The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic

A consensus species tree is reconstructed from 11 gene trees for human,
bat, and pangolin beta coronaviruses from samples taken early in the
pandemic (prior to April 1, 2020). Using coalescent theory, the shallow
(short branches relative to the hosts) consensus species tree provides
evidence of recent gene flow events between bat and pangolin beta
coronaviruses predating the zoonotic transfer to humans. The consensus
species tree was also used to reconstruct the ancestral sequence of human
SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The
time to most recent common ancestor was estimated to be Dec 8, 2019, with
a bat origin. Some human, bat, and pangolin coronavirus lineages found in
China are phylogenetically distinct, a rare example of a class II
phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422,
1987). The consensus species tree is a product of evolutionary factors,
providing evidence of repeated zoonotic transfers between bat and pangolin
as a reservoir for future zoonotic transfers to humans.