On rooting and dating viral trees with a changing evolutionary rate following host-switching.

Publication date: Jul 07, 2025

Viral host-switching from host H1 to host H2 is often associated with changes in viral evolutionary rate r. The pre-switching rate r1 in H1 may stay the same or increase/decrease to a new rate r2 in H2 during the host-switching and host-adapting process, depending on the difference between H1 and H2. The changing rate has previously been modeled by a linear function when the time interval is short but is better modeled by a sigmoidal function. I present the mathematical model, illustrate its application, and implement the rooting and dating methods in a new version of the user-friendly TRAD program, which is freely available at https://dambe. bio. uottawa. ca/TRAD/TRAD. aspx. Application of the method to a phylogeny of early SARS-CoV-2 genomes revealed 1) an increase in r in late February 2020 contributed mainly by the D614G lineage, 2) a significantly better fit of the sigmoidal-rate model to the SARS-CoV-2 evolution than the constant-rate model, and 3) the common ancestor of the included SARS-CoV-2 genomes dated to 2019/11/20.

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Semantics

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