O-4 - Early SARS-CoV-2 split into two lineages A and B differing by two linked substitutions
Analysis of the early genome collection (787 near-full-length lineage A/B genomes sampled by 14 Feb 2020) shows two dominant co-circulating haplotypes separated by two linked positions. This two-mutation gap with two large clades is the structural fact the rest of the paper reasons about.
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Why this is evidence
H-5 (two or more introductions) reads two co-dominant early lineages separated by a clean two-linked-mutation gap as a topology that single-introduction epidemic simulations reproduce only rarely, so the structure favours separate introductions. H-16 (single introduction) explains the same two-lineage structure as ordinary within-human diversification from one seeding and disputes that the topology is improbable under one introduction. The members predict this structural fact differently.