| Version | Summary | Created by | Modification | Content Size | Created at | Operation |
|---|---|---|---|---|---|---|
| 1 | Nagendra Kaushik | -- | 1886 | 2022-06-10 09:35:38 | | | |
| 2 | Camila Xu | Meta information modification | 1886 | 2022-06-10 09:50:21 | | | | |
| 3 | Camila Xu | Meta information modification | 1886 | 2022-06-10 09:51:10 | | | | |
| 4 | RAJAN ROLTA | + 200 word(s) | 2086 | 2022-06-10 10:29:08 | | | | |
| 5 | RAJAN ROLTA | Meta information modification | 2086 | 2022-06-10 10:29:56 | | | | |
| 6 | Camila Xu | -135 word(s) | 1951 | 2022-06-10 10:39:20 | | |
Since November 2019, SARS-CoV-2 has been a matter of global concern due to its rapid spread, the millions of deaths it caused, and repeated waves of infections. One after another, many variants of this novel virus have come into existence due to its constant mutability, specifically in the spike glycoprotein region. The tally for variants of concern (VOCs), which already include Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2), has increased to five with the latest appearance of Omicron (B.1.1.529).
Figure 1. Major amino acid mutations marked on the entire SARS-CoV-2 sequence: (a) Wild-type strain, (b) Alpha variant, (c) Beta variant, (d) Gamma variant, (e) Delta variant and (f) Omicron variant. (M: membrane protein, E: envelope protein, S: Spike protein, N: Nucleocapsid protein, ORF: Open Reading Frame, UTR: Untranslated Region).
Figure 2. Spike glycoprotein of SARS-CoV-2; (i): S1/S2 protease cleavage site; SP: signal peptide; NTD: N-terminal domain; RBD: receptor-binding domain; RBM: receptor-binding motif; FP: fusion peptide; HR1: heptapeptide domain 1; HP2: heptapeptide domain 2; TM: transmembrane domain; CD: cytoplasmic domain 3. (ii): SARS-CoV-2 spike glycoprotein trimeric structure showing chains A (pink), B (blue) and C (green) of (a) closed state (7DF3), (b) 1 RBD up (7LWT), (c) 2 RBD up (7LYK) and (d) 3 RBD up (7CAK) (figure visualized using USF Chimera).
Figure 3. The entry and immunopathology of SARS-CoV-2 in the human body. Adapted from “Mechanism of SARS-CoV-2 Viral Entry, Acute Respiratory Distress Syndrome (ARDS), Adaptive Immunity and Interferons”, by biorender.com (accessed on 5 January 2022). Retrieved from https://app.biorender.com/biorender-templates; image for “memory cell and IFN gamma” from <https://reactome.org/PathwayBrowser/#/R-HSA-168256&SEL=R-HSA-1280218> and image for “ACE2” from https://reactome.org/PathwayBrowser/#/R-HSA-2022377&SEL=R-HSA-2022344&PATH=R-HSA-392499,R-HSA-2980736&FLG=Q9BYF1. Reactome, (all accessed on 30 December 2021).
Figure 4. Maps showing global country-wise sequence count of all variants of concern as of 13 September 2021. (a) Sequence count of B.1.1.7 (Alpha variant), (b) sequence count of B.1.351 (Beta variant), (c) sequence count of P.1 (Gamma variant), (d) Sequence count of B.1.617.2 (Delta variant) and (e) sequence count of B.1.1.529 (Omicron variant) (data source: GISAID, Figure redrawn using GeoMaps).| WHO Label | Pango Lineage | Potential Emergence | Number of Countries Affected | Important Spike Mutations | Sequenced Genomes (GISAID) |
Impact of Mutations |
Transmissibility of Variant |
|---|---|---|---|---|---|---|---|
| Alpha | B.1.1.7 | UK, September 2020 | 170 | N501Y P681H |
11,49,443 | P681H: Slightly increases the S1–S2 cleavage [32]. N501Y: Enhances binding affinity between spike RBD domain and hACE2 receptor [33]. E484K *, L452R * |
~70% increase with respect to wild type |
| Beta | B.1.351 | South Africa, May 2020 |
112 | K417N E484K N501Y |
39,604 | K417N: Responsible for antibody-escape property of the virus [34]. N501Y: Same as above. E484K: Reduces antibody neutralisation and is responsible for increased infectivity [35]. |
20–113% increase with respect to wild type |
| Gamma | P.1 | Brazil, November 2020 | 80 | K417T E484K N501Y |
1,17,675 | K417T: Responsible for antibody escape property of the virus [34]. N501Y: Same as above. E484K: Same as above. |
~161% increase with respect to wild type |
| Delta | B.1.617.2 | India, October 2020 |
105 | L452R T478K P681R |
34,37,588 | T478K: Helps evade neutralising antibodies. Enhances viral infectivity [36]. L452R: Impairs antibody neutralization. Increases viral infectivity [34][37]. P681R: Increases the rate of S1–S2 cleavage, and hence results in enhanced transmissibility [35]. |
|
| Omicron | B.1.1.529 | Multiple countries, November 2021 |
- | H655Y N679K P681H E484A Q498R N501Y |
5352 | N501Y: Same as above. H655Y: May be associated with increased transmissibility as it is proximal to the Furin cleavage site, hence aids in increased spike cleavage (CoVariants-GISAID). N679K: Associated with increased transmissibility (CoVariants-GISAID). P681H: Slightly increases the S1–S2 cleavage [32]. E484A: May be associated with immune escape (CoVariants-GISAID). Q498R: Enhances binding affinity with ACE2 receptor in combination with N501Y (CoVariants-GISAID). |
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