There are issues with contamination that are worth mentioning again in light of the Shin et. al. study.
Contamination is only a big issue with two testing methods, both of which is based on polymerase chain reaction, PCR. PCR amplifies genetic material - so even a small amount is amplified and becomes detectable if it matches the starting primer. Nested PCR has the potential to further amplify the genetic material.
Culturing relies on PCR testing to identify the virus, iirc. Chance mouse contamination will probably have a small risk (due to being able to test for mouse DNA), this is a major problem only if the contamination is a live virus that can replicate in culture. The problem with a culture is that it is at risk from the environment on more occasions. Otherwise the risk is mostly from the PCR testing itself, because trace amounts of DNA in the culture will be amplified.
DNA and especially RNA are very vulnerable molecules. They are easily destroyed. So old sources of mouse contamination are not likely to be a problem, ongoing sources of mouse DNA is the issue, which means something is continually putting mouse DNA into the lab. Lab reagents are a possibility, but there are many other potential sources. To prove contamination, somebody has to definitively identify the source, lab by lab (because different labs might have different sources). I still think we should consider infected people as potential sources of MLV contamination, mice do not have to be a vector.
Antibody based tests, including immunohistochemistry, have a different problem. They are subject to cross-reactivity. Antibodies typically react to epitopes, small amino acid sequences with a particular configuration. Because these sequences are so small, many different proteins may have the same sequence present. This is why we can get cross-reactivity. These proteins need to be isolated and sequenced in full in order to determine what they are.
Isolation and sequencing of proteins is essential for immunological techniques to be robust. If something binds to your antibodies, it is always possible to use standard techniques to isolate the protein, after which it can be sequenced. If the sequence is a match for a known virus, or family of viruses, you have evidence for that virus, although there is always risk that another virus will have the same protein.
So contamination claims could explain the XMRV findings, but this is much more likely to be contamination from real XMRV than from mouse DNA, if for no other reason than mouse contamination is routinely tested for. I find this extremely unlikely, as the claim is that different strains are being detected - and contamination would most likely be from one single strain in any particular lab. I wont bother discussing the control issue again, as it has already been discussed at length.
Multiple contamination sources are the only way to explain this, although if the source is live, such as a person, they could easily carry multiple strains. Multiple sources will however make it easier to find the source, which makes me suspicious of this hypothesis.
Cross-reactivity could be due to proteins with similar amino acid sequences. It is always possible to isolate these proteins, but I am not sufficienty up to date to discuss the quantities necessary for sequencing. We need sequencing to be sure of the identity of the protein, but there might be difficulty in obtaining enough of any one protein to be able to sequence it. Alternatively this could be a gap in study design due to lack of resources, which includes funding and lab time.
These are all technical issues that can be resolved. It takes time, funding and will to do so. How many labs researching ME/CFS have adequate funding or other resources? I have a strong suspicion that the primary problem we are experiencing with the science is not the science, as this is a tough area of research, but the almost total lack of political will and funding. Its hard to do good science on a shoestring budget.
Bye
Alex
PS Doh, I forgot to get to a major point of this post. Singh has mostly found XMRV in prostate and other cancers using immunohistological techniques. She is finding something, but it might not be from XMRV. Does anyone recall it has been published that these proteins have been definitively identified as XMRV proteins? If the technology is effective at isolating and sequencing XMRV proteins in prostate tissue, there is no technical reason, provided we pick the right tissues, that this can't be done in ME/CFS.
