Two basal SARS-CoV-2 lineages are statistically improbable under a single spillover event
5 events · 4 assessments
Reassessed: still Contested
verdict confidence 0.73 → 0.74
Reassessed: still Contested
verdict confidence 0.72 → 0.73
Reassessed: still Contested
verdict confidence 0.70 → 0.72
Assessed Contested
verdict confidence 0.70
Early SARS-CoV-2 sampled in Wuhan fell into two basal lineages, A and B, separated by two nucleotide mutations. Whether this pattern is statistically improbable under a single spillover — and therefore points to two separate introductions — remains genuinely contested among qualified researchers. The influential analysis by Pekar et al. (Science, 2022) used epidemic simulations and a Bayesian comparison to conclude that a single introduction was unlikely to reproduce the observed two-lineage structure, a finding later cited by the WHO's SAGO review in judging a single-introduction origin "highly unlikely." Critics have raised two lines of objection: that intermediate A–B genomes among early human cases (which would make a single introduction plausible) were improperly excluded, and, more durably, that the statistical support is an artefact of an imbalanced hypothesis-testing framework and is fragile to more realistic modelling assumptions. The intermediate-genome objection has been substantially rebutted in peer review — the proposed intermediates appear to be derived from lineage A or B rather than true intermediates — which shifts the balance toward the two-spillover reading. The methodological objection to the phylodynamic inference itself, however, remains a live and unresolved disagreement, and a published erratum correcting a coding error in the original single-introduction frequency has kept scrutiny on the result. Resolving the question would require either agreement on the correct statistical framework and its robustness, or new early-case sequence data.
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