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Related Experiment Video

Updated: Sep 16, 2025

Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm

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On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching.

¹Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada.

Genome Biology and Evolution

|July 7, 2025

Summary

This summary is machine-generated.

Viral host switching can alter evolutionary rates, with sigmoidal models better capturing these changes than linear ones. This study introduces a new model and software for analyzing viral evolution, applied to SARS-CoV-2.

Keywords:

COVID-19 SARS-CoV-2 Zoonosis evolutionary rate rooting sigmoidal function tip-dating

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Last Updated: Sep 16, 2025

Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Area of Science:

Virology
Evolutionary Biology
Computational Biology

Background:

Viral host-switching events can lead to significant changes in viral evolutionary rates.
Previous models often used linear functions to describe rate changes over short time intervals.

Purpose of the Study:

To present a novel mathematical model for viral evolutionary rates during host switching.
To implement and apply this model using user-friendly software for phylogenetic analysis.
To investigate the evolutionary dynamics of early SARS-CoV-2.

Main Methods:

Development of a sigmoidal function to model viral evolutionary rate changes.
Implementation of rooting and dating methods in the TRAD program.
Application of the model to a phylogeny of early SARS-CoV-2 genomes.

Main Results:

The sigmoidal-rate model provided a significantly better fit to SARS-CoV-2 evolution compared to a constant-rate model.
An increase in the evolutionary rate of SARS-CoV-2 was observed in late February 2020, primarily driven by the D614G lineage.
The common ancestor of the analyzed SARS-CoV-2 genomes was dated to November 20, 2019.

Conclusions:

Sigmoidal models are superior to linear models for describing viral evolutionary rate changes during host adaptation.
The TRAD program offers a valuable tool for phylogenetic analysis of viral evolution.
The findings provide insights into the early evolutionary trajectory of SARS-CoV-2.