Description

Nextstrain.org displays data about mutations that occur in the current 2019/2020 outbreak. Nextstrain has a powerful user interface for viewing the timestamped molecular phylogeny tree that it infers from the patterns of mutations in sequences worldwide using the TreeTime algorithm.

Nextstrain defines clades named by year and letter, anticipating that SARS-CoV-2 will become a seasonal virus in the coming years. For more information about the rationale and properties of current clades, see https://github.com/nextstrain/ncov/blob/master/docs/src/reference/naming_clades.md.

The Nextstrain Mutations track contains all mutations shown on Nextstrain, of which this track's mutations are a very small subset.

Methods

Nextstrain downloads SARS-CoV-2 genomes from GISAID as they are submitted by labs worldwide. Nextstrain identifies mutations that define clades of interest and puts them in the file clades.tsv. The genome sequences and metadata including clades.tsv are processed by an automated pipeline and annotations are written to a data file that UCSC downloads and extracts annotations for display.

Data Access

You can download the bigBed file underlying this track (nextstrainClade.bb) from our Download Server. The data can be explored interactively with the Table Browser or the Data Integrator. The data can also be accessed from scripts through our API.

Credits

Thanks to nextstrain.org for sharing its analysis of genomes collected by GISAID, and to researchers worldwide for sharing their SARS-CoV-2 genome sequences.

References

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018 Dec 1;34(23):4121-4123. PMID: 29790939; PMC: PMC6247931