippant. But that was an odd claim. Also - we all know lab mice don't get to party - even before they're 'sacrificed' : (
 

oceanblue

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UK
Fair question - one of the bods was carrying on as if mouse DNA was on every surface in the land (or at least the labs)- which raises the question of sterilising efficacy (or rather, non-efficacy) - already brought up on one of these threads. It sounds like the lab mice have wild parties every night in all the labs, rolling all over the surfaces of everything- or wild mice are living it up- while no-one's looking, possibly in the evening?(

It might be hard to believe for anyone who hasn't worked in this kind of lab, but contamination is a real issue, and not just of mice dna. Everyone in the virology field commentating on xmrv takes the contamination issue seriously, including Judy Mikovits who has stressed the importance of carrying out the work in mice-free labs (that's labs that have NEVER been used for mice-work) and Ila Singh. Contamination isn't some Phantom issue conjured up by those who don't want to belive in a connection between XMRV and CFS; it's a real and important factor. Contamination could explain the xmrv results, whether or not it does explain the results is the key question.
 

Angela Kennedy

Senior Member
Messages
1,026
Location
Essex, UK
It might be hard to believe for anyone who hasn't worked in this kind of lab, but contamination is a real issue, and not just of mice dna. Everyone in the virology field commentating on xmrv takes the contamination issue seriously, including Judy Mikovits who has stressed the importance of carrying out the work in mice-free labs (that's labs that have NEVER been used for mice-work) and Ila Singh. Contamination isn't some Phantom issue conjured up by those who don't want to belive in a connection between XMRV and CFS; it's a real and important factor. Contamination could explain the xmrv results, whether or not it does explain the results is the key question.

We non-lab types might well have to take your word for that Oceanblue (mouse DNA all over the place) - but you have to admit it sounds a little - dodgy? THAT level of contamination? Except on the control specimens? I have a background in nursing, so am very aware of cross-infection issues, but this level of 'mouse DNA' contamination in ALL labs anywhere near mice, on ALL surfaces?
 

oceanblue

Guest
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UK
mouse DNA all over the place... - but you have to admit it sounds a little - dodgy? THAT level of contamination?
Well, I can see where you are coming from!
I have a background in nursing, so am very aware of cross-infection issues, but this level of 'mouse DNA' contamination in ALL labs anywhere near mice, on ALL surfaces?
Part of the problem is that mouse dna is used so widely; mice are just so handy for cloning and expressing human genes. Then add to the mix that with xmrv you are using incredibly sensitive assays because xmrv exists in such low levels. If you were dealing with a virus that was far more abundant (ie exists at higher levels in humans) you could use a much less sensitive test - and such tests would never pick up mouse dna contaminants at trace leves. The problem is that when you push detection technology to its absolute limits contamination becomes a much bigger issue because the technology will pick up even a whiff of anything. i guess it's like dealing with immune-compromised patients who will pick up an infection from the slightest trace of a bug - where another patient wiht a stronger immune system might easily deal with such tiny amounts of the same bug.
 

Angela Kennedy

Senior Member
Messages
1,026
Location
Essex, UK
Well, I can see where you are coming from!

Part of the problem is that mouse dna is used so widely; mice are just so handy for cloning and expressing human genes. Then add to the mix that with xmrv you are using incredibly sensitive assays because xmrv exists in such low levels. If you were dealing with a virus that was far more abundant (ie exists at higher levels in humans) you could use a much less sensitive test - and such tests would never pick up mouse dna contaminants at trace leves. The problem is that when you push detection technology to its absolute limits contamination becomes a much bigger issue because the technology will pick up even a whiff of anything. i guess it's like dealing with immune-compromised patients who will pick up an infection from the slightest trace of a bug - where another patient wiht a stronger immune system might easily deal with such tiny amounts of the same bug.

Ok Oceanblue- thanks for taking the time to discuss this. I appreciate it.
 

Megan

Senior Member
Messages
233
Location
Australia
Contamination isn't some Phantom issue conjured up by those who don't want to belive in a connection between XMRV and CFS; it's a real and important factor. Contamination could explain the xmrv results, whether or not it does explain the results is the key question.


I agree it is an issue that needs to be taken seriously especially because the viruses are carried by mice which necessarily puts a very high onus of proof on those finding the virus to show it is not contamination. But as many people have already pointed out in other places in these forums it is also clear that these viruses can infect people, so no matter how much contamination is around, the question still remains about how many people might be infected.

Thus far the WPI and Lo/Alter seem to have done what they can to exclude mouse contamination except for running the IAP test, which I expect they will have to do. What concerns me is that even if they run this test and it comes out negative then they will still be accussed of contaminating their samples from the 22Rv1 cell line (hard for them to win!). How to prove your samples are not contaminated from this cell line? It seems to me that this would be a thorny problem for any scientist but the only way would be to get consistently different results from patient samples vs controls that have all been treated the same way.

Then again as many have pointed out on the other thread antibodies have been found in both the WPI and Lo/Alter samples, though I'm not sure if they were found in all cases. Patient antibodies might have to become an increasingly important part of the equation in any analysis.
 

Angela Kennedy

Senior Member
Messages
1,026
Location
Essex, UK
Back to the mice DNA, everywhere, again, and the claims made in the negative UK/European studies made at the beginning of this year... Do British and European lab or wild mice have XMRV? Is mouse DNA everywhere in British labs as well?