Authors
Kimberly R Andrews, Jennifer Chang, Cornelius Roemer, James Hadfield, Victor Lin, Anderson F Brito, Richard Olumide Daodu, Isabel A Joia, Kathryn Kistler, Allison Li, Louise H Moncla, Miguel I Paredes, Denise Kühnert, Laura Marcela Torres, Laura Voitl, Ivan Aksamentov, Emma B Hodcroft, John Huddleston, John T McCrone, John S J Anderson, Thomas R Sibley, Jover Lee, Richard A Neher, Trevor Bedford
Published in
Bioinformatics (Oxford, England). Sep 25, 2026. Epub Sep 25, 2026.
Abstract
Genome sequencing provides an exceptional window into the evolutionary and epidemiological dynamics of endemic and emerging pathogens, and thus allows for better, more targeted, public health interventions. Online genomic surveillance platforms can provide near real-time insight into these dynamics.
Nextstrain provides continually updated real-time genomic surveillance for 21 viruses and the bacterial pathogen Mycobacterium tuberculosis, with most analyses relying solely on open sequence data. Each pathogen includes steps to fetch and curate open data, classify sequences using established nomenclature systems, perform phylogenetic analyses, and share the results publicly. These analyses are automated, with most running daily to provide continually updated snapshots of pathogen evolution.
All source code is available at https://github.com/nextstrain and a snapshot is archived at Zenodo (https://doi.org/10.5281/zenodo.22697730). Phylogenetic results can be visualized and downloaded at https://nextstrain.org/pathogens, and open sequence data and curated metadata are available at https://nextstrain.org/pathogens/files.
Supplementary data are available at Bioinformatics online.
PMID:
42788655
Bibliographic data and abstract were imported from PubMed on 25 Sep 2026.
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