@misc{andrews_nextstrain_2026,
 abstract = {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. 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.},
 area = {virus evolution},
 author = {Andrews, Kimberly R. and Chang, Jennifer and Roemer, Cornelius and Hadfield, James and Lin, Victor and Brito, Anderson F. and Daodu, Richard Olumide and Joia, Isabel A. and Kistler, Kathryn and Li, Allison and Moncla, Louise H. and Paredes, Miguel I. and Kühnert, Denise and Torres, Laura Marcela and Voitl, Laura and Aksamentov, Ivan and Hodcroft, Emma B. and Huddleston, John and McCrone, John T. and Anderson, John S. J. and Sibley, Thomas R. and Lee, Jover and Neher, Richard A. and Bedford, Trevor},
 copyright = {© 2026, Posted by openRxiv. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
 date = {2026-07-17},
 doi = {10.64898/2026.03.23.713807},
 journal = {bioRxiv},
 language = {en},
 month = {July},
 note = {ISSN: 2692-8205
Pages: 2026.03.23.713807
Section: New Results},
 title = {Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens},
 url = {https://www.biorxiv.org/content/10.64898/2026.03.23.713807v2},
 urldate = {2026-09-04},
 year = {2026}
}