Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution
Journal:
arXiv
Published Date:
Dec 5, 2024
Abstract
Computational multi-scale pandemic modelling remains a major and timely
challenge. Here we identify specific requirements for a new class of pandemic
models operating across three scales: (1) rapid pathogen evolution, punctuated
by emergence of new variants, (2) human interactions within a heterogeneous
population, and (3) public health responses which constrain individual actions
to control the disease transmission. We then present a pandemic modelling
framework satisfying these requirements and capable of simulating multi-scale
dynamic feedback loops. The developed framework comprises a stochastic
agent-based model of pandemic spread, coupled with a phylodynamic model of the
within-host pathogen evolution. It is validated with a case study, modelling a
rapid punctuated evolution of SARS-CoV-2, based on global and contemporary
genomic surveillance data, during the COVID-19 transmission within a large
heterogeneous population. We demonstrate that the model captures the essential
features of the COVID-19 pandemic and the novel coronavirus evolution, while
retaining computational tractability and scalability.
