Last Update: March 2021
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).
Mutations related to the new variants of the Spike protein.
Mutations: HV 69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H, T716I,S982A and D1118H.
Mutations: L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G and A701V.
Mutations: HV 69-70 deletion, Y453F, D614G, I692V, S1147L, and M1229I.
derived from B.1.1.28)
Clade B.1.1.28 (E484K) - E484K and V1176F.
derived from B.1.1.28)
Clade B.1.1.28 (K417N/E484K/N501Y) - L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.
GISAID ID: EPI_ISL_792680
Mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.
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.
2. WHO SARS-CoV-2 variant—United Kingdom of Great Britain and Northern Ireland.
3. Paola Cristina Resende et al. Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020.
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.
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;
6. Abdool Karim. The 2nd Covid-19 wave in South Africa:Transmissibility & a 501.V2 variant. 18 December 2020. Available from:
7. Republic of South Africa -Department of Health. Update on Covid-19.18 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].
9. Nuno R. Faria et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings.
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;
11. Brief report: New Variant Strain of SARS-CoV-2Identified in Travelers from Brazil.
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.
*Models built based on PDB 6VYB returned to its wild-type form and fully glycosylated,
thanks to Universitá della Tuscia, DIBAF Department,
thanks to The Department of Biotechnology of the High Institute of Biotechnology of Sidi Thabet (University of Manouba, Tunisia)
thanks to The Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy (University of Monastir, Tunisia).
**Models built based on heteromer PDB 7A94 SPIKE with ACE2_HUMAN bound,
thanks to Swiss intitute of Bioinformatics.