Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021.

ABSTRACT: Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission rate differences between simultaneously circulating variants in phylodynamic inference is crucial. In this study, we present and empirically validate an extension to the BEAST2 package birth-death skyline model (BDSKY), BDSKY[Formula: see text], which introduces a scaling factor for the transmission rate between independent, jointly inferred trees. In an extensive simulation study, we

SUBMITTER: Weber A 

PROVIDER: S-EPMC10725310 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature