Table 1.
High frequency mutations in the 7213 SARS-CoV-2 genome.a
| SARS-CoV-2 region | Mutation | Africa | Asia | Europe | Oceania | North America | South America | Total | % incidence |
|---|---|---|---|---|---|---|---|---|---|
| S protein | D614G | 696 (97.1%) | 1452 (58.4%) | 1113 (89.8%) | 1689 (83.3%) | 321 (91.5%) | 361 (92.3%) | 5632 | 78% |
| N protein | P13L | 2 (0.3%) | 248 (10%) | 116 (5.7%) | 366 | 5% | |||
| S194L | 2 (0.3%) | 314 (12.6%) | 11 (0.9%) | 14 (0.7%) | 10 (2.8%) | 1 (0.3%) | 352 | 5% | |
| R203K | 489 (68.2%) | 502 (20.2%) | 435 (35.1%) | 1348 (66.5%) | 47 (13.4%) | 252 (64.5%) | 3073 | 43% | |
| G204R | 489 (68.2%) | 495 (19.9%) | 432 (34.8%) | 1348 (66.5%) | 45 (12.8%) | 252 (64.5%) | 3061 | 42% | |
| I292T | 2 (0.2%) | 4 (0.2%) | 113 (28.9%) | 119 | 2% | ||||
| ORF3a | Q57H | 49 (6.8%) | 774 (31.1%) | 295 (23.8%) | 192 (9.5%) | 238 (67.8%) | 63 (16.1%) | 1611 | 22% |
| G251V | 3 (0.4%) | 61 (2.5%) | 29 (2.3%) | 67 (3.3%) | 3 (0.9%) | 4 (1%) | 167 | 2% | |
| ORF8 | S24L | 64 (18.2%) | 64 | 1% | |||||
| L84S | 12 (1.7%) | 259 (10.4%) | 60 (4.8%) | 171 (8.4%) | 24 (6.8%) | 12 (3.1%) | 538 | 7% | |
| ORF1ab; nsp2 | T265I | 20 (2.8%) | 79 (3.2%) | 188 (15.2%) | 148 (7.3%) | 207 (59%) | 28 (7.2%) | 670 | 9% |
| D448del | 5 (0.7%) | 4 (0.2%) | 4 (0.3%) | 13 | 0% | ||||
| ORF1ab; nsp3 | T2016K | 2 (0.3%) | 254 (10.2%) | 24 (1.2%) | 280 | 4% | |||
| ORF1ab; nsp5 | G3278S | 67 (9.3%) | 1 (0.04%) | 13 (1%) | 2 (0.6%) | 1 (0.3%) | 84 | 1% | |
| ORF1ab; nsp6 | L3606F | 35 (4.9%) | 425 (17.1%) | 56 (4.5%) | 152 (7.5%) | 11 (3.1%) | 6 (1.5%) | 685 | 9% |
| ORF1ab; nsp12 | A4489V | 2 (0.3%) | 256 (10.3%) | 25 (1.2%) | 1 (0.3%) | 1 (0.3%) | 285 | 4% | |
| P4715L | 697 (28%) | 1532 (61.6%) | 1088 (87.7%) | 1689 (83.3%) | 316 (90%) | 357 (91.3%) | 5679 | 79% | |
| ORF1ab; nsp13 | P5828L | 7 (0.3%) | 50 (2.5%) | 14 (4%) | 2 (0.5%) | 73 | 1% | ||
| Y5865C | 7 (0.3%) | 51 (2.5%) | 14 (4%) | 2 (0.5%) | 74 | 1% |
Key: One letter code for corresponding amino acid: A – Alanine, R – Arginine, N – Asparagine, D – Aspartic acid, C – Cysteine, E – Glutamate, Q – Glutamine, G – Glycine, H – Histidine, I – Isoleucine, L – Leucine, K – Lysine, M – Methionine, F – Phenylalanine, P – Proline, S – Serine, T – Threonine, W – Tryptophan, Y – Tyrosine, V – Valine.
a
The mutation positions are with respect to the reference (hCoV-19/Wuhan/WIV04/2019). The percentage (%) incidence is calculated as number of observed mutations across regions from the total 7213 viral samples. Highly recurrent mutations were observed in nsp12; P4715L, ORF3a; Q57H, N protein; R203K and G204R, and S protein; D614G.