Variant

Last updated: 2022 Jan 10
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Original Article
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The trimer organisation of the Omicron spike protein ectodomain is similar to that of the original strain and all the earlier variants, according to cryo-EM structural study. The Omicron variant has 37 mutations in the spike protein, and 15 of which are in the receptor binding region (RBD) The Omicron variant spike protein contains 3-5 times the number of mutations found in prior SARS-CoV-2 strains. Understanding the effects of these mutations on ACE2 receptor binding and neutralising antibody evasion is critical for developing effective therapies to stop the spread of the Omicron and related variations.
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 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
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Date of Entry 2022 Jan 10

Cryo-EM structure of the Omicron variant spike protein in complex with human ACE2 reveals salt bridge between RBD N417 and ACE2 D30 is lost. R493, R498 form salt bridge with ACE2 residues E35, D38, respectively and S496 forms a hydrogen bond with ACE2 residue K353. Compared to the Delta variant, new interactions are formed as a result of the mutations Q493R, G496S and Q498R, and the salt bridge between RBD K417 and ACE2 D30 is lost.
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 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
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Date of Entry 2022 Jan 10

Structural analysis was done to show the position of mutated residues in the Lambda spike regions (NTD and RBD). Three mutations (G75V, T76I, and RSYLTPGD246-253N) were presentin theN-terminal domain (NTD)and the deletion mutation (RSYLTPGD246-253N)mutation was observedin a loop structure(loop 5).Another protein region (Receptor binding domain) containstwo mutations (L452Q and F490S). In addition, the T859N mutation wasfound in a specificSpikesubunit (S2heptad repeat 1). Loop 5 contains 246-260 residues, which was a loop structure designated in a previous study.
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 		Pre-print (bioRXiv)
Title SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
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Date of Entry 2021 Dec 15

The cryo-EM structure of the S protein of the Alpha variant in the apo form and receptor ACE-2 bound form were charecterised. The A570D mutation modulates the opening and closing of the receptor binding domain (RBD) by introducing a salt bridge. The N501Y mutation increases ACE-2 binding affinity by introducing pi-pi interaction.
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 		Pre-print (bioRXiv)
Title Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations
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Date of Entry 2021 Sep 13