Schema for Variants of Concern - Mutations in Variants of Concern (VOC), Interest (VOI), or Under Monitoring (VUM) (configure to show more lineages)
  Database: wuhCor1    Primary Table: variantNucMutsV2_C_37 Data last updated: 2021-09-29
Big Bed File Download: /gbdb/wuhCor1/strainMuts/variantNucMuts_C.37_2021_09_10.bb
Item Count: 27
The data is stored in the binary BigBed format.

Format description: Browser Extensible Data
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart21785Start position in chromosome
chromEnd21786End position in chromosome
nameG21786TName of item.

Sample Rows
 
chromchromStartchromEndname
NC_045512v22178521786G21786T
NC_045512v22178821789C21789T
NC_045512v22229822319del_22299
NC_045512v22291622917T22917A
NC_045512v22303023031T23031C
NC_045512v22340223403A23403G
NC_045512v22373023731C23731T
NC_045512v22413724138C24138A
NC_045512v22825228253C28253T
NC_045512v22827028271A28271T

Variants of Concern (variantMuts) Track Description
 

Description

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.

  • 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 representative sequences.

Display Conventions

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:

ColorWHO label Pangolin lineageNextstrain cladeGISAID clade First detectedDate VOC/VOIType
      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., T22918G
Insertions and deletions in both tracks are named:
        [del/ins]_[1-based genomic coordinate of first affected nucleotide].  E.g., del_21991

Methods

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.

Data Access

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:

Release Notes

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.

Credits

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.

References

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. PMID: 32669681

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