Jones
is an epidemologist (well, he's a historian of medicine now, but you get the point). Indeed, the supposed mortality rates of 90%-95% would sound insane to an epidemologist more than to any anthropologist. To quote him in
Beyond Germs:
When I first encountered the literature on the Columbian Encounter as a medical student, I was startled by the ubiquitous—and impossible—assertions of “no immunity.” Reading more, I found the work by scholars who emphasized contingency, as well as work in medical anthropology about social suffering and embodiment. When I returned to the medical literature on race, genetics, and immunology, I found more reasons to be skeptical of the simplistic claims made by Diamond and so many others.
Diamond is an ornithologist. There are very good reasons to be sceptical of whatever he says. He has interesting overarching theories but whenever he writes about something I know anything about, all the details he bases his theories on are wrong. But Diamonds claims and research standard is by no means representative of the field, and he should not be assumed to be representative of it.
The thing is, virgin soil epidemics are not a theory. They are an observed, well-recorded phenomenon through modern history. For example, we have very good records of epidemics in late-contacted Pacific populations. Dysentery in Fijii in 1802-1803 killed over 20 % of the population. A Measles virgin soil epidemic in Alaska in 1900 spread from village to village with mortality rates between 25 and 50 % of the population. A study of
contact-related epidemics in Amazonia looked at 117 epidemics between 1875 and 2008, found mortality rates ranging from 1 to 97 %. Seven epidemics had a mortality of 80 % or above. (They also found mortality dropping with the number of years since contact). The average virgin soil epidemic seem to have a mortality of about 20-25 % outside the Americas. Smallpox a bit higher. These are not disputed theories. There is a wealth of recorded facts.
Now you may ask how we get to a mortality of 95 % and above among native Americans, when only about 1 in 25 of the recent contact epidemics have mortalities above 80 % ? Well, all those epidemics were single-disease epidemics. The native americans were subjected to smallpox, measles, diphtheria, typhus, croup, leprosy, influenza, bubonic plague, yellow fever, Lyme disease, Q-fever, dengue, various parasitic diseases, malaria, salmonella (cocoliztli), paratyphus, chickenpox, scarlet fever, whopping cough, etc, etc at the same time or in sucession. And surviving one did not actually indicate that you had any better chance of surviving the next. Often the opposite. Some of the diseases such as measles had immunosuppressant effects and made you more susceptible to other diseases. If you survived.
Additionally, there is a cumulative effect where a large number of people in a society falling ill means there is no one to nurse or feed the sick. Or bury the dead. (Diphtheria virgin soil in Hawaii 1804 "Not enough alive to bury the dead").
See, sometimes when a scientist wants to make a name for him or herself, they try to overturn something established that they feel iffy about. Sometimes that leads to an established paradigm being overturned and science advancing. But mostly it leads to some headlines and later research buring the new notion. As a somewhat relevant example, Cocoliztli was an old world disease that devastated Mexico from the 1500s. It was a fairly classic case of virgin soil from Europe, with contemporary physicians reporting on its selectivity for native Americans with Europeans left untouched, and Africans somewhere in between. Someone published some badly supported theory that it was an American indigenous disease, and had it taken seriously until the genes of the disease got sequenced.
Trying to overturn the idea of virgin soil epidemics... it would take a fantastic amount of results to overturn practically every physicians records from the age of exploration and quite a few from then until now. Now there is a discussion going about how much of a role genetics had in the devastation of the Americas, but they got an uphill battle too, because there are a lot of records.