Purported quantitative support for multiple introductions of SARS-CoV-2 into humans is an artefact of an imbalanced hypothesis testing framework
2025/02/27 by Angus McCowan, McCowan, Angus · 5 voices · 1 citation
Biochemistry, Genetics and Molecular Biology · Mathematics · Medicine · #Alternative hypothesis #COVID-19 Clinical Research Studies #COVID-19 epidemiological studies #Inference #SARS-CoV-2 and COVID-19 Research #Statistical hypothesis testing #Test (biology) #q-bio.QM
paper · pdf · doi:10.48550/arxiv.2502.20076
openalex publication_date 2025/02/27 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Abstract
A prominent report claimed substantial support for two introductions of SARS-CoV-2 into humans using a calculation that combined phylodynamic inferences and epidemic models. Inspection of the calculation identifies an imbalance in the hypothesis testing framework that confounds this result; the single-introduction model was tested against more stringent conditions than the two-introduction model. Here, I show that when the two-introduction model is tested against the same conditions, the support disappears.
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Discussions
- A recent critique by Angus McCowan (i.e., "Nod") claims that the quantitative support for multiple SARS-CoV-2 introductions in our Pekar et al. 2022 is an “artifact” of "imbalanced" hypothesis testing [bsky, 64 points, 1 comments]
- PS I've only just noticed - since I last looked at this, the person who first spotted all those errors has revealed his name and has published a preprint (last version March 2025) arxiv.org/abs/2502.2 [bsky, 3 points, 1 comments]
- The author who identified a coding error in Pekar et al (2022) has found a major statistical inference error too. Pekar et al appear to have applied stricter conditions for single spillover than for d [bsky, 2 points, 1 comments]
- My bad 🧪https://arxiv.org/abs/2502.20076 [bsky, 1 points, 1 comments]
- 1\ @kgandersen.bsky.social critiques this paper: arxiv.org/abs/2502.20076 This critique is unsound. Multiple spillovers could result in a large range of divergence in the spillover lineages, and could [bsky, 0 points, 1 comments]
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