Excluding intermediate lineage A/B SARS-CoV-2 genomes materially affects Pekar et al.'s inferred number of spillovers
3 events · 2 assessments
Reassessed: still Contested
verdict confidence 0.70
Assessed Contested
verdict confidence 0.70
Whether Pekar et al.'s exclusion of "intermediate" lineage A/B genomes changes their conclusion of at least two zoonotic spillovers is an active, unresolved dispute in the phylogenetics literature. Lineages A and B differ by two nucleotides; a genome with only one of those changes is an "intermediate," and under the two-spillover hypothesis such a genome would have to have arisen in an unsampled animal host, so a genuine human intermediate would instead point toward a single introduction. Critics (notably Kumar, Pipes, and colleagues) argue that Pekar et al. excluded these intermediate genomes on questionable grounds and that including them, together with the study's treatment of recombinants and sampling, materially weakens the two-spillover inference. Pekar, Wertheim, Worobey and co-authors counter that the reported intermediates are sequencing artifacts rather than authentic genomes—a position reinforced by later analyses finding the sequences are more likely erroneous or derived—so that their exclusion is warranted and the inference stands. The disagreement therefore turns largely on an empirical question that remains open: are the intermediate genomes real? Resolving it would require access to the underlying raw sequencing data and reads for the disputed samples, which have not been fully available for independent inspection.
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