Nextstrain-maintained pathogen analyses

These data represent analyses and situation-reports produced by the core Nextstrain team. We aim to provide a continually-updated view of publicly available data to show pathogen evolution and epidemic spread. The pipeline used to generate each dataset is available on our GitHub page or by loading a dataset and clicking the “built with” link at the top of the page. While we strive to keep datasets updated, there may be some staleness; the date when the dataset was updated can be found in the footer of each visualisation. In particular, data with a datestamp in the table below (YYYY-MM-DD) reflects an analysis at a point in time.

To learn more about nextstrain please see our documentation or ask a question on the discussion forum.

Click here to scroll down to all Nextstrain-maintained pathogen analyses.

Hadfield et al., Nextstrain: real-time tracking of pathogen evolution, Bioinformatics (2018)

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to must be provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Josh Batson, David Blazes, Jesse Bloom, Peter Bogner, Anderson Brito, Matt Cotten, Ana Crisan, Tulio de Oliveira, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Nate Grubaugh, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Duncan MacCannell, Erick Matsen, Sebastian Maurer-Stroh, Placide Mbala, Danny Park, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Cecile Viboud for comments, suggestions and data sharing.

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