I am really not here do debate the XMRV(/HGRV) hypothesis (I don't even have access to this paper

), but there is something that I feel needs mentioning in the context of the discussion of this paper.
With some experiments you could at least entertain the thought that scientists had been messing with the samples/data (although I personally don't subscribe to these ideas). However, even if you truly believe this to have taken place with some of the XMRV research, this study would still be a whole different ballpark.
Why? Because all the experimental data that was used to do the analysis in the paper is freely available to everybody in the world.
Remember, Lo/Alter, as well as the Lombardi team, performed phylogenetic analysis to substantiate their respective findings. The thing however with the Lo study is that Lo/Alter only performed phylogenetic analysis on the
original samples. I am not critiquing this here by the way, as this choice was understandable: they retested the patients only after they found out about the conflicting CDC study. And because they felt the paper shouldn't really be held up any longer and the retesting results (apparently) confirmed their findings, they published their paper without doing a new analysis involving
all of the found sequences.
Now, Lo/Alter are still free to do this. Lo/alter have the means and knowledge to do so. Mikovits is also free to do the analysis on her computer(s), as well as Ruscetti or any other scientist you do consider to be trustworthy. Even Gerwyn or somebody from the forums can give it a try. If any of these people could show that these reported conclusions are faulty by simply running them through
one of the many free phylogenetic computer programs of their own choice, this new study would be instantly regarded as a waste of space by the scientific community and the authours would be exposed as the incompetent/dishonest people that they then would be. It would be even worse for the authors if someone could show that the use of the same program (that was probably written way before the whole XMRV controvery) would or could produce very different results than these authors reported. And even if Alter/Lo/Mikovits or anybody else would "just" show that these results are ambiguous in the sense that only a very specific set of parameters could
possibly lead to the conclusion that the old Lo/Alter sequences are ancestral to the newly found sequences, they would put serious doubt on the validity of this study.
It therefore makes no sense to me at all that the authors of the paper here under discussion would/could produce faulty and/or fraudulent results that cannot be trusted.