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

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Conflicts of Interest

Identified Weaknesses

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Paper Summary

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COVID's "Two-Entry" Story Was Just Bad Math: New Look Says Only One!

This re-analysis demonstrates that previous claims of strong statistical support for multiple SARS-CoV-2 introductions into humans were an artifact of an imbalanced hypothesis testing framework. The original study unfairly applied stricter conditions to the single-introduction model, and when these conditions are made consistent for both models, the evidence for multiple introductions disappears, reversing the initial conclusion.

Possible Conflicts of Interest

None identified

Identified Weaknesses

Imbalanced Hypothesis Testing Framework

The original study tested the single-introduction model under more stringent conditions (relative size, evolutionary separation, root shape) than the two-introduction model, creating a bias that skewed the Bayes factor.

Errors in Original Calculation

The original paper contained critical errors including a syntax error, erroneous normalization, and non-exclusive marginalization, which collectively inflated the reported support for two introductions.

Improper Bayesian Tests

The relative size and evolutionary separation conditions used in the original paper are identified as improper tests for Bayesian analysis, as they test sidedness rather than agreement, potentially introducing bias.

Inconsistent Filtering of Lineages

Minor imbalances arose in filtering early samples and short-lived lineages, with different criteria applied based on whether a one- or two-introduction model was assumed, which could differentially benefit one model.

Implicit Upstream Diversity Assumptions

The original approach implicitly assumed very specific upstream diversity characteristics (e.g., 100% probability of a two-mutation separation, >50% probability of introducing ancestor-descendant pairs), which might not be biologically justified.

Rating Explanation

This paper provides a rigorous and thorough re-analysis of a prominent scientific claim regarding SARS-CoV-2 introductions. It meticulously identifies critical methodological flaws and inconsistencies in the original study's hypothesis testing framework, demonstrating how these led to a reversal of conclusions. The detailed explanation significantly contributes to scientific accuracy.

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