Few days ago I was talking to a friend about the outbreak of Black Plague and he explained me an interesting theory according to which Plague became less common 'cause of the diffusion of grey rats that substituted black rats (Grey rats' fleas when rats die move to other rats and not to humans therefore Plague cannot spread.).

(Assuming he was right.)
What if grey rats' fleas moved to humans as black rats' ones?

Plague (Bubbonic? Black?) Strikes Back during the Thirty Years War or the Wars of the Austrian/Polish/Spanish succession?
What about the Seven Years War?
More Europeans colonizing the Americas in order to escape the disease?
Is it possible to have butterflies delaying Plague vaccine?
 
A big fact is that we all have some inate resistance to diseases, some more than others, some to different diseases.
Also, once you had a disease and survived, it's harder to suffer from it again as your antibodies know it already.

With that in mind, the first waves and resurgences killed all the weak ones, people without defense against that strain. Interestingly enough, it came back every so often and always killed the younger people, the ones that did not live through the previous plague
 
Brown rats became dominant in Europe in the XVIIth-XVIIIth century, with plague epidemics still popping out in Europe in the XVIIth-XVIIIth centuries (such as the Plague of London or the Plague of Marseille) without much rupture.
The main difference with these epidemics is that the experience of the great plague and accumulation of sanitary measures since then did managed to prevent them to widespread regionally contrary to what happened in Asia after the XVIIIth century, with the Plague of China

Assuming that, for any reason, a plague epidemic in Europe devellops from an IOTL one (and frankly, you have only to pick one), it would indeed be more feasible in a region devasted by war (such as the TYW)and might have quite interesting consequences, but I don't think it would be enough for a whole pandemic/second wave of the medieval pandemic at this point, without people suddenly forgotting about what they did IOTL.
 
Just to clarify it immediately: I wasn't thinking about anything of continental dimensions, I was just wondering about something like a German Plague or a Polish Plague.

Also, brown rats like humid environments (Black rats don't.). What about XVIIIth century expanding cities (And public Sewerages too.) and the increasing unemployed poor urban population?
 
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