Nextstrain Clades Track Settings
 
Situation report zoom "clades" from nextstrain.org/ncov   (All Variation and Repeats tracks)

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Data last updated: 2020-04-23 10:03:56

Description

Nextstrain.org displays data about variants 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 variants in sequences worldwide using the TreeTime algorithm. Nextstrain also produces weekly situation reports (e.g. March 20th, 2020), in which they highlight certain branches of the tree. They define clades in terms of a small number of variants that define the branches as the mechanism to highlight the branches of interest in the situation reports. Nextstrain cautions that these clades are not officially recognized and should not be over-interpreted, but since the clades are an interesting feature of Nextstrain and can be used to label and color nodes in Nextstrain's tree display, we display each clade as a feature that spans the genome, with tall boxes at the locations of mutations that occurred on the path from the reference to the clade.

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

cladeSituation report section & date
A1a Possible hidden transmission in Italy (2020-03-05);
Sequence data can cross-check travel histories (2020-03-20)
A2 Global Spread from Lombardy, Italy (2020-03-05);
Circulation across Europe (2020-03-13)
A2a Evidence for local transmission in Kinshasa, Congo (2020-03-27)
A3 Export of COVID-19 from Iran (2020-03-27);
Local transmission in New South Wales (2020-03-27)
A6 (not used in any situation report as of March 30, 2020)
A7 Likely two local transmission chains in California (2020-03-27)
B (not used in any situation report as of March 30, 2020)
B1 How outbreaks grow: an example (2020-03-20);
Transmission across the U.S. is complex and not well-understood (2020-03-27)
B2 (not used in any situation report as of March 30, 2020)
B4 (not used in any situation report as of March 30, 2020)

Methods

Nextstrain downloads SARS-CoV-2 genomes from GISAID as they are submitted by labs worldwide. Nextstrain identifies variants 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 VCF files underlying this track (nextstrainClade) 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