The conventional view is that smallpox has been around since antiquity, but more recent evidence has suggested it's actually only around 500 years old.

So I have a research/rationality question: how conclusive is the "500 years old hypothesis"? I don't really have the expertise to evaluate it.

The wikipedia entry briefly notes the new findings, but doesn't seem to have rewritten the overall history section:

The earliest credible clinical evidence of smallpox is found in the smallpox-like disease in medical writings from ancient India (as early as 1500 BC),[54][55]Egyptian mummy of Ramses V who died more than 3000 years ago (1145 BC)[56] and China (1122 BC).[57] It has been speculated that Egyptian traders brought smallpox to India during the 1st millennium BC, where it remained as an endemic human disease for at least 2000 years. Smallpox was probably introduced into China during the 1st century AD from the southwest, and in the 6th century was carried from China to Japan.[26] In Japan, the epidemic of 735–737 is believed to have killed as much as one-third of the population.[14][58] At least seven religious deities have been specifically dedicated to smallpox, such as the god Sopona in the Yoruba religion. In India, the Hindu goddess of smallpox, Sitala Mata, was worshiped in temples throughout the country.[59]

A different viewpoint is that smallpox emerged 1588 AD and the earlier reported cases were incorrectly identified as smallpox.[60][61]

Paper: 17th Century Variola Virus Reveals the Recent History of Smallpox

The paper arguing the 500 years hypothesis is here.

Highlights:

• Variola virus genome was reconstructed from a 17th century mummified child

• The archival strain is basal to all 20th century strains, with same gene degradation

• Molecular-clock analyses show that much of variola virus evolution occurred recently

Abstract

Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1, 2, 3, 4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4, 5, 6, 7, 8, 9].

In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4, 5, 6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone.

To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650.

Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.