Bayesian Re-Analysis of the Phylogenetic Topology of Early SARS-CoV-2 Case Sequences

Abstract

A much-cited 2022 paper by Pekar et al. claimed that Bayesian analysis of the molecular phylogeny of early SARS-CoV-2 cases indicated that it was more likely that two successful introductions to humans had occurred than that just one had. Here I show that after correcting a fundamental error in Bayesian reasoning the results in that paper give larger likelihood for a single introduction than for two.

~5k words in main text, v2 has small tweaks, v3 more tweaks + useful histogram, v4 tweaks + include post-introduction pre-root mutations. v5 restores accidentally dropped histogram. closely related to extended version in March 2026 Econ Journal Watch https://econjwatch.org/file_download/1405/WeissmanMarch2026.pdf