Targets the load-bearing exclusion step in Pekar et al. 2022 (S-1): since lineages A and B differ at two linked positions, a genuine single-introduction-plus-recombination or single-introduction-plus-recurrent-mutation scenario predicts some sampled genomes should carry an “intermediate” one-of-two-positions haplotype, and confirming such an intermediate would undercut the two-spillover claim. Pekar et al. identified 20 such candidate intermediate genomes in GISAID and excluded them from the main analysis (citing low read depth / likely sequencing error at the two defining positions). Massey et al. re-examine the GISAID quality metadata for these 20 genomes and argue many were sequenced to depths inconsistent with the stated exclusion criteria, i.e. the exclusions look post hoc rather than principled, and reinstating them would be incompatible with the two-spillover conclusion.
relevance_note: the sharpest direct methodological challenge to the specific data-exclusion step the two-introduction inference depends on.