Substitute chickens for rats and Avian Flu for Bubonic Plague and Read This. The statistics are scary–30% of people died in the Middle Ages, like it’s predicted to happen now. Yet people built up immunity to the plague. The plague came in "waves". Given the fact that the rat/flea theory isn’t holding much credence these days, could people have been stricken by something like the Bird Flu? Poultry was everywhere, and widely traded in the Middle Ages. It’s not beyond the pale.
And just as in the fact that Rats really couldn’t have spread the plague far and wide by migrating–just isn’t possible to cover the areas as quickly as the disease spread–so too is it less likely that Migrating Birds will spread the Avian Flu far and wide. It takes Human intervention to spread disease far and wide. Transportation of the carrier. By their very nature, backyard poultry flocks and wild birds migrating are isolated. So while they may cause pockets of infection, here and there, it will take more than that to "fill in the blanks".
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I thought you might find this interesting as well. I work for JHU and saw this one our site a week or so ago:
http://www.jhsph.edu/flu/1957_Asianflu.html