Phylogenetics Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens
MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: 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 INFORMATION: Supplementary data are available at Bioinformatics online.
Authors
- Anderson Fernandes Brito (ORCID: https://orcid.org/0000-0001-5785-7222)
- John T. McCrone (ORCID: https://orcid.org/0000-0002-9846-8917)
- Emma B. Hodcroft (ORCID: https://orcid.org/0000-0002-0078-2212)
- Jover Lee (ORCID: https://orcid.org/0000-0002-2391-0512)
- Miguel I. Paredes (ORCID: https://orcid.org/0000-0002-9712-1663)
- Denise Kühnert (ORCID: https://orcid.org/0000-0002-5657-018X)
- I. A. Joia (ORCID: https://orcid.org/0009-0000-6241-7467)
- Richard A. Neher (ORCID: https://orcid.org/0000-0003-2525-1407)
- Cornelius Roemer (ORCID: https://orcid.org/0000-0002-6138-6539)
- Thomas R. Sibley (ORCID: https://orcid.org/0000-0001-5269-2297)
- Kimberly R. Andrews (ORCID: https://orcid.org/0000-0003-4721-1924)
- Louise H. Moncla (ORCID: https://orcid.org/0000-0001-5722-1988)
- Ivan Aksamentov (ORCID: https://orcid.org/0000-0002-7557-9673)
- Laura Marcela Torres (ORCID: https://orcid.org/0000-0001-9496-0595)
- Richard Olumide Daodu (ORCID: https://orcid.org/0009-0008-9568-4455)
- John S. J. Anderson
- Victor Lin (ORCID: https://orcid.org/0000-0002-8670-3377)
- Laura Voitl (ORCID: https://orcid.org/0009-0002-7987-1185)
- Allison Li (ORCID: https://orcid.org/0009-0001-2304-8248)
- John Huddleston
- Jennifer Chang
- Kathryn Kistler
- Trevor Bedford
- James Hadfield
Institutions
- SIB Swiss Institute of Bioinformatics (CH)
- Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa (ZA)
- Infectious Disease Research Institute (US)
- Howard Hughes Medical Institute (US)
- Swiss Tropical and Public Health Institute (CH)
- University of Basel (CH)
- University of Washington (US)
- Robert Koch Institute (DE)
- Fred Hutch Cancer Center (US)
- Instituto de Saúde (BR)
- Freie Universität Berlin (DE)
- University of Pennsylvania (US)
Publication Details
- Journal
- Bioinformatics
- Published
- 2026-09-25
- DOI
- https://doi.org/10.1093/bioinformatics/btag705
- Primary Topic
- Tuberculosis Research and Epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 0.00