Developing a systematic framework for reconstructing evolutionary histories of viruses with pandemic potential

The accurate estimation of molecular clock rates is crucial for characterising virus evolutionary dynamics and reconstructing their natural history. While modern sequencing software facilitates the inference of rates and dates of species divergence events, their use as a ‘blackbox’ without attention to the underlying assumptions can lead to spurious estimations. I have recently developed models to address rate variations in RNA and DNA viruses across different timescales. Here, I will develop methods to understand biological and methodological factors influencing evolutionary rate estimates. The goal is to establish a systematic framework for robust inference of rates and ages of viruses with pandemic potential. This framework will quantify the effects of selection, recombination, and site saturation on virus evolutionary rates. Initially focusing on viral rate estimation and determining the onset of epidemics in human populations, the research will extend to tracing the origins of these viruses back to their animal reservoirs, offering insights into historical outbreak patterns and their future likelihoods. This research will advance our understanding of virus evolutionary history, impacting public health by accurately inferring the timing of outbreaks, factors influencing evolutionary rates, and contributing to the development of treatments by shedding light on virus-host associations over time.