From a comment I posted on the Virology blog:
There seems to be an assumption that contamination and a wild-type virus are mutually exclusive hypotheses. A wild-type virus would be very likely to result in contamination prior to discovery. Contamination, by itself, does not distinguish competing hypotheses. Rather than plunge into the immediate debate I would like to offer a broader perspective.
Perspective: There is a certain purity and clarity to research which avoids all contact with diseased people, and there is a need for fundamental research on biology. Unfortunately, we have great uncertainty about many basic questions in biology as shown by changes in the field in the last 20 years. Our present understanding is unlikely to remain unchanged for so long.
We also have real public health problems to deal with. Many of these seem currently intractable. There is good reason to think our ignorance and that intractability are related.
Biomedical research has progressed largely through attention to specific examples. Polio might have been overrated as an epidemic, but there is no question the problems it posed led to a revolution in virology.
This brings me to questions about contamination. Assume, for the moment, there are undiscovered pathogenic viral infections, of whatever type, in the wild in humans. Assume we have no test assays to detect them at present. In this situation, researchers working with tissue samples from diseased people will have laboratory contamination. To avoid this they would have to avoid those patients. This is a good way to avoid criticism, but not good policy for investigating disease.
Prior to about 2004 there was simply no assay to detect XMRV. Stipulate there may have been such virus in the wild and the above situation would obtain.
One way to guarantee you have no contamination is to avoid finding any new pathogens. You will also likely avoid finding ways to treat pathogens.
Alexander Fleming was once shown a gleaming new laboratory. His host said, Think of what you could have discovered with such facilities! Fleming replied laconically, Not penicillin.