|Image Source: “Chinese Smallpox Inoculation” (or. image c. 1911), The Historical Medical Library of The College of Physicians of Philadelphia, History of Vaccines Project (2012).|
Few diseases have caused as much misery and death as smallpox. Smallpox has a 30% mortality rate in normal conditions, but in populations unexposed to the plague the death toll upon first contact is much, much higher. Originating in the urban slums of agrarian Eurasia, its presence was an accepted part of life in the great cities of Europe, the Middle East, India, and China. The peoples of the New World, Australia, and the Pacific Islands were blessed to live free of the disease for most of their histories. Contact with Europeans was first contact with their distinctive diseases; in many ways the history of European expansion across the globe is the story of one smallpox epidemic after another, missionaries, merchants, and conquerors bringing the dreaded disease wherever they roamed.
Resistance to the deadly maladies of the Old World has been described as one of the defining advantages of Eurasian civilization, but this tale is not unique to the European expansion. Not everyone in pre-modern Eurasia lived so intimately with illness and misery. Many peoples living in the cross roads of the Old World lived just as isolated from the filth and sickness of Eurasian urban centers as islanders living oceans away. Historian Peter Perdue explains:
Most notably, Central Asians remained nearly isolated front the European and Asian disease pools until the eighteenth century. Then smallpox, among other diseases, decimated the Mongolian population when it came into contact with Chinese settlers, just as Native American and Oceanic populations died off after the European conquests of the New World.
Mongols knew in the mid-fifteenth century that they could catch smallpox from the Chinese, and the Chinese in turn warned them not to settle too close to the border to avoid spreading it. The Ming dynasty held only sporadic horse fairs where Mongols and Chinese mingled; then Chinese bans on frontier trade in retaliation for nomadic raids had as a by-product the effect of protecting the Mongols from infection.” Chinese migrants who went beyond the Great Wall, however, could also spread the disease, and there were more than 100,000 of them in southern Mongolia by 1590. Still, few Mongols caught the disease under the Ming.
The Manchus, before the founding of the Qing, also rarely encountered smallpox, but they knew of its danger. Mongols and Manchus who had not been exposed to the disease were exempted from coming to Beijing to receive titles of succession. The main response of the Mongols and Manchus to those who did fall ill was quarantine. Li Xinheng commented that if anyone in a tribe caught smallpox, his relatives abandoned him in a cave or distant grassland. Seventy to 80 percent of those infected died. The German traveler Peter Simon Pallas, who visited the Mongols three times front 1768 to I771, commented that smallpox was the only disease they greatly feared. It occurred very seldom, but spread rapidly when it struck: “If someone catches it, they abandon him in his tent; they only approach front the windward side to provide food. Children who catch it are sold to the Russians very cheaply.” The Mongols whom Pallas visited lived far from the Chinese border, but they knew well that smallpox was highly contagious and nearly fatal.
The Chinese discovery of variolation-a method of inoculation-was of great aid in reducing the severity of attacks. The Kangxi emperor himself was selected as heir in part because he had survived the disease in childhood; his father had died of it. In 1687 he inaugurated regular inoculation of the royal family, and his successor extended mandatory inoculation to all Manchu children. The Manchus adopted this Chinese medical practice in order to protect themselves against the virulent strains that were absent from the steppe. Only Manchus who had survived the disease were allowed to be sent to the Mongolian steppe. Mongols close to the Manchu and Chinese border gradually grew immune, but those farther away suffered great losses in the nineteenth century when Chinese penetration increased. 
As was the case with the European conquests and expansion in the new world, smallpox played an important role in the Qing Dynasty’s conquest and expansion to the west:
Disease determined critical turning points in the conflict between the Manchus and Zunghars. Ligdan Khan, the first major Mongol rival to Manchu rule, died of smallpox. In 1745, when the Zunghar Khan Galdan Tsenen died, outbreaks of smallpox caused upheaval among the Zunghars; one report stated that 30 percent of them died. Another epidemic struck Zungharia in the 1750s, just as the Qianlong emperor launched his final campaign. The last rebel against Manchu domination, the young prince Amursana, died of smallpox at the age of thirty-five, opening the way to the complete conquest of Xinjiang. Wei Yuan estimated, after the Zunghars had vanished as a people, that 40 percent of them died of smaIlpox—more than lost their lives in battle or fled to Russia.
The Mongols for their part tried to avoid contact with Han Chinese as much as possible. Apparently they never learned the variolation techniques, so their only recourse was isolation. When negotiating licensed trade with the Qing in the 1740s, Galdan Tseren feared that his envoys would catch the disease when they passed through Chinese territory, so he asked for permission to avoid the northwestern towns of Hami and Suzhou and instead go direct to Dongkeer. Tibetans also tried to avoid traveling in the Chinese interior: the Panchen Lama used his lack of immunity to smallpox as an excuse to avoid an audience with the Kangxi emperor in Beijing. The Manchus themselves often tried to accommodate the Mongols in order to spare their lives. ‘The Kangxi emperor noted that many surrendered Mongols living in the capital were dying of diseases. He pitied them he cause “the capital’s food and drink are against their nature,‘ and they were “like caged birds and animals.” so he provided them with tents and settled them beyond the wall in Zhangjiakou and Guihua. When Mongol children flocked to Kangxi’s military camp in the Ordos while he was on campaign. called in a special doctor to inoculate them.
….The vulnerability of the Mongols to smallpox is eloquent testimony to their isolation from the germ pools of dense populations. At the same time, their constant contacts with the Manchus and Chinese made them aware of the danger, even though they could not prevent its incidence. The Manchus, by contrast, could take active measures against the disease, having closer regular contact with the Chinese, greater medical knowledge, and greater acquired immunity. They in turn used this knowledge to inoculate Mongols who surrendered to them, leaving those who resisted them to face the ravages of the disease. The disease environment itself significantly affected the outcome of the conflict, but the disease vectors acted through human agency.
Dr. Perdue slightly exaggerates his case–disease has traditionally been the most frequent cause of campaign deaths for armies the world over and is hardly extraordinary here–but his description points to an unappreciated attribute of traditional nomadic societies. The Mongols and Manchus had little resistance to diseases like smallpox because they were not normally exposed to diseases like smallpox.
For several millenia historians have tried to explain the generally superior strength and endurance of steppe warriors, often focusing on the demands of life in the saddle or the nomads’ protein-rich diets as the explanation for their vitality. A more powerful explanation may be the absence of the debilitating and deadly diseases of settled life among the peoples of the steppe.
 Peter Purdue. China Marches West: The Qing Conquest of Central Eurasia. (Cambridge: Harvard University Press, 2009). p.47.
 ibid., pp. 47-48.
What puzzles me about this is that it appears as if smallpox spread much more rapidly and virulently in the New World, outpacing the movement of European colonizers. By contrast, from this account, it sounds as if steppe nations like the Mongols and Manchus were exposed periodically to smallpox epidemics over an extended period of time.
Also, why would the Mongols have not been exposed prior to the Ming Dynasty during the Yuan?
While smallpox did outpace European colonizers in the Americas, "exposed periodically to smallpox epidemics over an extended period of time" describes what happened to Amerindian populations as well.
For example, see this table of all the different epidemics that struck the Valley of Mexico between 1518 and 1623. Of the ten epidemics listed, at least four of them were smallpox. On a similar vein, the best studied New World smallpox epidemic occurred in the 1770s, long after the first European colonizers arrived.
While there is substantial evidence that Eurasians-through centuries of contact with virulent diseases-evolved a more robust immune system than Amerindian populations (see the same book linked to above, p. 116-122 for a good introduction), what matters most is the immunity a population gains from constant exposure to a disease. This is why people occasionally voice concern about a smallpox epidemic in the future-though most of your ancestors were probably exposed to the diseases at one time or another, you and I have not been so exposed, and are thus quite vulnerable should another outbreak occur. The same principle applies to the Zunghar Mongols.
The Mongols of the Yuan period probably suffered from many deadly urban diseases – the Black Death's first appearance in Western chronicles, for example, was during the Mongol siege of Caffa, during which the Mongol camp besieging the city fell victim to the plague, prompting the Mongols to retreat–but not before they catapulted the bodies their dead over the city walls.
So Mongols of the 1300s probably had plenty of exposure to the diseases of urban civilization. I suspect after they retreated back to the steppe during Ming times opportunities for exposure shrank and new generations grew up without ever encountering the disease, leaving us with the situation Perdue describes.