Table 1.
SARS-CoV-2 variants, mutations and their impact.
| WHO variant name | Sub variants | Date first identified/Country | Spike protein mutations | Other mutations | Impact | Ref. |
|---|---|---|---|---|---|---|
| Alpha | B.1.1.7 | November 2020/UK | HV69-70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H | D3L, R203K, G204R, S235F | • Increased transmission • Increase in incidences of hospitalisations |
(27) |
| Beta | B.1.351 | May 2020/South Africa | L18F, D80A, D215G, 242-244del, R246I, K417N, E484K, N501Y, D614G, A701V | T205I | • Increased transmission | (28) |
| Gamma | B.1.1.248 (P.1 and P.2) | Nov-2020/Brazil | K417T, E484K, and N501Y | D138Y, R190S | • Increase affinity to ACE 2 receptor • Reduces the neutralizing activity |
(29, 30) |
| Delta | B.1.617.2 (Delta) | October 2020/India | T19R, G142D, EF156-157del, R158G, L452R, T478K, D614G, P681R, D950N | D63G, R203M, D377Y | • Decreased ability of immune system to identify the virus. • Increase affinity to ACE 2 receptor |
(31) |
| (Delta plus) | 03 March 2022/India | K417N, T19R, G142D, EF156-157del, R158G, L452R, T478K, D614G, P681R, D950N | D63G, R203M, D377Y | • It has higher tolerance to monoclonal antibodies compare to delta variant • Increase transmissibility and higher binding affinity towards lung epithelial cells compare to all other variants. |
(32) | |
| Omicron | BA.1 | 08 November 2021/ Botswana, South Africa | A67V, HV69-70del, T95I, G142D, VYY143-145del, N211del, 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 | nsp3 (K38R, V1069I, Δ1265, L1266I, A1892T), nsp4 (T492I), nsp5 (P132H), nsp6 (Δ105-107, A189 V), nsp12 (P323L), and nsp14 (I42V). Nsp3 (Plpro) and nsp5 (3Clpro, main protease) | • Changes in the shape of protein to which different class of antibody binds. • Compare to other variants has the highest transmission |
(23, 33–35) |
| BA.2 | 22 October 2021/Philippines | BA.2 shares 32 mutations with BA.1 but has 28 distinct ones. RBD mutations: 371F, T376A, D405N, and R408S, and BA.3 has S371F, D405N, and G446S | • All these variants have higher transmission and stronger immune invasion compare to BA.1 | (36–38) | ||
| BA.3 | 23 November 2021/northwest South Africa | N501Y, Q498R, H655Y, N679K, and P681H. BA.3 shares ten mutations (A67V, H69del, V70del, T95I, V143del, Y144del, Y145del, N211I, L212del, and G446S) from BA.1 and two (S371F and D405N) mutations from BA.2 to form its spike protein. |
||||
| BA.4 | 12 May 2022/South Africa, Botswana, Denmark, UK | S:del69/70, S:L452R, S:F486V, S:Q493R reversion | ||||
| BA.5 | 25 May 2022/Portugal | BA.2-like constellation in the spike protein + S:del69/70, S:L452R, S:F486V, S:Q493R reversion |