Table 1.
Genetic mutations in the S protein of SARS-CoV-2 and its variants of concern (VOC), as well as their consequences.
| SARS-CoV2 (Wuhan strain) | Alpha variant | Beta | Gamma | Delta | Omicron | References | |
|---|---|---|---|---|---|---|---|
| Lineage | B.1.1.7 | B.1.351 | P.1 | B.1.617.2 | B.1.1.529 | [1, 5, 6, 20, 28, 32, 38, 45, 61, 62, 64] | |
| Total mutations in spike protein | 1(D614G) | 9 (ΔH69-V70 deletion, ΔY144 deletion, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) | 10 (L18F, D80A, D215G, Δ242-244, R246I, K417N, E484K, N501Y, D614G, and A701V) | 12 (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F) | 17 (T19R, V70F, G142D, 156del, 157del, R158G, Δ213-214, A222V, W258L, K417N, L452R, T478K, E484Q, D614G, P681R, D950N, T95I) | 39 (A67V, H69del, V70del, T95I, G142del, V143del, Y144del, Y145D, N211del, L212I, ins214E, ins215P, ins216E, 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 | [2, 3, 8–10, 20–22, 32, 33, 37, 38, 45] |
| Mutations in NTD (14–305 aa) | 0 | 2 (Δ69-70 deletion, Δ144 deletion) | 5 (L18F, D80A, D215G, Δ242-244. R246I) | 5 (L18F, T20N, P26S, D138Y, R190S) | 9 (T19R, V700F, G142D, 156del, 157del, R158G, A222V, W258L, Δ213-214) | 13 (A67V, H69del, V70del, T95I, G142del, V143del, Y144del, Y145D, N211del, L212I, ins214E, ins215P, ins216E) | [2, 3, 5, 6, 8–10, 20–22, 32, 33, 37, 38, 45] |
| Mutation in RBD region (319–541 aa) | 0 | 1 (N501Y) | 3 (K417, E484K, N501Y) | 3 (K417T, E484K, N501Y) | 4 (K417N, L452R, T478K, E484K) | 15 (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H,) | [2, 3, 8, 9, 22, 28, 37, 38, 45] |
| Common mutations in NTD (14–305aa) | – | Δ69–70 deletion, Δ144 deletion | L18F | L18F | – | H69del, V70del, Y144del | [2, 3, 5, 6, 8–10, 20–22, 32, 33, 37, 38, 45] |
| Common Mutation in RBD region (319–541 aa) | – | N501Y | N501Y, E484K | K417N, E484K N501Y, | K417N, T478K, E484K | K417N. T478K, E484K, N501Y | [2, 3, 8, 9, 22, 28, 37, 38, 45] |
| Mutations in FCS (681PRRAR 685) | – | P681H | – | – | P681H | P681H | [10, 11, 33, 37, 38, 45] |
| Binding affinity with human ACE2 | Increased | Increased | Increased | Increased | Increased | Decreased | [8, 22, 32, 33, 34, 39, 40] |
| Impact on transmissibility | Increased | Increased | Increased | Increased | Increased | Increased | [24, 25, 30, 32, 33, 62, 63,69] |
| Disease severity | Not increased compared to SARS-CoV | Increased | Increased | Increased | Increased | Reduced | [12, 34, 38, 46, 47, 66, 69] |
| Impact on infectivity | Increased compared to SARS-CoV | Increased | Increased | Increased | Increased | Increased | [34, 38, 46, 47, 66, 69] |
| Hospitalization Risk | Increased | Increased | Increased | Increased | Increased | Reduced | [28, 29, 35, 61, 64, 66, 69] |
| Mortality rate | Increased | Increased | Increased | Increased | Increased | Reduced | [28, 29, 61, 64, 66, 69] |
| Testing kit failure | – | Yes | No | – | Yes | Yes | [2, 23, 29, 60] |
| Immune escape | Yes | Yes | Yes | Yes | Yes | [1, 23, 34, 41, 51] | |
| Impact on effectiveness of vaccine | 96% (Pfize- BioNTech) | No significant changes | No significant changes | No significant changes | No significant changes | Little change | [13, 14, 15, 16, 17, 18, 19, 26, 27, 36, 38, 42, 43, 44, 48–50] |