Pekar et al.'s two-spillover conclusion depends on the phylogenetic rooting of early SARS-CoV-2 sequences
3 events · 2 assessments
Reassessed: still Supported
verdict confidence 0.80
Assessed Supported
verdict confidence 0.80
Pekar et al. (2022, Science) argued that SARS-CoV-2 entered humans through at least two separate zoonotic spillovers, corresponding to the two earliest lineages (A and B) that differ by two mutations. That phylogenetic argument turns on how the early SARS-CoV-2 tree is rooted — specifically, on treating lineages A and B as two distinct basal clades rather than descendants of a single intermediate ("A/B") ancestor. This dependence is well established and is not itself the point of contention: the authors devote analysis to establishing their preferred ancestral haplotype, and critics engage the conclusion precisely by challenging the rooting. If the tree were instead rooted at an intermediate haplotype, a single introduction that later diversified into A and B becomes more plausible, weakening the case for two spillovers. The live disagreement is therefore not whether the conclusion depends on the rooting, but which rooting is correct: several groups (e.g., Bloom; Kumar et al.; Lv et al.) argue the data cannot confidently root the tree and that intermediate genomes may exist, while Pekar et al. and others (Débarre & Hensel; Crits-Christoph et al.) argue the root is lineage B and that reported intermediates are sequencing artifacts or later derived haplotypes. One caveat keeps this short of fully settled: the two-spillover case also rests on molecular-clock and epidemiological lines of evidence, so the overall conclusion is not contingent on rooting alone even though its core topological argument is.
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