According to Guns, Germs, and Steel, why did Eurasians have an advantage when it came to germs?

     The relative geographical isolation of North and South America may have given some early advantages to its inhabitants.  These isolated land masses protected their inhabitants from many of the epidemics that ravaged the Eurasian land mass throughout history.  The diseases in Eurasia spread quickly and effectively through trade and proximity to livestock. 
     The Silk Road in particular is thought to be a major vector of transmission in Eurasia.  No such intercontinental trade route existed in the Americas.  Until the Colombian exchange Eurasian diseases stayed in Eurasia and American diseases stayed in the Americas.  As is often the case this advantage was limited and ultimately proved more advantageous for European colonists. 
     When these two cultures began contact and trade the Eurasians had a much more expansive set of diseases and the related immunological responses.  This proved quite advantageous for Eurasians as the diseases would often spread in advance of the primary colonization effort decimating the Native American populations.  While Europeans would still contract these diseases their longer generational exposure provided them a much more protection.  This often left European colonists cultivated lands seemingly prepared for their benefit without any inhabitants.  

The answer to this, like most of the answers in Guns, Germs, and Steel, has to do with geographical advantages.  The Eurasians had better geographic luck.  Their luck gave them many domesticated animals that lived in close proximity to them.  The infectious diseases that the Eurasians carried came from those animals.
The Eurasians carried the germs for infectious diseases where Native Americans and other people did not.  This was because the Eurasians lived very close to their domesticated animals.  Germs from the animals would pass to the people and eventually become infectious diseases.  Table 11.1 on p. 207 shows us a number of infectious diseases that started out in domesticated animals and passed to people.  The Eurasians carried these germs, but did not all die from them because they had gradually developed some resistance to those diseases.  The people of other regions had not developed immunity and tended to die of the diseases in huge numbers.
So why did the Eurasians have domesticated animals while others did not?  Here, the answer is geographic luck.  In Chapter 9, Diamond discusses the fact that most of the kinds of large animals that exist in the world have proven to be unsuitable for domestication.  Table 9.1, on pp. 160-1, shows us that only one of the 14 most important large domesticated animals was native to a place other than Eurasia.  Because of this, people from other regions of the world could not live in close proximity to domesticated animals and could therefore not develop the kinds of germs that the Eurasians carried.  This is why the Eurasians had an advantage over others when it came to germs.