Amen to this. It almost feels like the Native Americans in a lot of ATLs are, to put it bluntly, simply "in the way" of the colonizing European powers. No discussion of cultures or anything like that beyond "colonists from XYZ nation fought the natives and won and now live there now."
Definitely! I think in many senses this is a rehashing of the "virgin land" myth which attempted to portray the vast majority of the Americas as unsettled/terra nullius, free for the Europeans to expand to. Except this version acknowledges the presence of Native Americans while explaining their disappearance in a way that absolves Europeans of guilt (after all, it isn't
their fault for introducing disease) and suggests it was something innate in the natives themselves that led to their demise. And while there's of course scientific basis to the notion of diseases wreaking havoc on populations with no prior immunity, to stop the analysis there doesn't do it justice. It reminds me of how until very recently, American doctors believed that African Americans were genetically predisposed to be more likely to have certain disorders, only for them to later realize that African Americans that didn't live in poor neighborhoods didn't get those diseases. In short, the racial difference in disease prevalence was created by societal conditions being worse for black people and not some weird racial heritage thing. Not the case for Native Americans because virgin immunity is a factor, but what would casualty rates look like if natives were exposed to disorders while not simultaneously trying to fight off European encroachment, or invasions from neighboring people's due to continent wide population movements? Presumably a lot lower.
Not to mention that there were Native American diseases that really only didn't cross-contaminate because a lot of the poor and hungry Native Americans really weren't anywhere near the Spanish themselves, and during the 1576 Cocoliztli epidemic there was a bit of chaos because the Spanish priests who were sent to tend to the dying started dying off themselves.
A TL where Cocoliztli ends up on a Spanish boat to Europe in the 1580's is a fascinating concept that hasn't really been explored yet. It's not like European sanitation or living conditions for the poor were that much better than in the Americas.
Cocoliztli is a really fascinating epidemic mostly because there's uncertainty as to what it actually was, although most studies have adopted a safe approach of saying it was probably multiple different disorders all spreading at once. The reasoning given is that the population was severely immunocompromised by one of the worst droughts in Mexican history, combined with really bad living conditions under the Spanish conquest. A sequencing study on some old bones (or maybe teeth I don't quite recall) suggested Salmonella was a major contributor, but the authors of that study say Salmonella was probably just one of many concurrent disorders. It's also been suggested to be the result of an endemic viral hemorrhaegic fever that jumped from bats.
If the authors are right and the epidemic was essentially the result of multiple disorders running haywire through an immunocompromised society, that presents two issues with cocoztli spreading to the Old World:
1) Given that it's a multi-disorder epidemic and not just one, obviously cocoliztli itself can't really be "transmitted" per se although maybe the indigenous fever and other unfamiliar pathogens could spread back?
2) If the major cause of the epidemic was as scholars suggest a
severe drought and a
severely immunocompromised society, then you'd have to replicate those conditions in an Old World country to get similar results; and even then it probably wouldn't result from a New World pathogen because Europeans had more than enough pathogens of their own to prey on them.
Having said that, I do love the idea of exploring a sort of reverse Columbian epidemic, and it can't be dismissed out of hand as a TL premise because we know so little for sure about Cocolizitli, only a lot of conjecture and some unconclusive sequencing revealing that
some people died of Salmonella around the same time; so if an author wanted they could certainly take the liberty of presuming the native bat fever was the major contributor and having it spread to Europe somehow. I'd read it!
EDIT: I looked up the Salmonella study just to check (Salmonella enterica serovar Paratyphi C for those interested), and there have been some criticisms of it as although the sequencing was valid, S. Paratyphi C. symptoms in current patients don't match with the historically recorded symptoms, and the team that sequenced the teeth didn't screen for other pathogens so they might have missed something. So with the information we have I'd say it's safe to say there was S. Paratyphi C. and one or more other pathogens that caused the recorded symptoms such as gastrointestinal bleeding. In short, definitely at least two bugs running around.