EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.

ABSTRACT: Accurately estimating the effective reproduction number (Rt) of a circulating pathogen is a fundamental challenge in the study of infectious disease. The fields of epidemiology and pathogen phylodynamics both share this goal, but to date, methodologies and data employed by each remain largely distinct. Here we present EpiFusion: a joint approach that can be used to harness the complementary strengths of each field to improve estimation of outbreak dynamics for large and poorly sampled epidemics, such as arboviral or respiratory virus outbreaks, and validate it for retrospective analysis. We propose a model of Rt that estimates outbreak trajectories conditional upon both phylodynamic (time-scaled trees estimated from genetic sequences) and epidemiological (case incidence) data. We simulate

SUBMITTER: Judge C 

PROVIDER: S-EPMC11581393 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature