Note: Omicron BA.4 and BA.5 added May, 2022
This track displays amino acid and nucleotide mutations in SARS-CoV-2 variants
as defined in December 2021 by
the World Health Organization (WHO). Note that the
Center for Disesase Control (CDC) classification of SARS-CoV-2
variants is slightly different than the WHO.
Mutations in this track were identified from viral sequences from
Variant incidence and geographic distribution information is available from links to the
Outbreak.info web resource
on the mutation details pages.
- Variants of Concern (VOC) have evidence for increased transmissibility,
virulence, and/or decreased diagnostic, therapeutic, or vaccine efficacy.
- Variants of Interest (VOI) contain mutations suspected or confirmed
to cause a change in transmissibility, virulence, or diagnostic / therapeutic /
vaccine efficacy, plus evidence of significant community transmission,
a cluster of cases, or detection in multiple countries.
- Variants under Monitoring (VUM) include variants with unclear
epidemiological impact. This track includes only the four VUMs which were previously
identified as Variants of Interest, now reclassified at this lower level of concern.
The related track
B.1.1.7 in USA
displays a phylogenetic tree of the first B.1.1.7 (Alpha) variant sequences collected
in the United States.
BV-BRC has a similar list of variants of concern and their mutations, but has added
Track colors are based on
The Greek-letter names assigned by the World Health Organization (WHO) are listed
in this table, along with lineage and clade designations:
||Pangolin lineage||Nextstrain clade||GISAID clade
||First detected||Date VOC/VOI||Type
||Sep 2020, United Kingdom
||May 2020, South Africa
||Nov 2020, Brazil
||Oct 2020, India
||Nov 2020, South Africa
||Dec 2020, Peru
||Jan 2021, Colombia
||Mar 2020, USA
||Nov 2020, USA
||Oct 2020, India
Mutations in the amino acid track are named with the format:
[Reference amino acid][1-based coordinate in peptide][Alternate amino acid]. E.g., L452R
Mutations in the nucleotide track are named with the format:
[Reference nucleotide][1-based coordinate in genome][Alternate nucleotide]. E.g., T22918G
Insertions and deletions in both tracks are named:
[del/ins]_[1-based genomic coordinate of first affected nucleotide]. E.g., del_21991
For each virus variant, SARS-CoV-2 genome sequences containing all characteristic
mutations of the lineage were downloaded from
using the lineage search feature
(restricting to complete, high-coverage genomes, and restricting to earliest sample
collection dates when there were too many results for the download limit of 10,000
sequences per query).
Sequences were aligned to the
SARS-CoV-2 reference genome
script from the
Single-nucleotide substitutions were extracted from the alignment using the UCSC tool
(available on the UCSC download server
or from bioconda;
also requires the
SARS-CoV-2 reference sequence).
Single-nucleotide substitutions present at a frequency
of at least 0.95 (.70 for Delta, .80 for Omicron) were retained while all others are discarded.
For indel detection, the
suite of tools was used as follows:
minimap2 --cs [Reference Sequence] [Set of Unaligned Sequences] | paftools.js call -L 10000 -
Indels present at a frequency of at least 0.85 (.50 for Delta, .70 for Omicron) were retained.
Less stringent cutoffs were applied to Delta and Omicron
variant sequences due to low quality of early sequences.
The results were then combined and formatted by
The entire pipeline was run using
You can download the bigBed data files for this track from the
UCSC Download Server.
The data can be explored interactively with the
or the Data Integrator. The data can be
accessed from scripts through our API.
For complete genome Fasta sequences of variants of concern, please visit the following
Version 2 of this track adds one new Variant of Concern (Delta), two new Variants of
Interest (Lambda, Mu), and three named variants previously VOI, now designated as less
concerning Variants under Monitoring (Eta, Iota, Kappa).
The track labels of all variants have been updated to include WHO labels. Track colors
reflect Nextstrain conventions at the time of track data update (September 10, 2021).
Omicron was added December 2, 2021.
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.
at the Australia National University for developing and maintaining the
sarscov2phylo web resource.
We also thank
and Andersen labs at Scripps Research for creating the
The lineageVariants scripts were developed and run at UCSC by Nick Keener,
Kate Rosenbloom and Angie Hinrichs.
Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
Nat Microbiol. 2020 Nov;5(11):1403-1407.
Rambaut A, Loman N, Pybus O, Barclay W, Barrett J,
Carabelli A, Connor T, Peacock T, Robertson DL, Volz E, et al.
Preliminary genomic characterization of an emergent SARS-CoV-2 lineage in the UK
defined by a novel set of spike mutations.
Virological. 2020 Dec 18.
Volz E, Mishra S, Chand M, Barrett JC, Johnson E,
Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O'Toole Á, et al.
Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking
epidemiological and genetic data.
Virological. 2020 Dec 31.
Tegally et al, December 21, 2020.
Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa medRxiv preprint.
Zhang al, January 20, 2021.
Emergence of a novel SARS-CoV-2 strain in Southern California, USA
Voloch et al, December 26, 2020.
Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil medRxiv preprint.
Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 sequences from GISAID. Zenodo DOI:
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100.
PMID: 29750242; PMC: PMC6137996
Gangavarapu, Karthik; Alkuzweny, Manar; Cano, Marco; Haag, Emily; Latif, Alaa Abdel;
Mullen, Julia L.; Rush, Benjamin; Tsueng, Ginger; Zhou, Jerry; Andersen, Kristian G.;
Wu, Chunlei; Su, Andrew I.; Hughes, Laura D.