Here's a rare instance where I get to contribute to AskHistorians. I am a biologist and so tend to look at the world through that lens. This conversation got me wondering if there is any genetic information about the plague, specifically Y. pestis, and it's evolution over time.
The Yersinia genus consists of 15 species, 3 of which are pathogenic to mammals. Y. pestis divereged genetlically from it's common ancestor, Y. pseudotuberculosis sometime in the last 1,500 to 20,000 years. Big gap, I know. History as it relates to genetics isn't as precise as history as it relates to humans.
The interesting thing here is that Y. pestis made a massive change when it diverged. Y. pseudotuberculosis is primarily an intestinal infection where as Y. pestis is a blood-borne and very deadly infection. Even among these two species of Yersinia, there are subsets known as biovar. Interestingly, the biovar in the Americas is different from the one in China, Mongolia, and the former Soviet Union. Let me clarify a bit, there are all Y. pestis. They are all the bubonic plague, but they are genetically different from each other to the point that we can tell them apart.
Here's the source for everything so far: http://iai.asm.org/content/77/6/2242.full
Now I just need to see if anyone has looked at the history of these different biovars and where they've come from.
Paydirt! And Nature no less. Nature is one of the top peer reviewed research journals. Source
This group sequenced Y. pestis from plague victims buried in a cemetery in East Smithfield around 1349. You can read the mumbo-jumbo if you like, but they got good sequencing results from these samples.
When this ancient sequence was compared to the current reference strain, only minor differences where found. (Reference strains are used in biology as a reference for comparison and are typically considered normal or prime. The idea is that they are elevated above other non-reference strains.) This is interesting outside of the historical context. ~700 years and little genetic change is pretty neat.
Based on differences in the genomes of the Y. pestis in East Smithfield and other acient sources, the group suggests that all Y. pestis capable of infecting humans shared a common ancestory around 700 years ago (1282-1343). This doesn't really answer the question posed in the origianl post, but it does suggest that all current plague came from the medivial plague. Or to quote the Nature paper:
This implies that the medieval plague was the main historical event that introduced human populations to the ancestor of all known pathogenic strains of Y. pestis.
They also speculate on the Justinian plague:
This further questions the aetiology of the sixth to eighth century Plague of Justinian, popularly assumed to have resulted from the same pathogen: our temporal estimates imply that the pandemic was either caused by a Y. pestis variant that is distinct from all currently circulating strains commonly associated with human infections, or it was another disease altogether.
And now I'm hitting a paywall and am not at work. If anyone has access to this article: http://www.nature.com/ng/journal/v42/n12/full/ng.705.html, it looks like they may go into some detail on the global diversity of Y. pestis. I'll see if I can get access to it later today and reply.