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

2025/10/01 by M. B. Weissman, Michael B. Weissman, Weissman, Michael B. · 2 voices
Biochemistry, Genetics and Molecular Biology · Medicine · #Data-Driven Disease Surveillance #FOS: Biological sciences #Fractal and DNA sequence analysis #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #Quantitative Methods (q-bio.QM) #q-bio.PE #q-bio.QM

paper · pdf · doi:10.48550/arxiv.2510.01484

openalex publication_date 2025/10/01 · arxiv published 2025/10/01 · openalex created_date 2025/10/10 · arxiv updated 2026/02/06 · openalex updated_date 2026/07/28

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.

Citations

• Purported quantitative support for multiple introductions of SARS-CoV-2 into humans is an artefact of an imbalanced hypothesis testing framework

Discussions

• The corrections to the Pekar 2022 Science paper claiming multiple SARS-CoV-2 introductions are factorizable and simple, using data contained in the paper and minimal assumptions. Their data and model [bsky, 4 points, 1 comments]
• "Here I show that after correcting a fundamental error in Bayesian reasoning [by Pekar et al] the results in that paper give larger likelihood for a single introduction than for two." arxiv.org/abs/25 [bsky, 3 points, 0 comments]

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• Purported quantitative support for multiple introductions of SARS-CoV-2 into humans is an artefact of an imbalanced hypothesis testing framework
• Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived
• The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2