Scheme explaining two alternative models for the location of the root of the SARS-CoV-2 genomes according to their chronologies. (A) Locating the root in haplogroup A would be consistent with a logical evolutionary time line that accounts for the number of mutations accumulated from an alleged pre-A ancestor originating from a zoonotic transmission between an intermediary animal and humans (occurring ∼November 12, 2019) and also consistent with TMRCA values estimated for Chinese A, B, B1, and B2 haplotypes (see text). The alternative of considering B1 as the root would enter into conflict (represented by a question mark) with mutation rates of SARS-CoV-2 genomes, coupled with the large unsampled period needed to explain the hypothetical first appearance of B1 on approximately November 12, 2019 and its first sampling on January 19, 2020, as well as TMRCA for haplogroups A, B, B1, and B2 (see text). (B) The scheme summarizes the two alternative evolutionary scenarios assuming roots in haplogroup A or B1, according to the time lines outlined in the upper panel.
