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The COVID-19 pandemic has underscored the need for efficient and mathematically rigorous methods to analyze epidemiological time series and genetic data. This project introduces and evaluates various methods for estimating infectious disease parameters. We employed a dynamic Markov chain model incorporating random variables tracking infected and susceptible individuals, as well as their coalescent times. Our objective was to assess the accuracy of different techniques in predicting disease characteristics based on this model. Simulation studies of various existing parameter estimation methods revealed that prediction accuracy falls drastically when a recovery rate is introduced. In response to the limitations of existing methods, we initiated the development of a novel model which would incorporate lineages, allowing us to use phylogenetic trees to estimate parameters. This would lead to an improvement in parameter estimates, especially with a recovery rate, as phylogenetic trees contain more information than the types of data used in existing parameter estimation methods.
Nair et al. (Mon,) studied this question.