I'm not sure I understand your reasoning here. What Paprotka et al did was trace the origin of 22Rv1 and their data is compelling. They then infer that because the sequences submitted by the Mikovits group are so similar to 22Rv1 then what they are picking up us 22Rv1 contamination. BTW even though Lombardi was the lead author on the original paper Mikovits is the PI and it's usual to refer to the work as hers.
Hi RedRuth, there is now compelling reason to suspect that this virus is easily transfered from cell culture to cell culture. MLVs have been found in many cell cultures. In a much earlier post I speculated that using only moderate assumptions, but indeed a string of such assumptions, the possible number of recombination events for related MLVs in the last century is about ten to the eighteenth. I would have to be out by more than six orders of magnitude to be wrong in my conclusions, but this implies that there is a good chance XMRV has arisen many times. These viruses are vertebrate viruses, we put too much emphasis on mice, although mice do seem to be a natural vector, with the exception of XMLVs.
If you start with the presumption there is no other XMRV out there, and people are not infected, then the ten to the twelfth calculation looks reasonable. However, if you start with the presumption that XMRV and related viruses are common and can be carried by people (perhaps even if they are not infected, but transfer on their clothes etc.), then you get a different result. Either way is begging the question, and I would prefer to see better evidence.
Which is more likely: that the XMRV virus arose in this one culture in a freak accident, or that the culture was contaminated with XMRV due to vulnerability? Given the ease with which we know MLVs can contaminate culture, I suspect it was contamination of the culture, and not the first time it was created. This is not proof of course, its just a suspicion, but it puts reasonable doubt on the origin claims.
If Switzer would do a follow-up paper to show how other MLV strains can recombine to make XMRV, this would increase the doubt. So far he has only made a vague claim in one paper, so I can't tell if it is accurate.
I have studied some recombination theory a long time ago, almost completely forgotten now, in association with genetic algorithms. What I do recall is that the combined computational power of any substantial subset of the global biome is immense. I also know that these recombination events and their power is not based on chance. There is subtle selective pressure that can turn very low probability events into moderate probability events. Given the size of the biome, and the inadequacy of probabilistic methods for this type of argument, I am not impressed with the probabalistic part of the Paprotka et al argument.
Paprotka has put forward an hypothesis. It might be right, but there are reasons to think it might be wrong. I have no problem with anyone claiming this as a supporting argument toward a recombination claim, but the way it is often commented on puts undue emphasis on it.
There is a further point is worth mentioning. The probability calculations by definition are based on an assumption of equal probability of each potential event. Genetic directed search aside, MLVs have been infecting mice for a long time, and MLLVs have been infecting vertebrates for a long time. I have not researched when this is supposed to have started - what is the timeline for MLVs? That could be interesting. In any case, the entire MLV biome subset will have a long history of co-evolution not just with vertebrate, mammalian and primate species, but with each other. Structure will tend to optimize over time, and some of that will be for optimized evolutionary crossover in an attempt to avoid immune defense. This makes recombination at a whole biome level of MLVs a less than random event in itself. The whole notion of a species of virus is highly problematic - there is too much emphasis on XMRV at the expense of all MLVs.
I think there is a good chance the culture discussed by Paprotka was contaminated by live virus. What level of biohazard security were they using? What about that we already know that MLVs can contaminate cultures under reasonable security? Were any of the lab workers tested for MLVs or XMRV - I seriously doubt it as I don't think this was considered a risk back in the early 90s, at least in part because earlier studies had failed to find any evidence of MLV infection in people.
I am prepared to accept Lipkin's findings unless they are somehow ambiguous - clear results are good, either way, but we don't need more results that are problematic.
This doesn't mean that Paprotka was wrong about the original source of XMRV by the way. It just means that the virus might have arisen from MLV infections and recombination in wild mice or even other species many times - murine endogenous viruses are a quiet reservoir.
All the arguments so far are not conclusive in my view. They are all "maybe" arguments, with alternative explanations. Given the importance that a new human retrovirus could have, especially being ignored for a very long time, we need to be as certain as we can be. Proving that XMRV and MLVs are not infecting people, whether or not it is pathogenic, would be a good start. I just don't want us to stop before the evidence is more clear.
Bye
Alex