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 Centers for Disease Control (CDC) classification of SARS-CoV-2 variants is slightly different than the WHO.
Mutations in this track were identified from viral sequences from GISAID. Variant incidence and geographic distribution information is available from links to the Outbreak.info web resource on the mutation details pages.
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 representative sequences.
Track colors are based on Nextstrain.org clade coloring:
The Greek-letter names assigned by the World Health Organization (WHO) are listed in this table, along with lineage and clade designations:
Color | WHO label | Pangolin lineage | Nextstrain clade | GISAID clade | First detected | Date VOC/VOI | Type |
---|---|---|---|---|---|---|---|
Alpha | B.1.1.7 | 20I (V1) | GRY | Sep 2020, United Kingdom | 18-Dec-2020 | former VOC | |
Beta | B.1.351 | 20H (V2) | GH/501Y.V2 | May 2020, South Africa | 18-Dec-2020 | former VOC | |
Gamma | P.1 | 20J (V3) | GR/501Y.V3 | Nov 2020, Brazil | 11-Jan-2021 | former VOC | |
Delta | B.1.617.2 | 21A | GK/478K.V1 | Oct 2020, India | 11-May-2021 | former VOC | |
Omicron | B.1.1.529/BA.1 | 21K | GR/484A | Nov 2021, Multiple countries | 26-Nov-2021 | former VOC | |
Omicron | BA.2 | 21L | GRA | Nov 2021, Multiple countries | 13-Dec-2021 | former VOC | |
Omicron | BA.4 | 22A | GRA | Jan. 2022 | 18-May-2022 | former VUM | |
Omicron | BA.5 | 22B | GRA | Jan. 2022 | 18-May-2022 | former VUM | |
Omicron | BA.2.12.1 | 22C | GRA | Dec. 2021 | 18-May-2022 | former VUM | |
Omicron | BA.2.75 | 22D | GRA | May 2022, India | 29-Jul-2022 | former VOC | |
Omicron | BQ.1 | 22E | GRA | Feb. 2021 | 12-Oct-2022 | former VUM | |
Omicron | XBB | 22F | GRA | Aug. 2022 | 12-Oct-2022 | VUM as of 29 January 2024 | |
Omicron | XBB.1.5 | 23A | GRA | Oct. 2022 | 11-Jan-2023 VUM, 15-Mar-2023 VOI | VOI as of 29 January 2024 | |
Omicron | XBB.1.16 | 23B | GRA | Jan. 2023 | 22-Mar-2023 VUM, 17-04-2023 VOI | VOI as of 29 January 2024 | |
Omicron | CH.1.1 | 23C | GRA | July 2022 | 9-Feb-2023 | former VUM | |
Omicron | XBB.1.9 | 23D | GRA | Dec. 2022 | 30-Mar-2023 | XBB.1.9.1 VUM as of 29 January 2024 | |
Omicron | XBB.2.3 | 23E | GRA | Sep. 2022 | 17-May-2023 | VUM as of 29 January 2024 | |
Omicron | EG.5.1 | 23F | GRA | Feb. 2023 | 9-Aug-2023 | EG.5 VOI as of 29 January 2024 | |
Omicron | XBB.1.5.70 | 23G | GRA | Mar. 2023 | n/a | n/a | |
Omicron | HK.3 | 23H | GRA | June 2023 | n/a | n/a | |
Omicron | BA.2.86 | 23I | GRA | July 2023 | 21-Nov-2023 | VOI | |
Omicron | JN.1 | 23I | GRA | Aug. 2023 | 18-Dec-2023 | VOI | |
Lambda | C.37 | 21G | GR/452Q.V1 | Dec 2020, Peru | 14-Jun-2021 | former VOI | |
Mu | B.1.621 | 21H | GH | Jan 2021, Colombia | 30-Aug-2021 | former VOI | |
Epsilon | B.1.429 | 21C | GH/452R.V1 | Mar 2020, USA | 06-Jul-2021 | former VUM | |
Eta | B.1.525 | 21D | G/484K.V3 | Dec 2020 | 20-Sep-2021 | former VUM | |
Iota | B.1.526 | 21F | GH/253G.V1 | Nov 2020, USA | 20-Sep-2021 | former VUM | |
Kappa | B.1.617.1 | 21B | G/452R.V3 | Oct 2020, India | 20-Sep-2021 | former VUM |
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., T22918GInsertions 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 GISAID 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 using the global_profile_alignment.sh script from the sarscov2phylo repository. Single-nucleotide substitutions were extracted from the alignment using the UCSC tool faToVcf (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 Minimap2 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 lineageVariants.py. The entire pipeline was run using lineageVariants.sh.
You can download the bigBed data files for this track from the UCSC Download Server. The data can be explored interactively with the Table Browser 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 third-party page:
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 BA.1 was added December 2, 2021 (called B.1.1.529 at the time of discovery).
Omicron lineages BA.4 and BA.5 were added in May 2022.
Omicron lineages BA.2, BA.2.12.1, BA.2.75, BQ.1, XBB, XBB.1.5, XBB.1.16, CH.1.1, XBB.1.9, XBB.2.3, and EG.5.1 were added in September 2023.
Omicron lineages XBB.1.5.70, HK.3, BA.2.86 and JN.1 were added in January 2024.
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. We thank Rob Lanfear at the Australia National University for developing and maintaining the sarscov2phylo web resource. We also thank the Su, Wu, and Andersen labs at Scripps Research for creating the Outbreak.info resource. The lineageVariants scripts were developed and run at UCSC by Nick Keener, Kate Rosenbloom and Angie Hinrichs.
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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 medRxiv preprint.
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: 10.5281/zenodo.3958883
Li, Heng 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. Outbreak.info