Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2.

ABSTRACT: Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasingly been used for population-scale monitoring of pathogen dynamics, including in low-resource settings. Broader adoption of wastewater genomic surveillance, however, is limited by a lack of flexibility across sequencing platforms and approaches, and adaptability to additional pathogens. Here, we describe "Freyja 2", an integrated bioinformatics tool enabling robust real-time inference of pathogen lineage prevalence and growth dynamics from wastewater and other complex samples. In Freyja 2, we develop new methods for estimating lineage prevalence and growth rates, and demonstrate robustness ac

SUBMITTER: Levy JI 

PROVIDER: S-EPMC12330420 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature