sars-cov-2

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Last Update: March 2021

Sars-CoV-2 SPIKE Variants

The Spike Mutants website aims to provide the scientific community with structural information on emerging variants involving the protein sequence of the Sars-CoV-2 Spike protein.

The emergence of new SARS-CoV-2 variants harboring mutations in the Spike protein that might impact viral fitness and transmissibility has been an issue of great concern, particularly after the recent identification of two independent emerging strains in UK and South Africa with a larger than usual number of mutations in the Spike protein that may have functional significance (virological.org).

Previous reports of the D614G mutation and the recent reports of virus variants from the Kingdom of Denmark, the United Kingdom of Great Britain and Northern Ireland, and the Republic of South Africa have raised interest and concern in the impact of viral changes (www.who.int).

Most Common SARS-COV-2 Spike variants


Mutations related to the new variants of the Spike protein.

UK variant

VOC 202012/01
(B.1.1.7 lineage)


Mutations: HV 69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H, T716I,S982A and D1118H.


Reference: 1,2,12

South Africa variant

501Y.V2
(B.1.351 lineage)


Mutations: L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G and A701V.


Reference: 5,6,7,10,12

Danish Mink variant



Mutations: HV 69-70 deletion, Y453F, D614G, I692V, S1147L, and M1229I.


Reference: 8,12

Brazilian variant

(B.1.1.248,
derived from B.1.1.28)


Mutations:
Clade B.1.1.28 (E484K) - E484K and V1176F.


Reference: 3,4,9

Brazilian variant

(B.1.1.248,
derived from B.1.1.28)


Mutations:
Clade B.1.1.28 (K417N/E484K/N501Y) - L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.


Reference: 3,4,9

Japan variant

GISAID ID: EPI_ISL_792680
to 792683


Mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.


Reference: 11

1. Andrew Rambaut, Nick Loman, Oliver Pybus, Wendy Barclay, Jeff Barrett, Alesandro Carabelli, Tom Connor, Tom Peacock, David L Robertson, Erik Volz, on behalf of COVID-19 Genomics Consortium UK (CoG-UK). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations.
https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563.
2. WHO SARS-CoV-2 variant—United Kingdom of Great Britain and Northern Ireland.
https://www.who.int/csr/don/21-december-2020-sars-cov2-variant-united-kingdom/en
 3. Paola Cristina Resende et al. Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020.
https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584.
 4. Felipe Naveca et al. Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein.
https://virological.org/t/phylogenetic-relationship-of-sars-cov-2-sequences-from-amazonas-with-emerging-brazilian-variants-harboring-mutations-e484k-and-n501y-in-the-spike-protein/585

5. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V,Giandhari J, et al. 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]. 22 December 2020;
Available from:
https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v151.Salim S.
 6. Abdool Karim. The 2nd Covid-19 wave in South Africa:Transmissibility & a 501.V2 variant. 18 December 2020. Available from:
https://www.scribd.com/document/488618010/Full-Presentation-by-SSAK-18-Dec
 7. Republic of South Africa -Department of Health. Update on Covid-19.18 December 2020.
Available from:
https://sacoronavirus.co.za/2020/12/18/update-on-covid-19-18th-december-2020/
 8. Statens Serum Institut (SSI). Preliminary rapport on SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data. SARS-CoV-2 spike mutations arising in Danish mink and their spread to humans.
24 December 2020].
Available from:
https://www.ssi.dk/-/media/arkiv/dk/aktuelt/nyheder/2020/mink-cluster-5-kort-rapport.pd

9. Nuno R. Faria et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings.
https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
10. Houriiyah Tegally et al. 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 2020.12.21.20248640;
doi: https://doi.org/10.1101/2020.12.21.20248640
 11. Brief report: New Variant Strain of SARS-CoV-2Identified in Travelers from Brazil.
https://www.niid.go.jp/niid/images/epi/corona/covid19-33-en-210112.pdf
 12. European Centre for Disease Prevention and Control. Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA –29 December2020. ECDC: Stockholm; 2020.
https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf

COVID-19 in VR: Spike Protein Mink Mutations

In this video we discuss the amino acid changes in the spike surface glycoprotein that appeared during the recent outbreak in Danish mink and their effect on the antigenicity of the SARS-CoV-2 virus.

Spike Protein Mink Mutations

UK Variant:


Mutant 1*

HV 69-70 deletion, Y144 deletion, N501Y, D614G, P681H.

Mutant 2*

HV 69-70 deletion, Y144 deletion, N501Y, P681H.

Mutant 9**

HV69-70del, Y144del, N501Y, D614G, P681H.

Mutant 10**

HV69-70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A,
D1118H.

South Africa Variant:


Mutant 6**

K417N, E484K, N501Y.

Mutant 11**

L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V.

Danish Mink Variant:


Mutant 5*

HV69-70 deletion and Y453F.

Mutant 8**

HV69-70del, Y453F.

Mutant 12**

HV69-70del, Y453F, D614G, I692V, S1147L, M1229I.

Brazil Variant:


Mutant 7**

E484K.

Mutant 13**

E484K, V1176F.


Brazil Variant:


Mutant 6**

K417N, E484K, N501Y.

Japan Variant:


Mutant 6**

K417N, E484K, N501Y.

Mutant 14**

L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F.


We acknowledge ENI and CINECA
for the support and concession of the HPC5 and Marconi100 super-computers,
indispensable high-performance processing resources for the molecular dynamics experiments.

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developed by Anna Fava for Nuovi S.O.C.I.