Applies a mutation-order reconstruction method (adapted from tumor phylogenetics) to ~160,000+ early SARS-CoV-2 genomes to infer a single “progenitor” genotype (proCoV2) as the most recent common ancestor of the sampled diversity. Finds the progenitor differs from every one of the earliest-sampled Wuhan genomes by 3 mutations, and estimates it was already circulating ~5.8–8.1 weeks before the first officially reported cases — i.e. that none of the earliest documented Wuhan patients carry the literal ancestral genotype, and that undetected transmission preceded the recognized outbreak by more than a month. This “missing progenitor” / “no true index genome sampled” finding is one of the two main empirical planks (with the SRA-deletion story, S-4) for the argument that the released Chinese genomic record is an incomplete or curated window onto the true early outbreak.
relevance_note: primary source for the claim that the earliest released Wuhan genomes are all several mutations removed from the actual root, feeding both “market cluster may be a superspreading event, not ground zero” and “record was curated” readings.