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Estimating transmission rates is a challenging yet essential aspect of comprehending and controlling the spread of infectious diseases. There are various methods available for this purpose, each with its own assumptions, data requirements, and limitations. This paper introduces a phylogenetic approach called transRate, designed to estimate inter-population transmission rates. The phylogenetic method, which maintains statistical consistency under the multi-population Susceptible-Infected-Recovered (SIR) model, integrates genetic information with traditional epidemiological approaches. This integration improves the accuracy of transmission rate estimates, facilitating more effective disease control and prevention strategies. Simulation analyses validate the precision of transRate in estimating transmission rates. With the growing abundance of public databases for genomic sequences, transRate is becoming more prevalent in tracking and preventing the spread of such diseases. 

Abstract 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.