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
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 clades displayed in this track are Nextstrain's "old" clades, i.e. the letter-number-letter
designations used from March 5th through the morning of June 2nd, 2020, at which point they
switched over to the current year-letter system.
The Nextstrain Variants track contains all variants shown on Nextstrain,
of which this track's variants are a very small subset.
Nextstrain assigns both an old clade (if applicable) and a new clade to each sample,
and has an option to color by old clade.
Nextstrain downloads SARS-CoV-2 genomes from
as they are submitted by labs worldwide.
Nextstrain identifies variants that define clades of interest and puts them in the file
(note: these "old" clades are defined in
The genome sequences and metadata including clades.tsv are processed by an
and annotations are written to a data file
that UCSC downloads and extracts annotations for display.
You can download the bigBed file underlying this track (nextstrainOldClade.bb) from our
Download Server. The data can be explored interactively with the
or the Data Integrator. The data can also be
accessed from scripts through our API.
sharing its analysis of genomes collected by
and to researchers worldwide for sharing their SARS-CoV-2 genome sequences.
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher
Nextstrain: real-time tracking of pathogen evolution.
Bioinformatics. 2018 Dec 1;34(23):4121-4123.
PMID: 29790939; PMC: PMC6247931