Estimating Epidemic Incidence and Prevalence from Genomic Data.

ABSTRACT: Modern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death, or behavior change). Birth-death and coalescent processes have been introduced to model the stochastic dynamics of epidemic spread under common epidemiological models such as the SIS and SIR models and are successfully used to infer phylogenetic trees together with transmission (birth) and removal (death) rates. These methods either integrate analytically over past incidence and prevalence to infer rate parameters, and thus cannot explicitly infer past incidence or prevalence, or allow such inference only in the coalescent limit of large population size. Here, we introduc

SUBMITTER: Vaughan TG 

PROVIDER: S-EPMC6681632 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature