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)
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart21766Start position in chromosome
chromEnd21772End position in chromosome
nameH69-Mutation name: amino acid, position, substitution
score0Score (always 0)
strand.Strand (always .)
thickStart21766n/a
thickEnd21772n/a
color0,0,255Color, based on date first sequenced (blue oldest, red most recent)
seqDate2020-01-05Date first sequenced
sourcecovariants.orgSource site for this item
clinicalNotesMay 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
geographyNotesn/aNotes pertaining to geographical distribution
geographyChartsUrlhttps://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.H69-_table.mdLink to charts and tables describing geographical distribution
nextstrainBuildUrlhttps://nextstrain.org/groups/neherlab/ncov/S.H69-?c=gt-S_69,501,453Link to Nextstrain build phylogeny visualization
publicationsUrlshttps://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/10.1101/2020.11.19.389916v1Comma separated list of links to relevant publications

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndcolorseqDatesourceclinicalNotesgeographyNotesgeographyChartsUrlnextstrainBuildUrlpublicationsUrls
NC_045512v22176621772H69-0.21766217720,0,2552020-01-05covariants.orgMay alter the recognition by antibodies, possibly impacting some antibody-therapy treatments, or immunity. In one study, was ide ...n/ahttps://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.H69-_table.mdhttps://nextstrain.org/groups/neherlab/ncov/S.H69-?c=gt-S_69,501,453https://www.medrxiv.org/content/10.1101/2020.12.05.20241927v2, https://www.biorxiv.org/content/10.1101/2020.12.14.422555v3, http ...
NC_045512v22179921802D80Y0.21799218020,0,25520-07-16covariants.orgn/aFound in at least 10 countries across Europehttps://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.D80Y_table.mdhttps://nextstrain.org/groups/neherlab/ncov/S.D80Y?f_region=Europehttps://www.biorxiv.org/content/10.1101/2020.05.01.072330v1
NC_045512v22185321856S98F0.21853218560,0,2552020-03-21covariants.orgn/aMostly found in Belgium and the Netherlands - predominantly Belgiumhttps://github.com/hodcroftlab/covariants/blob/master/cluster_tables/S.S98F_table.mdhttps://nextstrain.org/groups/neherlab/ncov/S.S98F?c=gt-S_98&f_region=Europen/a
NC_045512v22222522228A222V0.22225222280,0,2552020-06-01covariants.orgMutation 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 travelhttps://github.com/hodcroftlab/covariants/blob/master/cluster_tables/20A.EU1_table.mdhttps://nextstrain.org/groups/neherlab/ncov/20A.EU1?f_region=Europehttps://www.medrxiv.org/content/10.1101/2020.10.25.20219063v2
NC_045512v22287622879N439K0.2287622879255,0,02020-05-13covariants.orgMutation 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 extincthttps://nextstrain.org/groups/neherlab/ncov/S.N439K?c=gt-S_439&f_region=Europehttps://www.sciencedirect.com/science/article/pii/S0022283620304563, https://www.biorxiv.org/content/10.1101/2020.11.30.405472v1 ...
NC_045512v22291522918L452R0.2291522918255,0,02020-09-12covariants.orgMutation 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.L452Rhttps://www.biorxiv.org/content/10.1101/2020.11.06.372037v1, https://www.medrxiv.org/content/10.1101/2021.01.18.21249786v1
NC_045512v22291822921Y453F0.2291822921128,0,1282020-04-25covariants.orgMay 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=Minkhttps://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008449, https://science.sciencemag.org/content/369/6506/ ...
NC_045512v22299022993S477N0.2299022993128,0,1282020-07-09covariants.orgMutation 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 outbreakhttps://github.com/hodcroftlab/covariants/blob/master/cluster_tables/20A.EU2_table.mdhttps://nextstrain.org/groups/neherlab/ncov/20A.EU2?f_region=Europehttps://www.sciencedirect.com/science/article/pii/S0022283620304563, https://www.biorxiv.org/content/10.1101/2020.11.03.367391v1 ...
NC_045512v22301123014E4840.2301123014255,0,02020-03-09covariants.orgMutations 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.mdhttps://nextstrain.org/groups/neherlab/ncov/S.E484?c=gt-S_484&f_region=Europehttps://www.biorxiv.org/content/10.1101/2020.12.31.425021v1, https://www.preprints.org/manuscript/202101.0132/v1, https://www.bi ...
NC_045512v22306223065N5010.2306223065255,0,02020-03-19covariants.orgVariant 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.mdhttps://nextstrain.org/groups/neherlab/ncov/S.N501https://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
 

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 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)
BlueOther

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.

Credits

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.

References

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