Speculation

This is one possible scenario – don't know how likely it is.

Someone at W labs contaminated the patient samples with plasmid. Either Dr. M or Dr. L did it.

Dr. S was duped into doing some PCR&sequencing with samples contaminated with plasmid. But most PCR&sequencing was done at W labs, or at the Genomics Center of the same university of which W labs shares the campus. I think neither Dr. S, nor the Genomics Center did anything wrong except being duped.

Dr. R and his lab got on board to do the serology once the PCR was already going (don't know, needs checking) and showing positive patient samples by PCR. But one possible scenario was that Dr. R's lab didn't find positive serology. So if X was a real pathogen, and they fudged the results to show positive serology, nobody would ask questions how correct the results were – history would prove them right, after all, and they'll get fame and fortune. This would not have been necessarily been Dr. R, it could have been a postdoc feeling the pressure to come up with positive serology results.

Now let's look at Dr. L. He had a strong incentive to come up with the diagnostic test for X at V labs. If he was the one doing the plasmid thing at W lab, he knew what to do at V lab. If on the other hand Dr. M did the plasmid thing at W lab, he would be under pressure to come up with a test at V lab that would produce positive results.

I think Dr. M works alone. It is my impression that Dr. M does not play along with others. Whatever Dr. M did, I think she did not coordinate with Dr. L. And if Dr. L did it, he would not have told it to Dr. M – that's for sure. So did it Dr. M dupe Dr. L? Or did Dr. L dupe Dr. M? Or did they both do something independently, duping each other?

Dr. L was either really stupid and got results at V lab by accidental contamination – something I can't rule out. Or he must have known what was going on.

Dr. M showed initially 100% confidence in the results of V lab's testing, but after being fired discard the results of V lab. Equally, Dr. M showed initially 100% confidence in the results of PCR&sequencing, but then discarded the results of PCR testing and sequencing. The only thing Dr. M seems to confident of is the serology done at Dr. R's lab – Dr. M basically discarded everything done by Dr. M or Dr. L, done at W lab or done at V lab.

I think Dr. M knows that everything done at W lab or V lab was fake – and Dr. M does not know what happened at Dr. R's lab – that is why Dr. M thinks that X/M/P/whatever is a human pathogen, because Dr. R's lab found something. But as shown above, that could have been Dr. R's lab just playing along and fudging the results for fame and fortune.

So who was it? Was it Professor Plum in the library with the candlestick? I guess we'll need to have a bit more information first…

[Update]
Plus, we should factor in the housing crisis that started in 2008 (and the problems were felt at least one year before) and probably affected the W's and put pressure on the W lab.