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Covid-19 is changing: the emerging variants involving the protein sequence of the Sars-CoV-2 Spike protein are now our fear.
But how do they act? Exscalate4CoV tries to answer this difficult question with the Spike Mutants project.
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.
All viruses, including SARS-CoV-2, change over time. Some changes may affect the virus’s properties, such as how easily it spreads, the associated disease severity, or the performance of vaccines, therapeutic medicines, diagnostic tools, or other public health and social measures. WHO, in collaboration with partners, expert networks, national authorities, institutions and researchers have been monitoring and assessing the evolution of SARS-CoV-2 since January 2020. During late 2020, the emergence of variants that posed an increased risk to global public health prompted the characterisation of specific Variants of Interest (VOIs) and Variants of Concern (VOCs). (www.who.int).
A variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.
Lineage: B.1.1.7
WHO Label: Alpha
Predicted Attributes:
Lineage: B.1.351
WHO Label: Beta
Predicted Attributes:
Lineage: P.1
WHO Label: Gamma
Predicted Attributes:
Lineage: B.1.617.2
WHO Label: Delta
Lineage: BA.1, BA.5
WHO Label: Omicron
Predicted Attributes:
A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity
Lineage: B.1.427, B.1.429
WHO Label: Epsilon
Predicted Attributes:
Lineage: P.2 (484 K.V2)
WHO Label: Zeta
Predicted Attributes:
Lineage: B.1.525
WHO Label: Eta
Predicted Attributes:
Lineage: B.1.526
WHO Label: Iota
Predicted Attributes:
Lineage: B.1.617.1, B.1.617.3
WHO Label: Kappa
A SARS-CoV-2 variant with genetic changes that are suspected to affect virus characteristics with some indication that it may pose a future risk, but evidence of phenotypic or epidemiological impact is currently unclear, requiring enhanced monitoring and repeat assessment pending new evidence.
Lineage: B.1.640.1
WHO Label: Ihu
(*) Provided by Istituto Spallanzani
Predicted Attributes:
For each country, we show the main 3D model in the colored box. In addition, we show other structures with different mutations (MUTANT) in the white boxes.
Lineage: B.1.1.7
Mutations: AHV69-70Δ, Y144Δ, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
Mutations: HV 69-70Δ, Y144 Δ, N501Y, P681H. This mutant is for UK variant without D614G
Mutations: HV69-70Δ, Y144Δ, N501Y, D614G, P681H
Mutations: HV69-70Δ, Y144Δ, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
Lineage: B.1.351
Mutations: D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V, Δ241-243
Lineage: BA.1
Mutations: A67V, H69Δ, V70Δ, T95I, G142D, V143Δ, Y144Δ, Y145Δ, N211Δ, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
Lineage: BA.5
Mutations: Δ25/27, Δ69/70, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K,L452R,S477N,T478K,E484A,F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Lineage: P.1
Mutations: D138Y, R190S, K417T, E484K,N501Y, D614G, H655Y, T1027I
Lineage: P.2 (484 K.V2)
Mutations: E484K, D614G, V1176F
Mutations: K417N, E484K, N501Y
Mutations: E484K
Mutations: E484K, V1176F
Mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F
Lineage: B.1.617.2
Mutations: EE156/157Δ, R158G, L452R, T478K, D614G, P681R, D950N
Lineage: B.1.617.1, B.1.617.3
Mutations: E154K, E484Q, D614G, P681R, Q1071H
Lineage: B.1.427, B.1.429
Mutations: S13I, W152C, L452R, D614G
Lineage: B.1.525
Mutations: Q52R, A67V, Δ69/70, Δ144/144, E484K, D614G, Q677H, F888L
Lineage: B.1.526
Mutations: L5F, T95I, D253G, S477N, D614G
Lineage: B.1.526
Mutations: L5F, T95I, D253G, E484K, D614G
Lineage: B.1.640.1
Mutations: E96Q, CNDPFLGVY136-144Δ, R190S, I210T, R346S, N394S, Y449N, F490R, N501Y, D614G, P681H, T859N, D936H, K1191N
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.
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[doi:10.3390/ijms22115464]