Nextstrain SARS-CoV-2 resources

Labs from all over the world are sequencing SARS-CoV-2 and sharing genomic data. The Nextstrain team analyzes these data on a global and continental level. More specific analyses are often performed by public health and academic groups from around the world. This page lists a sample of such analyses. In addition to exploring SARS-CoV-2 evolution in finished analyses, you can use Nextclade to compare your sequences to the SARS-CoV-2 reference genome, assign them to clades, and see where they fall on a SARS-CoV-2 phylogeny.

All SARS-CoV-2 datasets

This section is an index of public Nextstrain datasets for SARS-CoV-2, organized by geography. Some of these datasets are maintained by the Nextstrain team and others are maintained by independent research groups. If you know of a dataset not listed here, please let us know! Please note that inclusion on this list does not indicate an endorsement by the Nextstrain team.

All SARS-CoV-2 situation reports

We have been writing interactive situation reports using Nextstrain Narratives to communicate how COVID-19 is moving around the world and spreading locally. These are kindly translated into a number of different languages by volunteers and Google-provided translators — click on any language below to see the list of situation reports available.

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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© 2015–2023 Trevor Bedford and Richard Neher