Spike Mutations Track Settings
Spike protein mutations from community annotation (Feb 2021)   (All Variation and Repeats tracks)

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Data schema/format description and download
Assembly: SARS-CoV-2 Jan. 2020 (NC_045512.2)
Data last updated at UCSC: 2021-03-10 21:29:20


The SARS-CoV-2 spike protein, which binds the virus to host cells, is a key target of vaccine development to combat COVID-19, and mutations in this protein have potential to change infectivity and response to disease treatments as well as vaccine efficacy. As of February 2021 more than a dozen mutations in this protein have been detected via sequencing worldwide, and specific mutations have been identified to be associated with viruses that are significantly more transmissible.

This track presents amino acid mutations identified in the SARS-CoV2 Spike protein, based on the community annotation at CoVariants.org, supplemented by the Variants of SARS-CoV-2 Wikipedia page.

Mutations in this track (with nicknames): H69-, D80Y, S98F, A222V, N439K (Nick), L452R, Y453F, S477N, E484 (Eeek), N501 (Nelly), D614G (Doug), A626S, P681H (Pooh), A701B, V1122

Information provided for each mutation, if available, includes:

  • Date first sequenced
  • Notes of clinical significance
  • Notes regarding geographic incidence
  • Link to charts and tables presenting geographic distribution
  • Link to Nextstrain build
  • Links to relevant publications

Display Conventions

The track items are colored as follows:

RedIdentified as strong antibody escape by Bloom Lab RBD-mutation screen
PurpleACE2 receptor binding region (RBD)

The mutation name, e.g. N501 as well as alternative identifiers (e.g. N501Y, 501Y) or nickname if present, can be typed in to the browser position box to navigate the browser to the mutation position and highlight the mutation in the browser window.

Release Notes

This track was updated to include the L453R mutation in the B.1.429 variant (first identified in California), as displayed in the Variants of Concern track. The color scheme was also changed in this track update.

Data Access

The raw data can be explored interactively with the Table Browser, or Data Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server. Data files for earlier versions of this track can be downloaded from our archive download server. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.


Thanks to Emma B. Hodcroft, Institute of Social and Preventive Medicine, University of Bern, Switzerland for leading and maintaining the community annotation resource on which this track is largely based.


CoVariants: SARS-CoV-2 Mutations and Variants of Interest Emma B. Hodcroft, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland

Variants of SARS-CoV-2, Wikipedia