ArticleGenome biology and evolution2025
On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching.
Article in Genome biology and evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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1 citing paper in PubMed.
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1 author.
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Abstract
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. The author presents the mathematical model, illustrates its application, and implements 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 (i) an increase in r in late February 2020 contributed mainly by the D614G lineage, (ii) a significantly better fit of the sigmoidal-rate model to the SARS-CoV-2 evolution than the constant-rate model, and (iii) the common ancestor of the included SARS-CoV-2 genomes dated to November 20, 2019.
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