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Genomic epidemiology, which links pathogen genomes with associated metadata to understand disease transmission, has become a key component of outbreak response. Decreasing costs of genome sequencing and increasing computational power provide opportunities to generate and analyse large viral genomic datasets that aim to uncover the spatial scales of transmission, the demographics contributing to transmission patterns, and to forecast epidemic trends. Emerging sources of genomic data and associated metadata provide new opportunities to further unravel transmission patterns. Key challenges include how to integrate genomic data with metadata from multiple sources, how to generate efficient computational algorithms to cope with large datasets, and how to establish sampling frameworks to enable robust conclusions.

Original publication

DOI

10.1016/j.pt.2021.08.007

Type

Journal article

Journal

Trends in parasitology

Publication Date

04/10/2021

Addresses

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. Electronic address: verity.hill@ed.ac.uk.