Schema for Spike Mutations - Spike protein mutations from community annotation (Feb 2021)
Database: wuhCor1 Primary Table: spikeMuts Data last updated: 2021-03-10|
Big Bed File: /gbdb/wuhCor1/spikeMuts/spikeMuts.Feb21.bb
Item Count: 15
Format description: COVID spike mutations (BED 9+7)
|chrom||NC_045512v2||Reference sequence chromosome or scaffold|
|chromStart||21766||Start position in chromosome|
|chromEnd||21772||End position in chromosome|
|name||H69-||Mutation name: amino acid, position, substitution|
|score||0||Score (always 0)|
|strand||.||Strand (always .)|
|color||0,0,255||Color, based on date first sequenced (blue oldest, red most recent)|
|seqDate||2020-01-05||Date first sequenced|
|source||covariants.org||Source site for this item|
|clinicalNotes||May alter the recognition by antibodies, possibly impacting some antibody-therapy treatments, or immunity. In one study, was identified as a 'recurrent deletion region' (found multiple times in public sequences), but did not impact the 2 monoclonal antibodies tested.||Notes pertaining to clinical significance|
|geographyNotes||n/a||Notes pertaining to geographical distribution|
|geographyChartsUrl||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.H69-_table.md||Link to charts and tables describing geographical distribution|
|nextstrainBuildUrl||https://nextstrain.org/groups/neherlab/ncov/S.H69-?c=gt-S_69,501,453||Link to Nextstrain build phylogeny visualization|
|publicationsUrls||https://www.medrxiv.org/content/10.1101/2020.12.05.20241927v2, https://www.biorxiv.org/content/10.1101/2020.12.14.422555v3, https://www.biorxiv.org/content/10.1101/2020.11.19.389916v1||Comma separated list of links to relevant publications|
|NC_045512v2||21766||21772||H69-||0||.||21766||21772||0,0,255||2020-01-05||covariants.org||May alter the recognition by antibodies, possibly impacting some antibody-therapy treatments, or immunity. In one study, was ide ...||n/a||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.H69-_table.md||https://nextstrain.org/groups/neherlab/ncov/S.H69-?c=gt-S_69,501,453||https://www.medrxiv.org/content/10.1101/2020.12.05.20241927v2, https://www.biorxiv.org/content/10.1101/2020.12.14.422555v3, http ...|
|NC_045512v2||21799||21802||D80Y||0||.||21799||21802||0,0,255||20-07-16||covariants.org||n/a||Found in at least 10 countries across Europe||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.D80Y_table.md||https://nextstrain.org/groups/neherlab/ncov/S.D80Y?f_region=Europe||https://www.biorxiv.org/content/10.1101/2020.05.01.072330v1|
|NC_045512v2||21853||21856||S98F||0||.||21853||21856||0,0,255||2020-03-21||covariants.org||n/a||Mostly found in Belgium and the Netherlands - predominantly Belgium||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.S98F_table.md||https://nextstrain.org/groups/neherlab/ncov/S.S98F?c=gt-S_98&f_region=Europe||n/a|
|NC_045512v2||22225||22228||A222V||0||.||22225||22228||0,0,255||2020-06-01||covariants.org||Mutation in the non-terminal domain (NTD), which is not known to play a direct role in receptor binding or membrane fusion. Subc ...||Associated with a cluster that initially expanded in Spain and spread across Europe via holiday travel||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/20A.EU1_table.md||https://nextstrain.org/groups/neherlab/ncov/20A.EU1?f_region=Europe||https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v2|
|NC_045512v2||22876||22879||N439K||0||.||22876||22879||255,0,0||2020-05-13||covariants.org||Mutation is in the receptor binding domain (RDB), important to ACE2 binding and antibody recognition. May increase ACE2 binding. ...||Has emerged twice independently in Europe, but was exclusive to Scotland in the first wave and went extinct||https://nextstrain.org/groups/neherlab/ncov/S.N439K?c=gt-S_439&f_region=Europe||https://www.sciencedirect.com/science/article/pii/S0022283620304563, https://www.biorxiv.org/content/10.1101/2020.11.30.405472v1 ...|
|NC_045512v2||22915||22918||L452R||0||.||22915||22918||255,0,0||2020-09-12||covariants.org||Mutation is in the receptor binding domain (RDB), important to ACE2 binding and antibody recognition. In a study co-incubating p ...||First detected in September 2020 in the US. On January 17, 2021, the California Dept. of Public Health announced that an L452R v ...||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.L452R_table.md|| https://nextstrain.org/groups/neherlab/ncov/S.L452R||https://www.biorxiv.org/content/10.1101/2020.11.06.372037v1, https://www.medrxiv.org/content/10.1101/2021.01.18.21249786v1|
|NC_045512v2||22918||22921||Y453F||0||.||22918||22921||128,0,128||2020-04-25||covariants.org||May be a mink-specific adaptation, increasing binding to mink ACE2. May also increase ACE2 binding in humans. Does confer resist ...||Associated with the 'cluster 5' 'mink' variant in Denmark and the Netherlands.||https://nextstrain.org/groups/neherlab/ncov/netherlands?c=gt-S_453&f_country=Netherlands&f_host=Mink||https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008449, https://science.sciencemag.org/content/369/6506/ ...|
|NC_045512v2||22990||22993||S477N||0||.||22990||22993||128,0,128||2020-07-09||covariants.org||Mutation is in the receptor binding domain (RDB), important to ACE2 binding and antibody recognition. May slightly increase ACE2 ...||Has arisen independently in Australia and was responsible for much of the summer 2020 outbreak||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/20A.EU2_table.md||https://nextstrain.org/groups/neherlab/ncov/20A.EU2?f_region=Europe||https://www.sciencedirect.com/science/article/pii/S0022283620304563, https://www.biorxiv.org/content/10.1101/2020.11.03.367391v1 ...|
|NC_045512v2||23011||23014||E484||0||.||23011||23014||255,0,0||2020-03-09||covariants.org||Mutations at S:E484 may significantly reduce convalescent serum neutralization. There has been a case of reinfection associated ...||Primarily associated with the 501Y.V2 variant that arose in South Africa in the winter of 2020 and a variant predominantly found ...||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.E484_table.md||https://nextstrain.org/groups/neherlab/ncov/S.E484?c=gt-S_484&f_region=Europe||https://www.biorxiv.org/content/10.1101/2020.12.31.425021v1, https://www.preprints.org/manuscript/202101.0132/v1, https://www.bi ...|
|NC_045512v2||23062||23065||N501||0||.||23062||23065||255,0,0||2020-03-19||covariants.org||Variant of Concern. First detected in October 2020 in the UK, correlated with significant increased rate of infection. Mutation ...||Associated with recently reported 'new variants' in the UK and South Africa. Smaller clusters also seen in Wales, USA, & Austral ...||https://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.N501_table.md||https://nextstrain.org/groups/neherlab/ncov/S.N501||https://www.biorxiv.org/content/10.1101/2020.12.14.422555v3, https://www.thelancet.com/article/S0140-6736(20)31757-8/fulltext, h ...|
Spike Mutations (spikeMuts) Track Description
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
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
The track items are colored as follows:
|Red||Identified as strong antibody escape by Bloom Lab RBD-mutation screen|
|Purple||ACE2 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.
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
The color scheme was also changed in this track update.
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
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