HERE is the CDC article discussing the disease.
Recent epidemiologic research suggests that the events in 1545 and 1576, associated with a high death rate and referred to as cocoliztli (Nahuatl for "pest"), may have been due to indigenous hemorrhagic fevers (4,5)...
Many of the symptoms described by Dr. Hernandez occur to a degree in infections by rodent-borne South American arenaviruses, but no arenavirus has been positively identified in Mexico. Hantavirus is a less likely candidate for cocoliztli because epidemics of severe hantavirus hemorrhagic fevers with high death rates are unknown in the New World. The hypothesized viral agent responsible for cocoloztli remains to be identified, but several new arenaviruses and hantaviruses have recently been isolated from the Americas and perhaps more remain to be discovered (11)they suspected it was spread by a rodent, similar to hanta virus or the plague.
as for the remarks that maybe the Indians knew about small pox before the Europeans arrived, one wonders if they were describing chicken pox (or even secondary syphilis aka the great pox) which has a similar rash.
Discovery magazine has a less technical article.
Then, four centuries later, Acuña-Soto improbably decided to reopen the investigation. Some key pieces of information—details that had been sitting, ignored, in the archives—just didn't add up. His studies of ancient documents revealed that the Aztecs were familiar with smallpox, perhaps even before Cortés arrived. They called it zahuatl.
Spanish colonists wrote at the time that outbreaks of zahuatl occurred in 1520 and 1531 and, typical of smallpox, lasted about a year. As many as 8 million people died from those outbreaks.
But the epidemic that appeared in 1545, followed by another in 1576, seemed to be another disease altogether. The Aztecs called those outbreaks by a separate name, cocolitzli.
For them, cocolitzli was something completely different and far more virulent," Acuña-Soto says. "Cocolitzli brought incomparable devastation that passed readily from one region to the next and killed quickly."
After 12 years of research, Acuña-Soto has come to agree with the Aztecs: The cocolitzli plagues of the mid-16th century probably had nothing to do with smallpox. In fact, they probably had little to do with the Spanish invasion.so today the Atlantic magazine has an article discussing this dreaded disease. DNA studies on teeth show evidence of paratyphoid.
Now, DNA from 16th-century cocolitzli victims has offered up a somewhat unexpected new candidate: Salmonella enterica, or the bacteria that cause paratyphoid fever. The DNA evidence comes from the teeth of 11 people buried in a large Mixtec cemetery in southern Mexico. Prior archaeological work had linked the burials to the 1545 cocolitzli epidemic, and the city was likely abandoned after the disease killed so many of its inhabitants.,..
Acuña-Soto still favors his viral hemorrhagic-fever hypothesis, and he notes that Salmonella has never caused another epidemic as deadly as cocoliztli in recorded history. The strain most similar to the one found in the 16th-century teeth is rare and not well-studied, but it has a 10 to 15 percent mortality rate today. It is also not entirely known whether Salmonella was present in the Americas before contact with the Spanish or how pervasive it was in Europe..that was my impression also, that paratyphoid was not that virulent.
But diseases do change with time.
for example the Athenian plague victims tested positive for regular typhoid, but many dispute that too.
but when you read about how San Diego is being threatened by Hepatitis epidemic because the homeless spread feces on the street, just remember: Typhoid, paratyphoid, cholera and shigellosis, not to mention viral diarrheas, are also spread that way.
update: Long article in Nature discusses the disease but alas is behind a paywall if you want to read the whole thing.