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 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 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:

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

        [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:

• SARS-CoV-2 Variants and Lineages of Concern from the Bacterial and Viral Bioinformatics Resource Center.

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 was added December 2, 2021.

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